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07-352 | Anti-acetyl-Histone H3 (Lys9) Antibody
Anti-acetyl-Histone H3 (Lys9) Antibody is a Rabbit Polyclonal Antibody for detection of acetyl-Histone H3 (Lys9) also known as H3K9Ac, Histone H3 (acetyl K9) & has been validated in ChIP, WB, Mplex.
Anti-acetyl-Histone H3 (Lys9) Antibody is a Rabbit Polyclonal Antibody for detection of acetyl-Histone H3 (Lys9) also known as H3K9Ac, Histone H3 (acetyl K9) & has been validated in ChIP, WB, Mplex. Less<<
|Replacement Information
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Key Spec Table
|Species Reactivity
|Key Applications
|Antibody Type
|H, Yeast (S. cerevisiae), Vrt
|WB, ChIP, ChIP-seq, Mplex
|Polyclonal Antibody
|Product Information
|Antiserum containing 0.35% sodium azide and 30% glycerol.
|Physicochemical Information
|Materials Information
|Toxicological Information
|Safety Information according to GHS
|Safety Information
|Storage and Shipping Information
|Storage Conditions
|Stable for 1 year at -20°C from date of receipt. For maximum recovery of product, centrifuge the vial prior to removing the cap.
|Packaging Information
|Material Size
|100 µL
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|Supplemental Information
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References | 49 Available | See All References
|Reference overview
|Pub Med ID
|Promoter-associated small double-stranded RNA interacts with heterogeneous nuclear ribonucleoprotein A2/B1 to induce transcriptional activation.
Jia Hu,Zhong Chen,Ding Xia,Jia Wu,Hua Xu,Zhang-Qun Ye
The Biochemical journal 447 2012
Show Abstract
Several recent reports have demonstrated that small activating dsRNA [double-stranded RNA; saRNA (small activating dsRNA)] complementary to promoter regions can up-regulate gene expression in mammalian cells, a phenomenon termed RNAa (RNA activation). However, the mechanism of RNAa remains obscure with regard to what is the target molecule for promoter-targeted saRNA and what are the proteins involved in this process. p21Waf1/Cip1 (p21) [CDKN1A (cyclin-dependent kinase inhibitor 1A)], an important tumour suppressor gene, is among the genes that can be activated by RNAa in tumour cells. In the present study, we provide direct evidence that p21 promoter-targeted saRNA interact with its intended target on the p21 promoter to activate p21 expression. This process is associated with recruitment of RNA polymerase II and AGO2 (argonaute 2) protein to the saRNA-target site. Additionally, we found that several hnRNPs (heterogeneous nuclear ribonucleoproteins) (A1, A2/B1 and C1/C2) are associated with saRNA. Further studies show that hnRNPA2/B1 interacts with the saRNA in vivo and in vitro and is required for RNAa activity. These findings indicate that RNAa results from specific targeting of promoters and reveals additional mechanistic details of RNAa.
|Increasing phosphatidylinositol (4,5) bisphosphate biosynthesis affects plant nuclear lipids and nuclear functions.
Catherine B Dieck,Austin Wood,Irena Brglez,Marcela Rojas-Pierce,Wendy F Boss
Plant physiology and biochemistry : PPB / Société française de physiologie végétale 57 2012
Show Abstract
In order to characterize the effects of increasing phosphatidylinositol(4,5)bisphosphate (PtdIns(4,5)P(2)) on nuclear function, we expressed the human phosphatidylinositol (4)-phosphate 5-kinase (HsPIP5K) 1α in Nicotiana tabacum (NT) cells. The HsPIP5K-expressing (HK) cells had altered nuclear lipids and nuclear functions. HK cell nuclei had 2-fold increased PIP5K activity and increased steady state PtdIns(4,5)P(2). HK nuclear lipid classes showed significant changes compared to NT (wild type) nuclear lipid classes including increased phosphatidylserine (PtdSer) and phosphatidylcholine (PtdCho) and decreased lysolipids. Lipids isolated from protoplast plasma membranes (PM) were also analyzed and compared with nuclear lipids. The lipid profiles revealed similarities and differences in the plasma membrane and nuclei from the NT and transgenic HK cell lines. A notable characteristic of nuclear lipids from both cell types is that PtdIns accounts for a higher mol% of total lipids compared to that of the protoplast PM lipids. The lipid molecular species composition of each lipid class was also analyzed for nuclei and protoplast PM samples. To determine whether expression of HsPIP5K1α affected plant nuclear functions, we compared DNA replication, histone 3 lysine 9 acetylation (H3K9ac) and phosphorylation of the retinoblastoma protein (pRb) in NT and HK cells. The HK cells had a measurable decrease in DNA replication, histone H3K9 acetylation and pRB phosphorylation.
|RORγ directly regulates the circadian expression of clock genes and downstream targets in vivo.
Yukimasa Takeda,Raja Jothi,Veronique Birault,Anton M Jetten
Nucleic acids research 40 2012
Show Abstract
In this study, we demonstrate that the lack of retinoic acid-related orphan receptor (ROR) γ or α expression in mice significantly reduced the peak expression level of Cry1, Bmal1, E4bp4, Rev-Erbα and Per2 in an ROR isotype- and tissue-selective manner without affecting the phase of their rhythmic expression. Analysis of RORγ/RORα double knockout mice indicated that in certain tissues RORγ and RORα exhibited a certain degree of redundancy in regulating clock gene expression. Reporter gene analysis showed that RORγ was able to induce reporter gene activity through the RORE-containing regulatory regions of Cry1, Bmal1, Rev-Erbα and E4bp4. Co-expression of Rev-Erbα or addition of a novel ROR antagonist repressed this activation. ChIP-Seq and ChIP-Quantitative real-time polymerase chain reaction (QPCR) analysis demonstrated that in vivo RORγ regulate these genes directly and in a Zeitgeber time (ZT)-dependent manner through these ROREs. This transcriptional activation by RORs was associated with changes in histone acetylation and chromatin accessibility. The rhythmic expression of RORγ1 by clock proteins may lead to the rhythmic expression of RORγ1 target genes. The presence of RORγ binding sites and its down-regulation in RORγ(-)(/)(-) liver suggest that the rhythmic expression of Avpr1a depends on RORγ consistent with the concept that RORγ1 provides a link between the clock machinery and its regulation of metabolic genes.
|5-azacitidine in aggressive myelodysplastic syndromes regulates chromatin structure at PU.1 gene and cell differentiation capacity.
N Curik,P Burda,K Vargova,V Pospisil,M Belickova,P Vlckova,F Savvulidi,E Necas,H Hajkova,C Haskovec,J Cermak,M Krivjanska,M Trneny,P Laslo,A Jonasova,T Stopka
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K 26 2012
Show Abstract
Epigenetic 5-azacitidine (AZA) therapy of high-risk myelodysplastic syndromes (MDS) and acute myelogenous leukemia (AML) represents a promising, albeit not fully understood, approach. Hematopoietic transcription factor PU.1 is dynamically regulated by upstream regulatory element (URE), whose deletion causes downregulation of PU.1 leading to AML in mouse. In this study a significant group of the high-risk MDS patients, as well as MDS cell lines, displayed downregulation of PU.1 expression within CD34+ cells, which was associated with DNA methylation of the URE. AZA treatment in vitro significantly demethylated URE, leading to upregulation of PU.1 followed by derepression of its transcriptional targets and onset of myeloid differentiation. Addition of colony-stimulating factors (CSFs; granulocyte-CSF, granulocyte-macrophage-CSF and macrophage-CSF) modulated AZA-mediated effects on reprogramming of histone modifications at the URE and cell differentiation outcome. Our data collectively support the importance of modifying the URE chromatin structure as a regulatory mechanism of AZA-mediated activation of PU.1 and induction of the myeloid program in MDS.
|Trichostatin a modified histone covalent pattern and enhanced expression of pluripotent genes in interspecies black-footed cat cloned embryos but did not improve in vitro and in vivo viability.
Gómez MC, Pope CE, Biancardi MN, Dumas C, Galiguis J, Morris AC, Wang G, Dresser BL
Cellular reprogramming 13 315-29. doi 2011
Show Abstract
Abstract The black-footed cat (BFC; Felis nigripes), one of the smallest wild cats, is listed as threatened. Interspecies somatic cell nuclear transfer (Is-SCNT) offers the possibility of preserving endangered species. Development to term of interspecies BFC (Is-BFC) cloned embryos has not been obtained, possibly due to abnormal epigenetic reprogramming. Treatment of intraspecies cloned embryos with TSA improves nuclear reprogramming and in vitro and in vivo viability. In this study, we evaluated (1) whether covalent histone modifications differ between Is-BFC cloned embryos and their IVF counterparts, (2) the optimal TSA concentration and exposure times to modify the covalent histone patterns, (3) if TSA enhances in vitro and in vivo developmental competence of cloned embryos, and (4) expression of pluripotent genes. Results indicated that the covalent histone modifications of Is-BFC cloned embryos aberrantly differ from their DSH-IVF counterpart embryos. Aberrant epigenetic events may be due partially to the inability of the DSH cytoplasm to modify the restrictive epigenetic marks of the BFC nuclei after somatic cell nuclear transfer (SCNT). Incomplete remodeling of the histone H3K9me2 in Is-BFC cloned embryos possibly contributes to abnormal expression of pluripotent genes and low embryonic development. Treatment of Is-BFC cloned embryos with TSA remodeled the covalent pattern in H3K9ac and H3K9me2, resembling epigenetic patterns in IVF counterpart embryos, and resulted in activation of some pluripotent genes. However, genomic reprogramming of Is-BFC cloned blastocysts did not follow the same reprogramming pattern observed in DSH-IVF embryos, and in vitro and in vivo developmental competence was not enhanced.
|Sgf29 binds histone H3K4me23 and is required for SAGA complex recruitment and histone H3 acetylation.
Bian C, Xu C, Ruan J, Lee KK, Burke TL, Tempel W, Barsyte D, Li J, Wu M, Zhou BO, Fleharty BE, Paulson A, Allali-Hassani A, Zhou JQ, Mer G, Grant PA, Workman JL, Zang J, Min J.
The EMBO journal 30 2829-42 2011
Show Abstract
The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an important chromatin modifying complex that can both acetylate and deubiquitinate histones. Sgf29 is a novel component of the SAGA complex. Here, we report the crystal structures of the tandem Tudor domains of Saccharomyces cerevisiae and human Sgf29 and their complexes with H3K4me2 and H3K4me3 peptides, respectively, and show that Sgf29 selectively binds H3K4me2/3 marks. Our crystal structures reveal that Sgf29 harbours unique tandem Tudor domains in its C-terminus. The tandem Tudor domains in Sgf29 tightly pack against each other face-to-face with each Tudor domain harbouring a negatively charged pocket accommodating the first residue alanine and methylated K4 residue of histone H3, respectively. The H3A1 and K4me3 binding pockets and the limited binding cleft length between these two binding pockets are the structural determinants in conferring the ability of Sgf29 to selectively recognize H3K4me2/3. Our in vitro and in vivo functional assays show that Sgf29 recognizes methylated H3K4 to recruit the SAGA complex to its targets sites and mediates histone H3 acetylation, underscoring the importance of Sgf29 in gene regulation.
|The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in committed B cells.
McManus, S; Ebert, A; Salvagiotto, G; Medvedovic, J; Sun, Q; Tamir, I; Jaritz, M; Tagoh, H; Busslinger, M
The EMBO journal 30 2388-404 2011
Show Abstract
Pax5 is a critical regulator of B-cell commitment. Here, we identified direct Pax5 target genes by streptavidin-mediated ChIP-chip analysis of pro-B cells expressing in vivo biotinylated Pax5. By binding to promoters and enhancers, Pax5 directly regulates the expression of multiple transcription factor, cell surface receptor and signal transducer genes. One of the newly identified enhancers was shown by transgenic analysis to confer Pax5-dependent B-cell-specific activity to the Nedd9 gene controlling B-cell trafficking. Profiling of histone modifications in Pax5-deficient and wild-type pro-B cells demonstrated that Pax5 induces active chromatin at activated target genes, while eliminating active chromatin at repressed genes in committed pro-B cells. Pax5 rapidly induces these chromatin and transcription changes by recruiting chromatin-remodelling, histone-modifying and basal transcription factor complexes to its target genes. These data provide novel insight into the regulatory network and epigenetic regulation, by which Pax5 controls B-cell commitment.
|p53-paralog DNp73 oncogene is repressed by IFNαSTAT2 through the recruitment of the Ezh2 polycomb group transcriptional repressor.
Testoni B, Schinzari V, Guerrieri F, Gerbal-Chaloin S, Blandino G, Levrero M
Oncogene 2011
Show Abstract
The DNp73 proteins act as trans-repressors of p53 and p73-dependent transcription and exert both anti-apoptotic activity and pro-proliferative activity. DNp73s are frequently up-regulated in a variety of human cancers, including human hepatocellular carcinomas (HCCs). Increased levels of DNp73 proteins confer to HCC cells resistance to apoptosis and, irrespective to p53 status, a chemoresistant phenotype. Here, we show that interferon (IFN)α down-regulates DNp73 expression in primary human hepatocytes (PHHs) and HCC cell lines. IFNα has been used as pro-apoptotic agent in the treatment of malignancies and there is increasing evidence of IFNα effectiveness in HCC treatment and prevention of recurrence. The precise mechanisms by which class I IFNs exert their anti-proliferative and anti-tumor activity remain unclear. IFNα binding to its receptor activates multiple intracellular signaling cascades regulating the transcription of numerous direct target genes through the recruitment of a complex comprising of STAT1, STAT2 and IFN regulatory factor (IRF)9 to their promoters. We found that, in response to IFNα, the P2p73 promoter undergoes substantial chromatin remodeling. Histone deacetylases (HDACs) replace histone acetyl transferases. STAT2 is recruited onto the endogenous P2p73 promoter together with the polycomb group protein Ezh2, leading to increased H3K27 methylation and transcriptional repression. The reduction of DNp73 levels by IFNα is paralleled by an increased susceptibility to IFNα-triggered apoptosis of Huh7 hepatoma cells. Our results show, for the first time, that IFN-stimulated gene factor 3 recruitment may serve both in activating and repressing gene expression and identify the down-regulation of DNp73 as an additional mechanism to counteract the chemoresistance of liver cancer cells.Oncogene advance online publication, 14 March 2011; doi:10.1038/onc.2010.635.
|HBO1 is required for H3K14 acetylation and normal transcriptional activity during embryonic development.
Kueh AJ, Dixon MP, Voss AK, Thomas T
Mol Cell Biol 31 845-60. Epub 2010 Dec 13. 2011
Show Abstract
We report here that the MYST histone acetyltransferase HBO1 (histone acetyltransferase bound to ORC; MYST2/KAT7) is essential for postgastrulation mammalian development. Lack of HBO1 led to a more than 90% reduction of histone 3 lysine 14 (H3K14) acetylation, whereas no reduction of acetylation was detected at other histone residues. The decrease in H3K14 acetylation was accompanied by a decrease in expression of the majority of genes studied. However, some genes, in particular genes regulating embryonic patterning, were more severely affected than \"housekeeping\" genes. Development of HBO1-deficient embryos was arrested at the 10-somite stage. Blood vessels, mesenchyme, and somites were disorganized. In contrast to previous studies that reported cell cycle arrest in HBO1-depleted cultured cells, no defects in DNA replication or cell proliferation were seen in Hbo1 mutant embryo primary fibroblasts or immortalized fibroblasts. Rather, a high rate of cell death and DNA fragmentation was observed in Hbo1 mutant embryos, resulting initially in the degeneration of mesenchymal tissues and ultimately in embryonic lethality. In conclusion, the primary role of HBO1 in development is that of a transcriptional activator, which is indispensable for H3K14 acetylation and for the normal expression of essential genes regulating embryonic development.Full Text Article
|Carbon monoxide stimulates global protein methylation via its inhibitory action on cystathionine β-synthase.
Yamamoto T, Takano N, Ishiwata K, Suematsu M
J Clin Biochem Nutr 48 96-100. Epub 2010 Dec 28. 2011
Show Abstract
Although carbon monoxide derived from heme oxygenase has been reported to exert diverse biological actions in mammals, macromolecules responsible for its direct reception and functional outcomes of the gas binding remain largely unknown. Based on our previous results in vivo suggesting carbon monoxide serves as an inhibitor of cystathionine β-synthase that rate-limits transsulfuration pathway for generation of hydrogen sulfide, we have herein hypothesized that the gas might serve as a regulator of protein methylation through accelerating turnover of remethylation cycle residing at the upstream of the enzyme. Metabolomic analysis in human monoblastic leukemia U937 cells in culture revealed that application of carbon monoxide-releasing molecules caused increases in methionine and S-adenosylmethionine and a decrease in cystathionine in the cells, suggesting the cystathionine β-synthase inhibition by carbon monoxide. Under these circumstances, the cells exhibited global protein arginine methylation: this event was also reproduced by the cell treatment with hemin, a heme oxygenase-1 inducer. The protein arginine methylation elicited by carbon monoxide was attenuated by knocking down cystathionine β-synthase with its small interfering RNA or by blocking S-adenosylhomocysteine hydrolase with adenosine dialdehyde, suggesting remethylation cycling is necessary to trigger the methylation processing. Furthermore, proteins undergoing the carbon monoxide-induced arginine methylation involved histone H3 proteins, suggesting chromatin modification by the gas. Collectively with our studies in vivo showing its inhibitory action on endogenous hydrogen sulfide production, the current results suggest that not only inhibition of transsulfuration pathway for H(2)S generation but also activation of protein methylation accounts for notable biological actions of carbon monoxide via the cystathionine β-synthase inhibition.Full Text Article
|The FUN30 Chromatin Remodeler, Fft3, Protects Centromeric and Subtelomeric Domains from Euchromatin Formation.
Strålfors A, Walfridsson J, Bhuiyan H, Ekwall K
PLoS Genet 7 e1001334. Epub 2011 Mar 17. 2011
Show Abstract
The chromosomes of eukaryotes are organized into structurally and functionally discrete domains. This implies the presence of insulator elements that separate adjacent domains, allowing them to maintain different chromatin structures. We show that the Fun30 chromatin remodeler, Fft3, is essential for maintaining a proper chromatin structure at centromeres and subtelomeres. Fft3 is localized to insulator elements and inhibits euchromatin assembly in silent chromatin domains. In its absence, euchromatic histone modifications and histone variants invade centromeres and subtelomeres, causing a mis-regulation of gene expression and severe chromosome segregation defects. Our data strongly suggest that Fft3 controls the identity of chromatin domains by protecting these regions from euchromatin assembly.Full Text Article
|Epigenetic regulation of early Osteogenesis and Mineralized tissue formation by a hOXA10-PBX1-Associated complex.
Gordon JA, Hassan MQ, Koss M, Montecino M, Selleri L, van Wijnen AJ, Stein JL, Stein GS, Lian JB
Cells, tissues, organs 2011
Show Abstract
Homeodomain-containing (HOX) factors such as the abdominal class homeodomain protein HOXA10 and the TALE-family protein PBX1 form coregulatory complexes and are potent transcriptional and epigenetic regulators of tissue morphogenesis. We have identified that HOXA10 and PBX1 are expressed in osteoprogenitors; however, their role in osteogenesis has not been established. To determine the mechanism of HOXA10-PBX-mediated regulation of osteoblast commitment and the related gene expression, PBX1 or HOX10 were depleted (shRNA or genetic deletion, respectively) or exogenously expressed in C3H10T1/2, bone marrow stromal progenitors, and MC3T3-E1 (preosteoblast) cells. Overexpression of HOXA10 increased the expression of osteoblast-related genes, osteoblast differentiation and mineralization; expression of PBX1 impaired osteogenic commitment of pluripotent cells and the differentiation of osteoblasts. In contrast, the targeted depletion of PBX1 by shRNA increased the expression of bone marker genes (osterix, alkaline phosphatase, BSP, and osteocalcin). Chromatin-associated PBX1 and HOXA10 were present at osteoblast-related gene promoters preceding gene expression, but PBX1 was absent from promoters during the transcription of bone-related genes, including osterix (Osx). Further, PBX1 complexes were associated with histone deacetylases normally linked with chromatin inactivation. Loss of PBX1 but not of HOXA10 from the Osx promoter was associated with increases in the recruitment of histone acetylases (p300), as well as decreased H3K9 methylation, reflecting transcriptional activation. We propose PBX1 plays a central role in attenuating the activity of HOXA10 as an activator of osteoblast-related genes and functions to establish the proper timing of gene expression during osteogenesis, resulting in proper matrix maturation and mineral deposition in differentiated osteoblasts.Copyright © 2011 S. Karger AG, Basel.
|Additional sex comb-like (ASXL) proteins 1 and 2 play opposite roles in adipogenesis via reciprocal regulation of peroxisome proliferator-activated receptor {gamma}.
Park UH, Yoon SK, Park T, Kim EJ, Um SJ
J Biol Chem 286 1354-63. Epub 2010 Nov 3. 2011
Show Abstract
Our previous studies have suggested that the mammalian additional sex comb-like 1 protein functions as a coactivator or repressor of retinoic acid receptors in a cell-specific manner. Here, we investigated the roles of additional sex comb-like 1 proteins in regulating peroxisome proliferator-activated receptors (PPARs). In pulldown assays in vitro and in immunoprecipitation assays in vivo, ASXL1 and its paralog, ASXL2, interacted with PPARα and PPARγ. In 3T3-L1 preadipocyte cells, overexpression of ASXL1 inhibited the induction of PPARγ activity by rosiglitazone, as shown by transcription assays, and completely suppressed adipogenesis, as shown by Oil Red O staining. In contrast, overexpression of ASXL2 greatly enhanced rosiglitazone-induced PPARγ activity and enhanced adipogenesis. Deletion of the heterochromatin protein 1 (HP1)-binding domain from ASXL1 caused the mutant protein to enhance adipogenesis similarly to ASXL2, indicating that HP1 binding is required for the adipogenesis-suppressing activity of ASXL1. Adipocyte differentiation was associated with a gradual decrease in ASXL1 expression but did not affect ASXL2 expression. Knockdown of ASXL1 and ASXL2 had reciprocal effects on adipogenesis. In chromatin immunoprecipitation assays in 3T3-L1 cells, ASXL1 occupied the promoter of the PPARγ target gene aP2 together with HP1α and Lys-9-methylated histone H3, whereas ASXL2 occupied the aP2 promoter together with histone-lysine N-methyltransferase MLL1 and Lys-9-acetylated and Lys-4-methylated H3 histones. Finally, microarray analysis demonstrated that ASXL1 represses, whereas ASXL2 increases, the expression of adipogenic genes, most of which are PPARγ targets. These results suggest that members of the additional sex comb-like family provide complex regulation of adipogenesis via differential modulation of PPARγ activity.Full Text Article
|Specific histone lysine 4 methylation patterns define TR-binding capacity and differentiate direct T3 responses.
Bilesimo P, Jolivet P, Alfama G, Buisine N, Le Mevel S, Havis E, Demeneix BA, Sachs LM
Mol Endocrinol 25 225-37. Epub 2011 Jan 14. 2011
Show Abstract
The diversity of thyroid hormone T(3) effects in vivo makes their molecular analysis particularly challenging. Indeed, the current model of the action of T(3) and its receptors on transcription does not reflect this diversity. Here, T(3)-dependent amphibian metamorphosis was exploited to investigate, in an in vivo developmental context, how T(3) directly regulates gene expression. Two, direct positively regulated T(3)-response genes encoding transcription factors were analyzed: thyroid hormone receptor β (TRβ) and TH/bZIP. Reverse transcription-real-time quantitative PCR analysis on Xenopus tropicalis tadpole brain and tail fin showed differences in expression levels in premetamorphic tadpoles (lower for TH/bZIP than for TRβ) and differences in induction after T(3) treatment (lower for TRβ than for TH/bZIP). To dissect the mechanisms underlying these differences, chromatin immunoprecipitation was used. T(3) differentially induced RNA polymerase II and histone tail acetylation as a function of transcriptional level. Gene-specific patterns of TR binding were found on the different T(3) -responsive elements (higher for TRβ than for TH/bZIP), correlated with gene-specific modifications of H3K4 methylation (higher for TRβ than for TH/bZIP). Moreover, tissue-specific modifications of H3K27 were found (lower in brain than in tail fin). This first in vivo analysis of the association of histone modifications and TR binding/gene activation during vertebrate development for any nuclear receptor indicate that chromatin context of thyroid-responsive elements loci controls the capacity to bind TR through variations in histone H3K4 methylation, and that the histone code, notably H3, contributes to the fine tuning of gene expression that underlies complex physiological T(3) responses.
|Chromatin Immunoprecipitation (ChIP)
|Brain-specific Expression of N-Acetylglucosaminyltransferase IX (GnT- IX) Is Regulated by Epigenetic Histone Modifications.
Kizuka Y, Kitazume S, Yoshida M, Taniguchi N
The Journal of biological chemistry 286 31875-84. Epub 2011 Jul 19. 2011
Show Abstract
It is well known that biosynthesis of glycans takes place in organ- and tissue-specific manners and glycan expression is controlled by various factors including glycosyltransferases. The expression mechanism of glycosyltransferases, however, is poorly understood. Here we investigated the expression mechanism of a brain-specific glycosyltransferase, GnT-IX (N-acetylglucosaminyltransferase IX, also designated as GnT-Vb), which synthesizes branched O-mannose glycan. Using an epigenetic approach, we revealed that the genomic region around the transcriptional start site of the GnT-IX gene was highly associated with active chromatin histone marks in a neural cell-specific manner, indicating that brain-specific GnT-IX expression is under control of an epigenetic \"histone code.\" By EMSA and ChIP analyses we identified two regulatory proteins, NeuroD1 and CTCF that bind to and activate the GnT-IX promoter. We also revealed that GnT-IX expression was suppressed in CTCF- and NeuroD1-depleted cells, indicating that a NeuroD1- and CTCF-dependent epigenetic mechanism governs brain-specific GnT-IX expression. Several other neural glycosyltransferase genes are also found to be regulated by epigenetic histone modifications. This is the first report demonstrating a molecular mechanism at the chromatin level underlying tissue-specific glycan expression.
|Pbx1 represses osteoblastogenesis by blocking Hoxa10-mediated recruitment of chromatin remodeling factors.
Jonathan A R Gordon,Mohammad Q Hassan,Sharanjot Saini,Martin Montecino,Andre J van Wijnen,Gary S Stein,Janet L Stein,Jane B Lian
Molecular and cellular biology 30 2010
Show Abstract
Abdominal-class homeodomain-containing (Hox) factors form multimeric complexes with TALE-class homeodomain proteins (Pbx, Meis) to regulate tissue morphogenesis and skeletal development. Here we have established that Pbx1 negatively regulates Hoxa10-mediated gene transcription in mesenchymal cells and identified components of a Pbx1 complex associated with genes in osteoblasts. Expression of Pbx1 impaired osteogenic commitment of C3H10T1/2 multipotent cells and differentiation of MC3T3-E1 preosteoblasts. Conversely, targeted depletion of Pbx1 by short hairpin RNA (shRNA) increased expression of osteoblast-related genes. Studies using wild-type and mutated osteocalcin and Bsp promoters revealed that Pbx1 acts through a Pbx-binding site that is required to attenuate gene activation by Hoxa10. Chromatin-associated Pbx1 and Hoxa10 were present at osteoblast-related gene promoters preceding gene expression, but only Hoxa10 was associated with these promoters during transcription. Our results show that Pbx1 is associated with histone deacetylases normally linked with chromatin inactivation. Loss of Pbx1 from osteoblast promoters in differentiated osteoblasts was associated with increased histone acetylation and CBP/p300 recruitment, as well as decreased H3K9 methylation. We propose that Pbx1 plays a central role in attenuating the ability of Hoxa10 to activate osteoblast-related genes in order to establish temporal regulation of gene expression during osteogenesis.Full Text Article
|Enhanced histone acetylation in somatic cells induced by a histone deacetylase inhibitor improved inter-generic cloned leopard cat blastocysts.
Hyo-Sang Lee,Xian-Feng Yu,Jae-Il Bang,Su-Jin Cho,Gautam Kumar Deb,Byeong-Woo Kim,Il-Keun Kong
Theriogenology 74 2010
Show Abstract
The objective was to determine whether alterations of histone acetylation status in donor cells affected inter-generic SCNT (igSCNT)-cloned embryo development. Leopard cat cells were treated with trichostatin A (TSA; a histone deacetylase inhibitor) for 48 h, and then donor cells were transferred into enucleated oocytes from domestic cats. Compared to non-treated cells, the acetylated histone 3 at lysine 9 (AcH3K9) and histone 4 at lysine 5 (AcH4K5) in the TSA group increased for up to 48 h (P < 0.05). The AcH3K9 signal ratios of igSCNT group was higher than control group 3 h after activation (P < 0.05). Treatment with TSA significantly increased total cell number of blastocysts (109.1 ± 6.9 vs. 71.8 ± 2.9, mean ± SEM), with no significant effects on rates of cleavage or blastocyst development (71.1 ± 2.8 vs. 67.6 ± 2.9 and 12.2 ± 2.6 vs. 11.0 ± 2.6, respectively). When igSCNT cloned embryos were transferred into a domestic cat oviduct and recovered after 8 d, blastocyst development rates and total cell numbers were greater in the TSA-igSCNT group (20.7 ± 3.0% and 2847.6 ± 37.2) than in the control igSCNT group (5.7 ± 2.2% and 652.1 ± 17.6, P < 0.05). Average total cell numbers of blastocysts were approximately 4.4-fold higher in the TSA-igSCNT group (2847.6 ± 37.2, n = 10) than in the control group (652.1 ± 17.6, n = 8; P < 0.05), but were ∼2.9-fold lower than in vivo cat blastocysts produced by intrauterine insemination (8203.8 ± 29.6, n = 5; P < 0.001). Enhanced histone acetylation levels of donor cells improved in vivo developmental competence and quality of inter-generic cloned embryos; however, fewer cells in blastocysts derived from igSCNT than blastocysts produced by insemination may reduce development potential following intergeneric cloning (none of the cloned embryos were maintained to term).
|Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation.
Nugent RL, Johnsson A, Fleharty B, Gogol M, Xue-Franzén Y, Seidel C, Wright AP, Forsburg SL
BMC genomics 11 59 2010
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ABSTRACT: BACKGROUND: Histone acetyltransferase enzymes (HATs) are implicated in regulation of transcription. HATs from different families may overlap in target and substrate specificity. RESULTS: We isolated the elp3+ gene encoding the histone acetyltransferase subunit of the Elongator complex in fission yeast and characterized the phenotype of an Deltaelp3 mutant. We examined genetic interactions between Deltaelp3 and two other HAT mutants, Deltamst2 and Deltagcn5 and used whole genome microarray analysis to analyze their effects on gene expression. CONCLUSIONS: Comparison of phenotypes and expression profiles in single, double and triple mutants indicate that these HAT enzymes have overlapping functions. Consistent with this, overlapping specificity in histone H3 acetylation is observed. However, there is no evidence for overlap with another HAT enzyme, encoded by the essential mst1+ gene.Full Text Article
|c-MYC coordinately regulates ribosomal gene chromatin remodeling and Pol I availability during granulocyte differentiation.
Poortinga G, Wall M, Sanij E, Siwicki K, Ellul J, Brown D, Holloway TP, Hannan RD, McArthur GA
Nucleic Acids Res 2010
Show Abstract
Loss of c-MYC is required for downregulation of ribosomal RNA (rRNA) gene (rDNA) transcription by RNA Polymerase I (Pol I) during granulocyte differentiation. Here, we demonstrate a robust reduction of Pol I loading onto rDNA that along with a depletion of the MYC target gene upstream binding factor (UBF) and a switch from epigenetically active to silent rDNA accompanies this MYC reduction. We hypothesized that MYC may coordinate these mechanisms via direct regulation of multiple components of the Pol I transcription apparatus. Using gene expression arrays we identified a \'regulon\' of Pol I factors that are both downregulated during differentiation and reinduced in differentiated granulocytes upon activation of the MYC-ER transgene. This regulon includes the novel c-MYC target genes RRN3 and POLR1B. Although enforced MYC expression during granulocyte differentiation was sufficient to increase the number of active rRNA genes, its activation in terminally differentiated cells did not alter the active to inactive gene ratio despite increased rDNA transcription. Thus, c-MYC dynamically controls rDNA transcription during granulocytic differentiation through the orchestrated transcriptional regulation of core Pol I factors and epigenetic modulation of number of active rRNA genes.
|Maintenance of a constitutive heterochromatin domain in vertebrates by a Dicer-dependent mechanism.
KE Giles, R Ghirlando, G Felsenfeld
Nature cell biology 12 94-9; sup pp 1-6 2010
Show Abstract
The 16 kilobase (kb) heterochromatin domain between the chicken beta-globin locus and the folate receptor gene is used here to study the roles of RNA-dependent mechanisms and histone modifications in the maintenance of a constitutive heterochromatic structure. Inhibition of histone deacetylase (HDAC) activity is shown to both increase intergenic transcription and render the heterochromatin more accessible to MspI digestion. We show that short interfering RNA (siRNA)-mediated downregulation of the enzyme Dicer has similar effects: histone acetylation is increased, transcript levels rise and the compact chromatin structure becomes more accessible to restriction endonucleases. We also show that the chicken Argonaute 2 homologue binds the 16 kb region in a Dicer-dependent manner and is necessary for a condensed chromatin structure. Heterochromatic domains of this kind, which are widely distributed in vertebrate genomes, thus seem to be maintained in their condensed form by highly conserved mechanisms.
|14-3-3 mediates histone cross-talk during transcription elongation in Drosophila.
Karam CS, Kellner WA, Takenaka N, Clemmons AW, Corces VG
PLoS Genet 6 e1000975. 2010
Show Abstract
Post-translational modifications of histone proteins modulate the binding of transcription regulators to chromatin. Studies in Drosophila have shown that the phosphorylation of histone H3 at Ser10 (H3S10ph) by JIL-1 is required specifically during early transcription elongation. 14-3-3 proteins bind H3 only when phosphorylated, providing mechanistic insights into the role of H3S10ph in transcription. Findings presented here show that 14-3-3 functions downstream of H3S10ph during transcription elongation. 14-3-3 proteins localize to active genes in a JIL-1-dependent manner. In the absence of 14-3-3, levels of actively elongating RNA polymerase II are severely diminished. 14-3-3 proteins interact with Elongator protein 3 (Elp3), an acetyltransferase that functions during transcription elongation. JIL-1 and 14-3-3 are required for Elp3 binding to chromatin, and in the absence of either protein, levels of H3K9 acetylation are significantly reduced. These results suggest that 14-3-3 proteins mediate cross-talk between histone phosphorylation and acetylation at a critical step in transcription elongation.Full Text Article
|Asf1 can promote trimethylation of h3 k36 by set2.
Lin LJ, Minard LV, Johnston GC, Singer RA, Schultz MC
Molecular and cellular biology 30 1116-29 2010
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Asf1 is a conserved histone H3/H4 chaperone that can assemble and disassemble nucleosomes and promote histone acetylation. Set2 is an H3 K36 methyltransferase. The functions of these proteins intersect in the context of transcription elongation by RNA polymerase II: both contribute to the establishment of repressive chromatin structures that inhibit spurious intragenic transcription. Here we characterize further interactions between budding yeast (Saccharomyces cerevisiae) Asf1 and Set2 using assays of intragenic transcription, H3/H4 posttranslational modification, coding region cross-linking of Asf1 and Set2, and cooccurrence of Asf1 and Set2 in protein complexes. We find that at some genes Asf1 and Set2 control chromatin metabolism as components of separate pathways. However, the existence of a low-abundance complex containing both proteins suggests that Asf1 and Set2 can more directly collaborate in chromatin regulation. Consistent with this possibility, we show that Asf1 stimulates Set2 occupancy of the coding region of a highly transcribed gene by a mechanism that depends on Asf1 binding to H3/H4. This function of Asf1 promotes the switch from di- to trimethylation of H3 K36 at that gene. These results support the view that Set2 function in chromatin metabolism can intimately involve histone chaperone Asf1.Full Text Article
|Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression.
Zhou J, Wang X, He K, Charron JB, Elling AA, Deng XW
Plant Mol Biol 72 585-95. 2010
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Lysine residue 9 of histone H3 can either be acetylated or mono-, di-, or tri-methylated. These epigenetic states have a diverse impact on regulating gene transcriptional activity and chromatin organization. H3K9ac is invariably correlated with transcriptional activation, whereas H3K9me2 has been reported to be mainly located in constitutive heterochromatin in Arabidopsis. Here, we present epigenetic landscapes for histone H3 lysine 9 acetylation (H3K9ac) and dimethylation (H3K9me2) in Arabidopsis seedlings. The results show that H3K9ac targeted 5,206 non-transposable element (non-TE) genes and 321 transposable elements (TEs), whereas H3K9me2 targeted 2,281 TEs and 1,112 non-TE genes. H3K9ac was biased towards the 5' end of genes and peaked at the ATG position, while H3K9me2 tended to span the entire gene body. H3K9ac correlated with high gene expression, while H3K9me2 correlated with low expression. Analyses of H3K9ac and H3K9me2 with the available datasets of H3K27me3 and DNA methylation revealed a correlation between the occurrence of multiple epigenetic modifications and gene expression. Genes with H3K9ac alone were actively transcribed, while genes that were also modified by either H3K27me3 or DNA methylation showed a lower expression level, suggesting that a combination of repressive marks weakened the positive regulatory effect of H3K9ac. Furthermore, we observed a significant increase of the H3K9ac modification level of selected target genes in hda19 (histone deacetylase 19) mutant seedlings, which indicated that HDA19 plays an important role in regulating the level of H3K9ac and thereby influencing the transcriptional activity in young seedlings.
|Preferential epigenetic suppression of the autonomous MusD over the nonautonomous ETn mouse retrotransposons.
Irina A Maksakova, Ying Zhang, Dixie L Mager, Irina A Maksakova, Ying Zhang, Dixie L Mager, Irina A Maksakova, Ying Zhang, Dixie L Mager
Molecular and cellular biology 29 2456-68 2009
Show Abstract
Nonautonomous retrotransposon subfamilies are often amplified in preference to their coding-competent relatives. However, the mechanisms responsible for such replicative success are poorly understood. Here, we demonstrate that the autonomous MusD long terminal repeat (LTR) retrotransposons are subject to greater epigenetic silencing than their nonautonomous cousins, the early transposons (ETns), which are expressed at a 170-fold-higher level than MusD in mouse embryonic stem (ES) cells. We show that, in ES cells, 5' LTRs and the downstream region of MusD elements are more heavily methylated and are associated with less-activating and more-repressive histone modifications than the highly similar ETnII sequences. The internal region of MusD likely contributes to their silencing, as transgenes with MusD, compared to those with ETnII sequences, show reduced reporter gene expression and a higher level of repressive histone marks. Genomic distribution patterns of MusD and ETn elements are consistent with stronger selection against MusD elements within introns, suggesting that MusD-associated silencing marks can negatively impact genes. We propose a model in which nonautonomous retrotransposons may gain transcriptional and retrotranspositional advantages over their coding-competent counterparts by elimination of the CpG-rich retroviral sequence targeting the autonomous subfamilies for silencing.Full Text Article
|The Mi-2/NuRD complex associates with pericentromeric heterochromatin during S phase in rapidly proliferating lymphoid cells.
Lisa Helbling Chadwick, Brian P Chadwick, David L Jaye, Paul A Wade
Chromosoma 118 445-57 2009
Show Abstract
Chromosomal replication results in the duplication not only of DNA sequence but also of the patterns of histone modification, DNA methylation, and nucleoprotein structure that constitute epigenetic information. Pericentromeric heterochromatin in human cells is characterized by unique patterns of histone and DNA modification. Here, we describe association of the Mi-2/NuRD complex with specific segments of pericentromeric heterochromatin consisting of Satellite II/III DNA located on human chromosomes 1, 9, and 16 in some but not all cell types. This association is linked in part to DNA replication and chromatin assembly and may suggest a role in these processes. Mi-2/NuRD accumulation is independent of Polycomb association and is characterized by a unique pattern of histone modification. We propose that Mi-2/NuRD constitutes an enzymatic component of a pathway for assembly and maturation of chromatin utilized by rapidly proliferating lymphoid cells for replication of constitutive heterochromatin.
|Native chromatin immunoprecipitation (N-ChIP) and ChIP-Seq of Schistosoma mansoni: Critical experimental parameters.
Céline Cosseau, Abdelhalim Azzi, Kristina Smith, Michael Freitag, Guillaume Mitta, Christoph Grunau, Céline Cosseau, Abdelhalim Azzi, Kristina Smith, Michael Freitag, Guillaume Mitta, Christoph Grunau, Céline Cosseau, Abdelhalim Azzi, Kristina Smith, Michael Freitag, Guillaume Mitta, Christoph Grunau, Céline Cosseau, Abdelhalim Azzi, Kristina Smith, Michael Freitag, Guillaume Mitta, Christoph Grunau
Molecular and biochemical parasitology 166 70-6 2009
Show Abstract
Histone modifications are important epigenetic marks that influence chromatin structure and consequently play a role in the control of eukaryotic transcription. Several histone modifying enzymes have been characterized in Schistosoma mansoni and it has been suggested that the regulation of gene transcription in schistosomes may require the action of these enzymes. However, the influence of chromatin structure on gene transcription in schistosomes has never been investigated. Chromatin immunoprecipitation (ChIP) is the technique of choice to study the relationship between histone modifications and gene expression. Although this technique has been widely used with cultured cells from model organisms and with many unicellular organisms, it remains challenging to apply this technique to non-conventional organisms that undergo complex life cycles. In this work, we describe a native ChIP procedure that is applicable to all the stages of the S. mansoni life cycle and does not require expensive equipment. Immunoprecipitated DNA was analysed on a whole-genome scale using massively parallel sequencing (ChIP-Sequencing or ChIP-Seq). We show that ChIP-Seq and conventional quantitative PCR deliver comparable results for a life-cycle regulated locus, smRHO, that encodes a guanine-protein coupled receptor. This is the first time that the ChIP-Seq procedure has been applied to a parasite. This technique opens new ways for analyzing epigenetic mechanisms in S. mansoni at a whole-genome scale and on the level of individual loci.
|REST selectively represses a subset of RE1-containing neuronal genes in mouse embryonic stem cells.
Helle F Jørgensen, Anna Terry, Chiara Beretta, C Filipe Pereira, Marion Leleu, Zhou-Feng Chen, Claire Kelly, Matthias Merkenschlager, Amanda G Fisher, Helle F Jørgensen, Anna Terry, Chiara Beretta, C Filipe Pereira, Marion Leleu, Zhou-Feng Chen, Claire Kelly, Matthias Merkenschlager, Amanda G Fisher, Helle F Jørgensen, Anna Terry, Chiara Beretta, C Filipe Pereira, Marion Leleu, Zhou-Feng Chen, Claire Kelly, Matthias Merkenschlager, Amanda G Fisher
Development (Cambridge, England) 136 715-21 2009
Show Abstract
REST is a transcriptional repressor that targets a group of neuronal genes in non-neuronal cells. In embryonic stem (ES) cells, REST has been implicated in controlling the expression of transcription factor genes that are crucial for lineage determination and for maintaining ES cell potential. Here, we asked whether REST directly regulates neural-specifying genes in mouse ES cells using siRNA-mediated REST knockdown and ES cells that lack functional REST protein as a result of gene targeting. Loss of REST did not affect the expression of any of ten transcription factor genes known to promote neural commitment and did not affect the expression of several microRNAs, including miR-21, a putative REST target in ES cells. REST-deficient ES cells retained the ability to self-renew and to undergo appropriate differentiation towards mesoderm, endoderm and ectoderm lineages upon LIF withdrawal. Genome-wide expression profiling showed that genes that were deregulated in the absence of REST were preferentially expressed in the brain and highly enriched for the presence of canonical REST binding sites (RE1). Chromatin immunoprecipitation studies confirmed these genes as direct targets of REST in ES cells. Collectively, these data show that REST selectively silences a cohort of neuronal genes in ES cells.
|p8/nupr1 regulates DNA-repair activity after double-strand gamma irradiation-induced DNA damage.
Gironella M, Malicet C, Cano C, Sandi MJ, Hamidi T, Tauil RM, Baston M, Valaco P, Moreno S, Lopez F, Neira JL, Dagorn JC, Iovanna JL
J Cell Physiol 221 594-602. 2009
Show Abstract
The stress protein p8 is a small, highly basic, unfolded, and multifunctional protein. We have previously shown that most of its functions are exerted through interactions with other proteins, whose activities are thereby enhanced or repressed. In this work we describe another example of such mechanism, by which p8 binds and negatively regulates MSL1, a histone acetyl transferase (HAT)-associated protein, which in turn binds the DNA-damage-associated 53BP1 protein to facilitate DNA repair following DNA gamma-irradiation. Contrary to the HAT-associated activity, MSL1-dependent DNA-repair activity is almost completely dependent on 53BP1 expression. The picture that has emerged from our findings is that 53BP1 could be a scaffold that gets the HAT MSL1-dependent DNA-repair activity to the sites of DNA damage. Finally, we also found that, although p8 expression is transiently activated after gamma-irradiation, it is eventually submitted to sustained down-regulation, presumably to allow development of MSL1-associated DNA-repair activity. We conclude that interaction of MSL1 with 53BP1 brings MSL1-dependent HAT activity to the vicinity of damaged DNA. MSL1-dependent HAT activity, which is negatively regulated by the stress protein p8, induces chromatin remodeling and relaxation allowing access to DNA of the repair machinery.
|The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.
Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine M Irvine, David A Hume, Alistair R R Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub, Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine M Irvine, David A Hume, Alistair R R Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub, Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine M Irvine, David A Hume, Alistair R R Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub
Genome biology 10 R40 2009
Show Abstract
In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along a differentiation time course of the human THP-1 cell line and under 52 systematic siRNA perturbations. In addition, data regarding chromatin status derived from ChIP-chip to elucidate the transcriptional regulatory interactions are included. Here we present these data to the research community as an integrated web resource.Full Text Article
|Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize.
Xiangfeng Wang, Axel A Elling, Xueyong Li, Ning Li, Zhiyu Peng, Guangming He, Hui Sun, Yijun Qi, X Shirley Liu, Xing Wang Deng, Xiangfeng Wang, Axel A Elling, Xueyong Li, Ning Li, Zhiyu Peng, Guangming He, Hui Sun, Yijun Qi, X Shirley Liu, Xing Wang Deng, Xiangfeng Wang, Axel A Elling, Xueyong Li, Ning Li, Zhiyu Peng, Guangming He, Hui Sun, Yijun Qi, X Shirley Liu, Xing Wang Deng, Xiangfeng Wang, Axel A Elling, Xueyong Li, Ning Li, Zhiyu Peng, Guangming He, Hui Sun, Yijun Qi, X Shirley Liu, Xing Wang Deng, Xiangfeng Wang, Axel A Elling, Xueyong Li, Ning Li, Zhiyu Peng, Guangming He, Hui Sun, Yijun Qi, X Shirley Liu, Xing Wang Deng
The Plant cell 21 1053-69 2009
Show Abstract
Maize (Zea mays) has an exceptionally complex genome with a rich history in both epigenetics and evolution. We report genomic landscapes of representative epigenetic modifications and their relationships to mRNA and small RNA (smRNA) transcriptomes in maize shoots and roots. The epigenetic patterns differed dramatically between genes and transposable elements, and two repressive marks (H3K27me3 and DNA methylation) were usually mutually exclusive. We found an organ-specific distribution of canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), indicative of their tissue-specific biogenesis. Furthermore, we observed that a decreasing level of mop1 led to a concomitant decrease of 24-nucleotide siRNAs relative to 21-nucleotide miRNAs in a tissue-specific manner. A group of 22-nucleotide siRNAs may originate from long-hairpin double-stranded RNAs and preferentially target gene-coding regions. Additionally, a class of miRNA-like smRNAs, whose putative precursors can form short hairpins, potentially targets genes in trans. In summary, our data provide a critical analysis of the maize epigenome and its relationships to mRNA and smRNA transcriptomes.Full Text Article
|Genome-wide analysis of histone H3 lysine9 modifications in human mesenchymal stem cell osteogenic differentiation.
J Tan, J Lu, W Huang, Z Dong, C Kong, L Li, L Gao, J Guo, B Huang
PloS one 4 e6792 2009
Show Abstract
Mesenchymal stem cells (MSCs) possess self-renewal and multi-lineage differentiation potentials. It has been established that epigenetic mechanisms such as histone modifications could be critical for determining the fate of stem cells. In this study, full human genome promoter microarrays and expression microarrays were used to explore the roles of histone modifications (H3K9Ac and H3K9Me2) upon the induction of MSC osteogenic differentiation. Our results revealed that the enrichment of H3K9Ac was decreased globally at the gene promoters, whereas the number of promoters enriched with H3K9Me2 was increased evidently upon osteogenic induction. By a combined analysis of data from both ChIP-on-chip and expression microarrays, a number of differentially expressed genes regulated by H3K9Ac and/or H3K9Me2 were identified, implicating their roles in several biological events, such as cell cycle withdraw and cytoskeleton reconstruction that were essential to differentiation process. In addition, our results showed that the vitamin D receptor played a trans-repression role via alternations of H3K9Ac and H3K9Me2 upon MSC osteogenic differentiation. Data from this study suggested that gene activation and silencing controlled by changes of H3K9Ac and H3K9Me2, respectively, were crucial to MSC osteogenic differentiation.Full Text Article
|Enhancer blocking activity of the insulator at H19-ICR is independent of chromatin barrier establishment.
Vikrant Singh, Madhulika Srivastava
Molecular and cellular biology 28 3767-75 2008
Show Abstract
Transcriptional insulators are cis regulatory elements that organize chromatin into independently regulated domains. At the imprinted murine Igf2/H19 locus, the H19-ICR insulator prevents the activation of the Igf2 promoter on the maternal allele by enhancers that activate H19 on the same chromosome. Given the well-demonstrated role of H19-ICR as an enhancer blocker, we investigated its ability to define a chromatin barrier, as the two activities are coincident on several insulators and may act in concert to define a functional chromatin boundary between adjacent genes with distinct transcriptional profiles. Allele-specific association of posttranslationally modified histones, reflecting the presence of active or inactive chromatin, was analyzed in the region encompassing H19-ICR using chromatin immunoprecipitation. The existence of differential histone modifications upstream and downstream of H19-ICR specifically on the maternal chromosome was observed, which is suggestive of a chromatin barrier formation. However, H19-ICR deletion analysis indicated that distinct chromatin states exist despite the absence of an intervening barrier. Also, the enhancers can activate the Igf2 promoter despite some parts of the intervening chromatin being in the silent state. Hence, H19-ICR insulator activity is not dependent on preventing the enhancer-mediated alteration of the histone modifications in the region between the Igf2 promoter and the cognate enhancers.Full Text Article
|Genome-wide analysis of abnormal H3K9 acetylation in cloned mice.
Takahiro Suzuki, Shinji Kondo, Teruhiko Wakayama, Paul E Cizdziel, Yoshihide Hayashizaki, Takahiro Suzuki, Shinji Kondo, Teruhiko Wakayama, Paul E Cizdziel, Yoshihide Hayashizaki, Takahiro Suzuki, Shinji Kondo, Teruhiko Wakayama, Paul E Cizdziel, Yoshihide Hayashizaki
PloS one 3 e1905 2008
Show Abstract
Somatic nuclear transfer is a cloning technique that shows great promise in the application to regenerative medicine. Although cloned animals are genetically identical to their donor counterparts, abnormalities in phenotype and gene expression are frequently observed. One hypothesis is that the cause of these abnormalities is due to epigenetic aberration. In this report, we focused our analysis on the acetylation of histone H3 at lysine9 (H3K9Ac). Through the use of whole genome tiling arrays and quantitative PCR, we examined this epigenetic event and directly compared and assessed the differences between a cloned mouse (C1) and its parental nuclear donor (D1) counterpart. We identified 4720 regions of chromosomal DNA that showed notable differences in H3K9Ac and report here many genes identified in these hyper- and hypo-acetylated regions. Analysis of a second clone (C2) and its parental donor counterpart (D2) for H3K9Ac showed a high degree of similarity to the C1/D1 pair. This conservation of aberrant acetylation is suggestive of a reproducible epigenetic phenomenon that may lead to the frequent abnormalities observed in cloned mice, such as obesity. Furthermore, we demonstrated Crp which was identified as a hyper-acetylated gene in this study is related to the body mass, suggesting that Crp is a possible candidate of a cause for the abnormal obesity in cloned mice. In this, one of the first reports describing genome-wide epigenetic aberration between parental and nuclear transfer-cloned mammals, we propose that aberrant acetylation of histones (H3K9Ac) flanking promoter regions highly correlates with gene-expression and may itself be an epigenetic change that accounts for variable expression patterns observed in cloned animals.Full Text Article
|PvALF and FUS3 activate expression from the phaseolin promoter by different mechanisms.
Danny W-K Ng, Timothy C Hall
Plant molecular biology 66 233-44 2008
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Transcription from the phaseolin (phas) promoter requires two major events: chromatin remodeling, mediated by PvALF, a B3 domain factor, and activation by an ABA-induced signal transduction cascade. Expression from phas is normally seed-specific, but high levels of expression in leaves can be obtained by ectopic expression of PvALF. Here, the system was used to compare the ability of PvALF and Arabidopsis FUS3, another B3 domain transcription factor that lacks the N-terminal activation and B1 domain present in PvALF, to activate phas expression in vegetative tissues. When compared to PvALF-mediated phas activation in the presence of ABA, a delay in phas activation was observed in the presence of both FUS3 and ABA in vegetative tissue. Significant differences in histone modifications at the phas promoter were mediated by FUS3 and PvALF, suggesting that they function through different epigenetic mechanisms. The relationship between PvALF and ABI5, a bZIP transcription factor, in mediating phas expression was also evaluated. Interestingly, over-expression of ABI5 rendered phas expression ABA-independent in the presence of PvALF. Changes in phas activity in different regions within seed embryos were demonstrated using abi5 mutants. Our results show that (1) redundant factors, such as PvALF and FUS3, employ different mechanisms to regulate their common target gene (phas); (2) ABI5, and possibly other redundant bZIP factors, act downstream of ABA in modulating phas expression in the presence of PvALF.
|Histone deacetylase inhibitors modify pancreatic cell fate determination and amplify endocrine progenitors.
Haumaitre, Cécile, et al.
Mol. Cell. Biol., 28: 6373-83 (2008) 2008
Show Abstract
During pancreas development, transcription factors play critical roles in exocrine and endocrine differentiation. Transcriptional regulation in eukaryotes occurs within chromatin and is influenced by posttranslational histone modifications (e.g., acetylation) involving histone deacetylases (HDACs). Here, we show that HDAC expression and activity are developmentally regulated in the embryonic rat pancreas. We discovered that pancreatic treatment with different HDAC inhibitors (HDACi) modified the timing and determination of pancreatic cell fate. HDACi modified the exocrine lineage via abolition and enhancement of acinar and ductal differentiation, respectively. Importantly, HDACi treatment promoted the NGN3 proendocrine lineage, leading to an increased pool of endocrine progenitors and modified endocrine subtype lineage choices. Interestingly, treatments with trichostatin A and sodium butyrate, two inhibitors of both class I and class II HDACs, enhanced the pool of beta cells. These results highlight the roles of HDACs at key points in exocrine and endocrine differentiation. They show the powerful use of HDACi to switch pancreatic cell determination and amplify specific cellular subtypes, with potential applications in cell replacement therapies in diabetes.
|Rapid induction of pluripotency genes after exposure of human somatic cells to mouse ES cell extracts.
Thierry Bru,Catriona Clarke,Michael J McGrew,Helen M Sang,Ian Wilmut,J Julian Blow
Experimental cell research 314 2008
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The expression of 4 pluripotency genes (Oct4, Sox2, c-Myc and Klf4) in mouse embryonic fibroblasts can reprogramme them to a pluripotent state. We have investigated the expression of these pluripotency genes when human somatic 293T cells are permeabilized and incubated in extracts of mouse embryonic stem (ES) cells. Expression of all 4 genes was induced over 1-8 h. Gene expression was associated with loss of repressive histone H3 modifications and increased recruitment of RNA polymerase II at the promoters. Lamin A/C, which is typically found only in differentiated cells, was also removed from the nuclei. When 293T cells were returned to culture after exposure to ES cell extract, the expression of the pluripotency genes continued to rise over the following 48 h of culture, suggesting that long-term reprogramming of gene expression had been induced. This provides a methodology for studying the de-differentiation of somatic cells that can potentially lead to an efficient way of reprogramming somatic cells to a pluripotent state without genetically altering them.Full Text Article
|Analysis of HSF4 binding regions reveals its necessity for gene regulation during development and heat shock response in mouse lenses.
Mitsuaki Fujimoto, Koji Oshima, Toyohide Shinkawa, Bei Bei Wang, Sachiye Inouye, Naoki Hayashida, Ryosuke Takii, Akira Nakai, Mitsuaki Fujimoto, Koji Oshima, Toyohide Shinkawa, Bei Bei Wang, Sachiye Inouye, Naoki Hayashida, Ryosuke Takii, Akira Nakai, Mitsuaki Fujimoto, Koji Oshima, Toyohide Shinkawa, Bei Bei Wang, Sachiye Inouye, Naoki Hayashida, Ryosuke Takii, Akira Nakai
The Journal of biological chemistry 283 29961-70 2008
Show Abstract
Heat shock transcription factors (HSFs) regulate gene expression in response to heat shock and in physiological conditions. In mammals, HSF1 is required for heat-mediated induction of classic heat shock genes; however, we do not know the molecular mechanisms by which HSF4 regulates gene expression or the biological consequences of its binding to chromatin. Here, we identified that HSF4 binds to various genomic regions, including the introns and distal parts of protein-coding genes in vivo in mouse lenses, and a substantial numbers of the regions were also occupied by HSF1 and HSF2. HSF4 regulated expression of some genes at a developmental stage when HSF1 and HSF2 expression decreased. Although HSF4 binding did not affect expression of many genes, it induces demethylated status of histone H3K9 on the binding regions. Unexpectedly, a lot of HSF4 targets were induced by heat shock treatment, and HSF4 is required for induction of a set of non-classic heat shock genes in response to heat shock, in part by facilitating HSF1 binding through chromatin modification. These results suggest novel mechanisms of gene regulation controlled by HSF4 in non-classic heat shock response and in lens development.Full Text Article
|Mammalian sirtuin 1 is involved in the protective action of dietary saturated fat against alcoholic fatty liver in mice.
Min You, Qi Cao, Xiaomei Liang, Joanne M Ajmo, Gene C Ness
The Journal of nutrition 138 497-501 2008
Show Abstract
This study was undertaken to elucidate the mechanism underlying the protective effect of a high saturated fat (HSF) diet against the development of alcoholic fatty liver in mice. We tested the effects of a HSF diet on the ethanol-mediated increase in hepatic sterol regulatory element binding protein 1 (SREBP-1) activity. Thirty-two male mice were divided into 4 groups and fed liquid diets consisting of either a high polyunsaturated fat (40% of energy from corn oil) or a HSF (40% of energy from cocoa butter) diet with or without ethanol for 4 wk. In the ethanol-containing diets, ethanol was substituted for an equivalent amount of carbohydrate to provide 27.5% of the total energy. Control mice were pair-fed the same volume of liquid diets as the ethanol-fed mice. The HSF diet suppressed the increase in mature SREBP-1 protein and prevented increased mRNA of the SREBP-1-regulated lipogenic enzymes in the ethanol-fed mice (P 0.05). Sirtuins 1 (SIRT1), a NAD+-dependent class III histone deacetylase, was upregulated by ethanol administration in mice fed the HSF diet (P 0.05). The HSF diet blocked histone H3 at lysine 9 (lys9) hyperacetylation and attenuated association of acetylated histone H3-Lys9 with the promoters of mitochondrial glycerol-3-phosphate acyltransferase and stearoyl-CoA desaturase 1 in the livers of the ethanol-fed mice. These results suggest that the protective effects of HSF diet against the development of alcoholic liver steatosis may occur via regulation of the hepatic SIRT1-SREBP-1-histone H3 axis, suppressing the expression of genes encoding lipogenic enzymes and slowing the synthesis of hepatic fatty acids.
|An epigenetic aberration increased in intergenic regions of cloned mice.
Hiromi Nishida, Shinji Kondo, Takahiro Suzuki, Yuki Tsujimura, Shunsuke Komatsu, Teruhiko Wakayama, Yoshihide Hayashizaki
Mammalian genome : official journal of the International Mammalian Genome Society 19 667-74 2008
Show Abstract
The causes of frequent abnormal phenotypes and low success rate in mammalian cloning are poorly understood. Although epigenetic aberration is suspected to be a cause, its connection to the phenotypes has yet to be investigated. To measure the level of reprogramming of an epigenetic mark, acetylation at lysine 9 of histone H3 (H3K9Ac), in cloned mice, we examined its conservation between two cloned mice derived from distinct cell nuclei and their natural donors by utilizing whole-genome tiling arrays and quantitative PCR. Pairwise comparison of the H3K9Ac enrichment profile between the four mice revealed that H3K9Ac is less conserved in intergenic regions than in promoter regions of protein-coding genes. Intriguingly, the variation of H3K9Ac enrichment in intergenic regions is the most prominent in comparison of the two clones, possibly reflecting an additive effect of aberrant reprogramming of this epigenetic information occurring specifically in each of the two clones.
|Paired-like homeodomain transcription factors 1 and 2 regulate follicle-stimulating hormone beta-subunit transcription through a conserved cis-element.
Pankaj Lamba, Vishal Khivansara,
Endocrinology 149 3095-108 2008
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Paired-like homeodomain transcription factors (PITX) regulate the activity of pituitary hormone-encoding genes. Here, we examined mechanisms through which the family of PITX proteins control murine FSH beta-subunit (Fshb) transcription. We observed that endogenous PITX1 and PITX2 isoforms from murine LbetaT2 gonadotrope cells could bind a highly conserved proximal cis-element. Transfection of PITX1 or PITX2C in heterologous cells stimulated both murine and human Fshb/FSHB promoter-reporter activities, and in both cases, mutation of the critical cis-element abrogated these effects. In homologous LbetaT2 cells, the same mutation decreased basal reporter activity and greatly reduced activin A-stimulated transcription from murine and human promoter-reporters. Transfecting dominant-negative forms of PITX1 or PITX2C or knocking down PITX1 or -2 expression by RNA interference in LbetaT2 cells inhibited murine Fshb transcription, confirming roles for endogenous PITX proteins. Both PITX1 and PITX2C interacted with Smad3 (an effector of the activin signaling cascade in these cells) in coprecipitation experiments, and the PITX binding site mutation greatly inhibited Smad2/3/4-stimulated Fshb transcription. In summary, both PITX1 and PITX2C regulate murine and human Fshb/FSHB transcription through a conserved cis-element in the proximal promoter. Furthermore, the data indicate both common and distinct mechanisms of PITX1 and PITX2C action.Full Text Article
|The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells.
Helle F Jørgensen, Véronique Azuara, Shannon Amoils, Mikhail Spivakov, Anna Terry, Tatyana Nesterova, Bradley S Cobb, Bernard Ramsahoye, Matthias Merkenschlager, Amanda G Fisher
Genome biology 8 R169 2007
Show Abstract
BACKGROUND: The time of locus replication during S-phase is tightly regulated and correlates with chromatin state. Embryonic stem (ES) cells have an unusual chromatin profile where many developmental regulator genes that are not yet expressed are marked by both active and repressive histone modifications. This poised or bivalent state is also characterized by locus replication in early S-phase in ES cells, while replication timing is delayed in cells with restricted developmental options. RESULTS: Here we used a panel of mutant mouse ES cell lines lacking important chromatin modifiers to dissect the relationship between chromatin structure and replication timing. We show that temporal control of satellite DNA replication is sensitive to loss of a variety of chromatin modifiers, including Mll, Eed, Dnmt1, Suv39h1/h2 and Dicer. The replication times of many single copy loci, including a 5 Mb contiguous region surrounding the Rex1 gene, were retained in chromatin modifier mutant ES cells, although a subset of loci were affected. CONCLUSION: This analysis demonstrates the importance of chromatin modifiers for maintaining correct replication of satellite sequences in pluripotent ES cells and highlights the sensitivity of some single copy loci to the influence of chromatin modifiers. Abundant histone acetylation is shown to correlate well with early replication. Surprisingly, loss of DNA methylation or histone methylation was tolerated by many loci, suggesting that these modifications may be less influential for the timing of euchromatin replication.Full Text Article
|COP9 signalosome subunit 8 is essential for peripheral T cell homeostasis and antigen receptor-induced entry into the cell cycle from quiescence.
Suchithra Menon, Hongbo Chi, Huiyong Zhang, Xing Wang Deng, Richard A Flavell, Ning Wei
Nature immunology 8 1236-45 2007
Show Abstract
Engagement of antigen receptors triggers the proliferation and functional activation of lymphocytes. Here we report that T cell homeostasis and antigen-induced responses require the COP9 signalosome (CSN), a regulator of the ubiquitin-proteasome system. Conditional deletion of the CSN subunit Csn8 in peripheral T lymphocytes disrupted formation of the CSN complex, reduced T cell survival and proliferation in vivo and impaired antigen-induced production of interleukin 2. Moreover, Csn8-deficient T cells showed defective entry into the cell cycle from the G0 quiescent state. This phenotype was associated with a lack of signal-induced expression of cell cycle-related genes, including G1 cyclins and cyclin-dependent kinases, and with excessive induction of p21(Cip1). Our data define a CSN-dependent pathway of transcriptional control that is essential for antigen-induced initiation of T cell proliferation.
|A modular enhancer is differentially regulated by GATA and NFAT elements that direct different tissue-specific patterns of nucleosome positioning and inducible chromatin remodeling.
Andrew G Bert, Brett V Johnson, Euan W Baxter, Peter N Cockerill
Molecular and cellular biology 27 2870-85 2007
Show Abstract
We investigated alternate mechanisms employed by enhancers to position and remodel nucleosomes and activate tissue-specific genes in divergent cell types. We demonstrated that the granulocyte-macrophage colony-stimulating factor (GM-CSF) gene enhancer is modular and recruits different sets of transcription factors in T cells and myeloid cells. The enhancer recruited distinct inducible tissue-specific enhanceosome-like complexes and directed nucleosomes to different positions in these cell types. In undifferentiated T cells, the enhancer was activated by inducible binding of two NFAT/AP-1 complexes which disrupted two specifically positioned nucleosomes (N1 and N2). In myeloid cells, the enhancer was remodeled by GATA factors which constitutively displaced an upstream nucleosome (N0) and cooperated with inducible AP-1 elements to activate transcription. In mast cells, which express both GATA-2 and NFAT, these two pathways combined to activate the enhancer and generate high-level gene expression. At least 5 kb of the GM-CSF locus was organized as an array of nucleosomes with fixed positions, but the enhancer adopted different nucleosome positions in T cells and mast cells. Furthermore, nucleosomes located between the enhancer and promoter were mobilized upon activation in an enhancer-dependent manner. These studies reveal that distinct tissue-specific mechanisms can be used either alternately or in combination to activate the same enhancer.Full Text Article
|Structure/function analysis of the phosphatidylinositol-3-kinase domain of yeast tra1.
A Irina Mutiu, Stephen M T Hoke, Julie Genereaux, Carol Hannam, Katherine MacKenzie, Olivier Jobin-Robitaille, Julie Guzzo, Jacques Côté, Brenda Andrews, David B Haniford, Christopher J Brandl
Genetics 177 151-66 2007
Show Abstract
Tra1 is an essential component of the Saccharomyces cerevisiae SAGA and NuA4 complexes. Using targeted mutagenesis, we identified residues within its C-terminal phosphatidylinositol-3-kinase (PI3K) domain that are required for function. The phenotypes of tra1-P3408A, S3463A, and SRR3413-3415AAA included temperature sensitivity and reduced growth in media containing 6% ethanol or calcofluor white or depleted of phosphate. These alleles resulted in a twofold or greater change in expression of approximately 7% of yeast genes in rich media and reduced activation of PHO5 and ADH2 promoters. Tra1-SRR3413 associated with components of both the NuA4 and SAGA complexes and with the Gal4 transcriptional activation domain similar to wild-type protein. Tra1-SRR3413 was recruited to the PHO5 promoter in vivo but gave rise to decreased relative amounts of acetylated histone H3 and histone H4 at SAGA and NuA4 regulated promoters. Distinct from other components of these complexes, tra1-SRR3413 resulted in generation-dependent telomere shortening and synthetic slow growth in combination with deletions of a number of genes with roles in membrane-related processes. While the tra1 alleles have some phenotypic similarities with deletions of SAGA and NuA4 components, their distinct nature may arise from the simultaneous alteration of SAGA and NuA4 functions.Full Text Article
|Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell.
Hiromi Nishida, Takahiro Suzuki, Shinji Kondo, Hisashi Miura, Yu-ichi Fujimura, Yoshihide Hayashizaki
Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 14 203-11 2006
Show Abstract
Nucleosome depletion in the promoters has been indicated in yeasts, suggesting that nucleosome depletion in promoter might be a fundamental feature of eukaryotic transcriptional regulation. We compared the relationship between histone H3 acetylation at lysine 9 (K9) in promoter, gene expression level, and nucleosome density in the vicinity of the transcription start site (TSS), in HepG2 cells (human hepatocellular liver carcinoma cells). We found that the density of nucleosome is relatively low in the close vicinity of TSS flanked by H3 K9 significantly acetylated promoter, compared with that for genes without marked H3 K9 acetylation in promoter, regardless of their transcriptional activation status. Our results imply that the relative nucleosome depletion in the vicinity of TSS is not necessarily associated with active transcription, but with histone H3 K9 acetylation in promoter.
|Snf1p-dependent Spt-Ada-Gcn5-acetyltransferase (SAGA) recruitment and chromatin remodeling activities on the HXT2 and HXT4 promoters.
Chris J C van Oevelen, Hetty A A M van Teeffelen, Folkert J van Werven, H Th Marc Timmers
The Journal of biological chemistry 281 4523-31 2006
Show Abstract
We previously showed that the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex is recruited to the activated HXT2 and HXT4 genes and plays a role in the association of TBP-associated factors. Using the HXT2 and HXT4 genes, we now present evidence for a functional link between Snf1p-dependent activation, recruitment of the SAGA complex, histone H3 removal, and H3 acetylation. Recruitment of the SAGA complex is dependent on the release of Ssn6p-Tup1p repression by Snf1p. In addition, we found that the Gcn5p subunit of the SAGA complex preferentially acetylates histone H3K18 on the HXT2 and HXT4 promoters and that Gcn5p activity is required for removal of histone H3 from the HXT4 promoter TATA region. In contrast, histone H3 removal from the HXT2 promoter does not require Gcn5p. In conclusion, although similar protein complexes are involved, induction of HXT2 and HXT4 displays important mechanistic differences.
|EGFR mutations in non-small-cell lung cancer: analysis of a large series of cases and development of a rapid and sensitive method for diagnostic screening with potential implications on pharmacologic treatment.
Antonio Marchetti,Carla Martella,Lara Felicioni,Fabio Barassi,Simona Salvatore,Antonio Chella,Pier P Camplese,Teodorico Iarussi,Felice Mucilli,Andrea Mezzetti,Franco Cuccurullo,Rocco Sacco,Fiamma Buttitta
Journal of clinical oncology : official journal of the American Society of Clinical Oncology 23 2005
Show Abstract
It has been reported that EGFR mutations in lung carcinomas make the disease more responsive to treatment with tyrosine kinase inhibitors. We decided to evaluate the prevalence of EGFR mutations in a large series of non-small-cell lung carcinomas (NSCLCs) and to develop a rapid and sensitive screening method. PATIENTS AND METHODS We examined 860 consecutive NSCLC patients for EGFR mutations in exons 18, 19, and 21 using a dual technical approach--direct sequencing of polymerase chain reaction (PCR) products and PCR single-strand conformation polymorphism (SSCP) analysis. Moreover, all lung adenocarcinomas were analyzed for K-ras mutations at codon 12 by allele-specific oligoprobe hybriditations.
|Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin.
Suka, N, et al.
Mol. Cell, 8: 473-9 (2001) 2001
Show Abstract
We have developed a highly specific antibody set for acetylation sites in yeast histones H4 (K5, K8, K12, and K16); H3 (K9, K14, K18, K23, and K27); H2A (K7); and H2B (K11 and K16). Since ELISA does not assure antibody specificity in chromatin immunoprecipitation, we have employed additional screens against the respective histone mutations. We now show that telomeric and silent mating locus heterochromatin is hypoacetylated at all histone sites. At the INO1 promoter, RPD3 is required for strongly deacetylating all sites except H4 K16, ESA1 for acetylating H2A, H2B, and H4 sites except H4 K16, and GCN5 for acetylating H2B and H3 sites except H3 K14. These data uncover the in vivo usage of acetylation sites in heterochromatin and euchromatin.
|Chromatin Immunoprecipitation (ChIP)
|ICI 125,211: a new gastric antisecretory agent acting on histamine H2-receptors.
Yellin TO, Buck SH, Gilman DJ, Jones DF, Wardleworth JM.
Life sciences 25 2001-9 2001
|Histone Modifications


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News and notes on health, medicine and fitness
Diet monitoring just a breath away, say Japanese researchers
Want to know whether your body is successfully burning fat while you diet? Thanks to a team of researchers in Japan, you may soon be able to find out simply by taking a breath test.
The team developed a breathalyzer-like device that measures the amount of acetone in a person's breath and can easily transfer the data to a smartphone or a computer. Acetone is produced as a byproduct when the liver breaks down fat for energy, so measuring how much is in someone's breath indicates how much fat their body is breaking down.
The Japanese researchers tested their device on a group of volunteers who exercised; dieted and exercised; or didn't do either. They measured the volunteers' body fat using another method and showed that for those who decreased their body fat (mostly in the diet-plus-exercise group), their device also showed higher acetone levels in the volunteers' breath.
"Because obesity increases the risk of lifestyle-related illnesses, enabling users to monitor the state of fat burning could play a pivotal role in daily diet management," said Satoshi Hiyama, the principal investigator in the study.
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Journal Sentinel TV and film critic Duane Dudek looks at life on the small and big screen, and some of the cool stuff on both.
Memories of Blockbuster: late nights and late fees
News that Blockbuster will be closing its remaining its remaining stores, stopping its DVD delivery service and folding the brand caused me to reflect a bit on the years spent going there. »Read Full Blog Post
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When I was living on the Eastside of Milwaukee in the mid to late 80s I was spoiled to live a couple blocks from Video Visions in Prospect Mall. They had a great selection of movies and I mined their catelog to see for the first time many films by the likes of Peckinpah, Scorcese, Hal Ashby, Michael Cimino, Robert Altman, etc. Then I moved to Tosa and was forced to go to Blockbuster where the selection was terrible. They had a bazzilion copies of the latest Shwarzegger junk, but not much else. One day in desparation I rented some crummy movie which I didn't watch. I went to bring it back, set the VHS tape on the roof of my car, forgot about it and drove to the Blockbuster. I frantically searched my car and couldn't find it. I drove home and found the VHS tape in the middle of the road in front of my house, smashed from having been run over. Blockbuster charged me a $90 replacement fee for that tape. I always hated Blockbuster.
Good anecdote backslapper. When I was 12, we only cared about 2 things..playing sports and hoping to watch R rated movies with sex scenes in them. Since my neighbor's older sister worked at Blockbuster, we'd usually walk up there on Friday night and she'd let us rent whatever we wanted. At that time, Christina Applegate or Marissa Tomei movies for beating and action films with Stalone or Van Damme for viewing...Plus the bonus for me, my buddy's sister at Blockbuster had HUGE CANS. Tan mountains of boobies with a valley of exposed cleavage erupting like a volcano from that Blockbuster polo shirt made those Fridays even better. I never told my buddy that or he would have pounded me. Haha.
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Softball Splits First Day Of Big West Action
Christina Clermont struck out 10 in a complete game shutout.
Tautalafua's Hot Bat Drives 49ers to Two Victories at UC Riverside
The freshman drove in 10 RBI, while hitting a grand slam as LBSU won two games at UCR on Friday.
Softball Notches Two Wins on Day One of San Diego State Classic II
The 49ers defeated Massachusetts 9-1 and Miami (OH) 4-2.
49ers Split at LBSU Invitational
The 49ers defeated North Dakota State 5-4, but fell to South Alabama 4-1 in the night cap.
49ers defeat Charleston Southern 6-1 at LBSU Invitational
Amanda Hansen allows only one run as Long Beach State improves to 13-8.
Long Beach State (2014): Threw 15.0 innings, third most on the team ... Seven appearances in the circle was also third-most out of the pitching staff ... Pitched 3.0 innings of relief against Utah (2/15) ... Saw 0.2 innings against LSU (2/20) ... Set a career high with 3.1 innings of work against Oklahoma State (2/22) ... Had a strikeout in 0.2 innings of hitless relief at San Diego State (3/14) ... Took the loss in her only decision of the year against San Jose State (3/22) ... Pitched two innings in a 15-4 win over UC Riverside (4/6) ... Allowed four hits in her final appearance of the season against UCLA (4/21).
(2013): Posted a 4.67 ERA in her first season with Long Beach State ... Made six appearances on the year as well as one start ... Debuted against Oregon State on February 16 ... Pitched a scoreless inning against Charleston Southern (3/9) ... Allowed just one hit in 2.1 innings of work against South Alabama (3/10) ... Pitched a career high three innings against Buffalo (3/13) ... Earned her only start against Miami, surrendering no earned runs in an inning of work (3/15) ... Finished her season with a 1.0 inning outing at UC Riverside (3/29).
High School: Attended Segerstrom High School, lettering in softball ... Golden West League MVP in 2012 with a .429 batting average and an ERA of 1.08 ... Also named first-team All-CIF and third-team All-County in 2012 ... Two-time Golden West League Pitcher of the Year (`11, `10) ... Had an ERA of 0.77 and batting average of .365 her junior year and .344 and 0.42 her sophomore season ... First-team all-league and first-team All-CIF in 2010 ... Was named first-team all-league and All-Freshman team in 2009 ... Was on the Principal's Honor Roll every year of high school, and received Scholar-Athlete awards.
Major: Political Science
Career Highs:
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Hawks pick up Dampier as insurance for rest of season
Mar 1, 2012, 1:23 PM EDT
Eric Dampier isn't brining a lot to the Atlanta Hawks the rest of this season. But the journeyman center provides some depth at a ravaged position in Atlanta.
The Hawks have picked up Dampier for the rest of the season, Marc Spears of Yahoo tweets.
Right now Zaza Pachulia is the starting center while everyone waits for the return of Al Horford. Jason Collins is still on the roster but is out a couple more weeks with elbow problems. Ivan Johnson is there, too, but that's the kind of guy that has you picking up Dampier just in case.
By the way, Horford could return to non-contact work with the team soon but may still be a month away from stepping on the court following his torn pectoral muscle.
- bowens3181 - Mar 1, 2012 at 1:36 PM
I swear Kurt is either:
1. hammered every time he writes anything
2. dyslexic
3. an elementary school drop out
…because he CANNOT spell to save his life
"Eric Dampier isn't brining a lot to the Atlanta Hawks"
Really!? At least get someone else to edit your work if you flat out refuse to.
- igeorgiaboy - Mar 1, 2012 at 2:05 PM
Dampie? Ok I can see that. But why they dont move Marvin Williams or force Joe Johnson to redo his contract is beyond me. Joe Johnson is not MAX contract material. Josh Smith I can deal with because he gets boards and pts… MARVIN AND JOE MUST GO….
- goforthanddie - Mar 1, 2012 at 4:38 PM
You can't "force" anyone with a guaranteed contract to do anything. That includes earning that contract.
- goforthanddie - Mar 1, 2012 at 4:37 PM
Insurance against what? Making sure the bench doesn't float away?
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|Product #: EMC6010024_TQ
My Bookmark (Book Project) (Resource Book Only) eBookGrade 5|Grade 6
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This individual book report project focuses on identifying story elements & directs a student to read a fiction book, review basic story elements, & create a bookmark. The unit includes directions, bookmark forms, & bookmarks of good reader strategies. (Find other book units by searching 'Reports 5-6')
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Was Justin Bieber Late to Concert After Throwing Tantrum? He Responds!
Justin Bieber is learning the importance of being on time.
The pop star was late to his London concert earlier this week, and now reports say that his tardiness was due to his own diva-like behavior, according to The Sun.
"He was arguing with members of his management, his family," says a source about his behavior prior to the start of the show. "It was a really uncomfortable atmosphere."
"His attitude was, 'I'm the star and I can do what I want,'" the source adds.
However, Justin is fighting back on Twitter, claiming that the rumors are untrue.
On March 6, he wrote:
rumors rumors and more rumors. nothing more nothing less. might talk about them 1 day. rt now im just gonna be positive. cant bring me down— Justin Bieber (@justinbieber) March 6, 2013
fake stories to sell papers i guess are part of the job. but im a good person. i know that. u cant tell me different. we know the truth— Justin Bieber (@justinbieber) March 6, 2013


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It's Dan Mount again and I'm here with the Tuesday NHL headlines. Today we look at the struggles of the Toronto Maple Leafs and the injuries surrounding the defending champion Chicago Blackhawks. We're close to the end of the regular season and both storied franchises are facing challenges. The champs are facing health issues, while the Leafs are fighting for their playoff lives.
If you like (or don't like) what I have to say, please leave comments below or you can tweet me @DanMountSports. I love getting feedback from the readers.
Falling Leafs
At the beginning of the season, the Toronto Maple Leafs were rolling along. The Buds had things going their way and looking to make some noise in the Eastern Conference playoff race. However, things have changed drastically for the Leafs as they've lost eight in a row heading into Tuesday night's game against Calgary.
There has been a lot of blame to go around from James Reimer, (ask his wife about that one) to captain and defenseman Dion Phaneuf, to coach Randy Carlyle (who former boxing champion and Leafs fan Riddick Bowe wants to knock out after a loss to Philadelphia.) Even double-shifted offensive star Phil Kessel is not immune to being criticized (although he's accounted for one-third of the offense for Toronto.)
So what's wrong in Toronto? How did they go from a playoff threat to a bubble team? Toronto is two points back in the wild card standings as of Tuesday night.
One of the main culprits has been Reimer, as he's been disastrous in relief of Jonathan Bernier. (Bernier did return in a loss to St. Louis and dropped a game against the Flyers.) However, Reimer shouldn't take all of the heat as his agent Ray Petkau pointed out the defense didn't exactly do the embattled netminder any favors. Bernier is clearly the number one, but Reimer isn't exactly awful. Plus, Randy Carlyle's system allows for more shots and it was only a matter of time before the goalies were going to lose the form that got Toronto into any position to contend.
There are other things to blame for the collapse. The Leafs power play couldn't help make up for the bad play of the even strength unit. The Buds power play only worked at a 14-percent efficiency rating in March, which is down almost eight points from the rest of the season. Toronto has lived dangerously by trying to outscore its opponents, but it is defense that rules this time of the year.
Another problem is that Carlyle has a short bench and doesn't really use his fourth line. The fourth line of Colton Orr, Frazer McLaren and others only gets over five minutes a game, but they are more than capable of getting about 10 minutes of time. Five minutes may not seem like a lot for a single game, but those minutes add up over the course of the season.
After the last loss to Detroit, Toronto has only a less than seven-percent chance to make the postseason. The main question will be do Carlyle, General Manager Dave Nonis and people like Phaneuf get a chance to right the wrong or is there going to be a massive overhaul. I'm leading towards Carlyle and possibly Nonis getting the axe in the offseason. The Leafs haven't won the Cup since 1967, and the fans and the media are clamoring for a title.
Blackhawks Down?
The Chicago Blackhawks were my favorite to win the Stanley Cup at the beginning of the season. However, the champs have taken a few hits over the last few weeks. The St. Louis Blues loaded up and took first in Central Division thanks to getting Ryan Miller at the trade deadline.
The main problem has been the injuries that Chicago has taken in the last couple of weeks. It started when Patrick Kane suffered a leg injury against St. Louis on March 20. The Hawks are missing Kane on the power play.
However, it went from bad to worse as Blackhawks' captain Jonathan Toews was injured after absorbing a hard hit from Pittsburgh Penguins defenseman Brooks Orpik. Toews is day-to-day according to Coach Joel Quenville. (Toews was holding his left arm when he was taken off the ice.)
Some are wondering if Chicago's chance to repeat is going up in smoke. The Blackhawks need to fix some things if they want to contend. Their normally solid defense has been shaky as of late, plus Corey Crawford has not been as good as he was during last year's Stanley Cup run. The Hawks are going to need players like Patrick Sharp and Marian Hossa to step up the offensive production before Toews and Kane get healthy.
It's that time of the week where look at the spectacular, the stupid and the silly with First star, Worst star and Who blew up the Death Star?
First star
Jonathan Quick makes what could be the save of the year against the Winnipeg Jets with this move called the scorpion kick.
Worst star
James Neal of the Penguins cross-checks the head of Detroit's Luke Glendening.
Who blew up the Death Star?
Dear Jeopardy contest,
Magic Johnson didn't play in the NHL. Hand in your man card.
Men of North America
That's it for this week. Take care, and I'll see you later in the week.
Dan Mount is an NHL columnist for TJRSports.com. He is based out of Watertown, NY.