where does mrna processing take place in eurkaryotic cells
nucleus
9850039
rRNAs: 18S, 5.8S, and 28S. The transcription of rRNA genes takes place in a specialised structure of the nucleus called the nucleolus, where the transcribed rRNAs are combined with proteins to form ribosomes. RNA polymerase II (Pol II) is responsible for the transcription of all mRNAs, some snRNAs, siRNAs, and all miRNAs. Many Pol II transcripts exist transiently as single strand precursor RNAs (pre-RNAs) that are further processed to generate mature RNAs. For example, precursor mRNAs (pre-mRNAs) are extensively processed before exiting into the cytoplasm through the nuclear pore for protein translation. RNA polymerase III (Pol III) transcribes small non-coding
Eukaryotic transcription
4187255
produce different proteins and RNAs such as mRNA, tRNA, and rRNA. The basic primary transcript modification process is similar for tRNA and rRNA in both eukaryotic and prokaryotic cells. On the other hand, primary transcript processing varies in mRNAs of prokaryotic and eukaryotic cells. For example, some prokaryotic bacterial mRNAs serve as templates for synthesis of proteins at the same time they are being produced via transcription. Alternatively, pre-mRNA of eukaryotic cells undergo a wide range of modifications prior to their transport from the nucleus to cytoplasm where their mature forms are translated. These modifications are responsible for the different
Primary transcript
8718188
the cap to the mRNA while it is produced by RNA polymerase II. Eukaryotic RNA must undergo a series of modifications in order to be exported from the nucleus and successfully translated into function proteins, many of which are dependent on mRNA capping, the first mRNA modification to take place. 5' capping is essential for mRNA stability, enhancing mRNA processing, mRNA export and translation. After successful capping, an additional phosphorylation event initiates the recruitment of machinery necessary for RNA splicing, a process by which introns are removed to produce a mature mRNA. The addition of the cap onto mRNA confers
Capping enzyme
6948823
SnRNP snRNPs (pronounced "snurps"), or small nuclear ribonucleoproteins, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs. The action of snRNPs is essential to the removal of introns from pre-mRNA, a critical aspect of post-transcriptional modification of RNA, occurring only in the nucleus of eukaryotic cells. Additionally, "U7 snRNP" is not involved in splicing at all, as U7 snRNP is responsible for processing the 3′ stem-loop of histone pre-mRNA. The two essential components of snRNPs are protein molecules and RNA. The RNA
SnRNP
773205
of the entire transcription process (that began with the production of the pre-mRNA chain) is a mature mRNA chain. The mature mRNA finds its way to a ribosome, where it gets translated. In prokaryotic cells, which have no nuclear compartment, the processes of transcription and translation may be linked together without clear separation. In eukaryotic cells, the site of transcription (the cell nucleus) is usually separated from the site of translation (the cytoplasm), so the mRNA must be transported out of the nucleus into the cytoplasm, where it can be bound by ribosomes. The ribosome reads the mRNA triplet codons,
Central dogma of molecular biology
9743981
of a wide variety of RNA species. In the cytoplasm of cells, it is involved in the turn-over of messenger RNA (mRNA) molecules. The complex can degrade mRNA molecules that have been tagged for degradation because they contain errors, through interactions with proteins from the nonsense mediated decay or non-stop decay pathways. In alternative fashion, mRNAs are degraded as part of their normal turnover. Several proteins that stabilize or destabilize mRNA molecules through binding to AU-rich elements in the 3' untranslated region of mRNAs interact with the exosome complex. In the nucleus, the exosome is required for the correct processing
Exosome complex
348235
that every three nucleotides (a codon) corresponds to one amino acid. In eukaryotic cells, once precursor mRNA (pre-mRNA) has been transcribed from DNA, it is processed to mature mRNA. This removes its introns—non-coding sections of the pre-mRNA. The mRNA is then exported from the nucleus to the cytoplasm, where it is bound to ribosomes and translated into its corresponding protein form with the help of tRNA. In prokaryotic cells, which do not have nucleus and cytoplasm compartments, mRNA can bind to ribosomes while it is being transcribed from DNA. After a certain amount of time, the message degrades into its
RNA
15446774
the mRNA translation, it can avoid this problem of molecular chaos. This is exactly what is found in eukaryotic cells, where the splicing of the primary RNA transcript occurs within the nucleus, and the spliced mRNA is transported to the cytoplasm, where the ribosomes translate them into proteins. The nuclear boundary provides a clear separation of the primary RNA splicing and the mRNA translation. These investigations thus led to the possibility that primordial DNA with essentially random sequence gave rise to the complex structure of the split genes with exons, introns and splice junctions. They also predict that the cells
Periannan Senapathy
331610
DNA strand from the 3-prime (3') end to the 5-prime (5') end, while it synthesizes a single strand of messenger RNA in the 5'-to-3' direction. The general RNA structure is very similar to the DNA structure, but in RNA the nucleotide uracil takes the place that thymine occupies in DNA. The single strand of mRNA leaves the nucleus through nuclear pores, and migrates into the cytoplasm. The first product of transcription differs in prokaryotic cells from that of eukaryotic cells, as in prokaryotic cells the product is mRNA, which needs no post-transcriptional modification, whereas, in eukaryotic cells, the first product
Protein biosynthesis
11318063
mRNAs (pre-mRNA) (see CPSF). The FIP1 motif of 40 amino acids on FIP1L1 is responsible for its binding to CPSF1. CPSF1 is an RNA processing protein that binds to uracil-rich sequences in pre-mRNA, concurrently binds with and stimulates POPOLA, i.e. Polynucleotide adenylyltransferase, and then proceeds to add adenylyl residues to pre-mRNA. This poly-adenylyl action increases pre-mRNA's maturation and movement from the nucleus to cytoplasm while also increasing the stability of the mRNA formed from pre-mRNA: FIP1L1 is a Pre-mRNA 3'-end-processing factor. "FIP1L1" gene fusions between it and either the platelet-derived growth factor receptor, alpha ("PGDFRA") or Retinoic acid receptor alpha
FIP1L1
387782
including bacteria, archaea, plants, yeast and humans. RNA splicing RNA splicing, in molecular biology, is a form of RNA processing in which a newly made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). During splicing, introns are removed and exons are joined together. For nuclear-encoded genes, splicing takes place within the nucleus either during or immediately after transcription. For those eukaryotic genes that contain introns, splicing is usually required in order to create an mRNA molecule that can be translated into protein. For many eukaryotic introns, splicing is carried out in a series of reactions
RNA splicing
387765
RNA splicing RNA splicing, in molecular biology, is a form of RNA processing in which a newly made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). During splicing, introns are removed and exons are joined together. For nuclear-encoded genes, splicing takes place within the nucleus either during or immediately after transcription. For those eukaryotic genes that contain introns, splicing is usually required in order to create an mRNA molecule that can be translated into protein. For many eukaryotic introns, splicing is carried out in a series of reactions which are catalyzed by the spliceosome, a
RNA splicing
7546160
mature mRNA molecule, while intron regions are spliced out (excised) during post-transcriptional processing. Indeed, the intron regions of a gene can be considerably longer than the exon regions. Once spliced together, the exons form a single continuous protein-coding regions, and the splice boundaries are not detectable. Eukaryotic post-transcriptional processing also adds a 5' cap to the start of the mRNA and a poly-adenosine tail to the end of the mRNA. These additions stabilise the mRNA and direct its transport from the nucleus to the cytoplasm, although neither of these features are directly encoded in the structure of a gene. The
Gene structure
15021442
roenbergensis", and thereby confers immunity to the population. CroV enters cells via phagocytosis. Once inside the cell, the CroV capsid disassembles and the viral proteins and genome are released. CroV does not use the transcription or translation machinery of the host cell. It remains in the cytoplasm, where a “virus factory” forms and replicates independent of the host cell nucleus. The CroV genome is not integrated into the host cell genome. CroV encodes eight subunits of DNA-dependent RNA polymerase and it also encodes at least six transcription factors, which allows the DNA genome to be transcribed into mRNA without the
Cafeteria roenbergensis virus
1373830
its mRNA target interact. While the majority of miRNAs are located within the cell, some miRNAs, commonly known as circulating miRNAs or extracellular miRNAs, have also been found in extracellular environment, including various biological fluids and cell culture media. miRNA biogenesis in plants differs from animal biogenesis mainly in the steps of nuclear processing and export. Instead of being cleaved by two different enzymes, once inside and once outside the nucleus, both cleavages of the plant miRNA are performed by a Dicer homolog, called Dicer-like1 (DL1). DL1 is expressed only in the nucleus of plant cells, which indicates that both
MicroRNA
10585822
associated with longer leukocyte telomere length, are associated with faster epigenetic aging rates in blood according to a molecular biomarker of aging known as epigenetic clock. Similarly, human TERT expression did not arrest epigenetic aging in human fibroblasts. The hTERT gene has become a main focus for gene therapy involving cancer due to its expression in tumor cells but not somatic adult cells. One method is to prevent the translation of hTERT mRNA through the introduction of siRNA, which are complimentary sequences that bind to the mRNA preventing processing of the gene post transcription. This method does not completely eliminate
Telomerase reverse transcriptase
4187261
on the level of DHFR pre-mRNA containing certain introns, which are sections of pre-mRNA that are usually cut out of the sequence as a part of processing. However, levels of total DHFR mRNA decreased two-fold in cells exposed to 1.0 μM FUra. There was no significant change in the half-life, which refers to the time it takes 50% of the mRNA to decay, of total DHFR mRNA or pre-mRNA observed in cells exposed to FUra. And nuclear/cytoplasmic RNA labeling experiments demonstrated that the rate of nuclear DHFR RNA changing to cytoplasmic DHFR mRNA decreased in cells treated with FUra. These
Primary transcript
773204
place during S phase of the cell cycle. Transcription is the process by which the information contained in a section of DNA is replicated in the form of a newly assembled piece of messenger RNA (mRNA). Enzymes facilitating the process include RNA polymerase and transcription factors. In eukaryotic cells the primary transcript is pre-mRNA. Pre-mRNA must be processed for translation to proceed. Processing includes the addition of a 5' cap and a poly-A tail to the pre-mRNA chain, followed by splicing. Alternative splicing occurs when appropriate, increasing the diversity of the proteins that any single mRNA can produce. The product
Central dogma of molecular biology
13224328
known to function within cells: the nonsense-mediated mRNA decay pathway (NMD); the nonstop mediated mRNA decay pathways (NSD); and the no-go mediated mRNA decay pathway (NGD). Nonsense-mediated decay is involved in detection and decay of mRNA transcripts which contain premature termination codons (PTCs). PTCs can arise in cells through various mechanisms: germline mutations in DNA; somatic mutations in DNA; errors in transcription; or errors in post transcriptional mRNA processing. Failure to recognize and decay these mRNA transcripts can result in the production of truncated proteins which may be harmful to the organism. By causing decay of C-terminally truncated polypeptides, the
MRNA surveillance
11484378
+ RNA(n) = diphosphate + RNA(n+1) Uridylation catalyzed by ZCCHC6 takes place readily on deadenylated mRNAs inside the cells. Purified ZZHC6 selectively recognizes and uridylates RNA molecules possessing short polyA-tails (less than 25 nucleotides) in vitro. In cells depleted of ZCCHC6, the majority of mRNAs lose the signature oligo-U-tails that are characteristic of ZCCHC6 reactivity, and the half-life of mRNA molecules are accordingly prolonged. In addition to mRNA degradation, uridylation is also thought to function in pre-microRNA maturation, with some group II pre-microRNA requiring 3' mono-uridylation for Dicer processing. ZCCHC6 is thought to work in redundancy with ZCCHC11 to mediate
ZCCHC6
7197511
P-bodies Processing bodies (P-bodies) are distinct foci within the cytoplasm of the eukaryotic cell consisting of many enzymes involved in mRNA turnover. P-bodies have been observed in somatic cells originating from vertebrates and invertebrates, plants and yeast. To date, P-bodies have been demonstrated to play fundamental roles in general mRNA decay, nonsense-mediated mRNA decay, adenylate-uridylate-rich element mediated mRNA decay, and microRNA induced mRNA silencing. Not all mRNAs which enter P-bodies are degraded, as it has been demonstrated that some mRNAs can exit P-bodies and re-initiate translation. Purification and sequencing of the mRNA from purified processing bodies showed that these mRNAs
P-bodies
7197518
identify them. Using this approach, Youn et al. identified 42 proteins that localize to processing bodies. P-bodies Processing bodies (P-bodies) are distinct foci within the cytoplasm of the eukaryotic cell consisting of many enzymes involved in mRNA turnover. P-bodies have been observed in somatic cells originating from vertebrates and invertebrates, plants and yeast. To date, P-bodies have been demonstrated to play fundamental roles in general mRNA decay, nonsense-mediated mRNA decay, adenylate-uridylate-rich element mediated mRNA decay, and microRNA induced mRNA silencing. Not all mRNAs which enter P-bodies are degraded, as it has been demonstrated that some mRNAs can exit P-bodies and
P-bodies
4187264
by Aedes. Ivo Melcak, Stepanka Melcakova, Vojtech Kopsky, Jaromıra Vecerova and Ivan Raska from the department of Cell Biology at the Institute of Experimental Medicine, at the Academy of Sciences of Czech Republic in Prague studied the influences of nuclear speckles on pre-mRNA. Nuclear speckles (speckles) are a part of the nuclei of cells and are enriched with splicing factors known for involvement in mRNA processing. Nuclear speckles have shown to serve neighboring active genes as storage places of these splicing factors. In this study, researchers showed that, in HeLa cells which derived from cells of a person who had
Primary transcript
10764808
ribonucleases in an energy-dependent mode of RNA degradation. "E. coli" does not have a 5'→3' degradation pathway. Its mRNA does not have 5' capped ends and there are not any 5'→3' exonucleases known. The same thing happens to other eubacteria, hence the 5'→3' degradation pathway could be an exclusive treat of eukaryotic cells. Degradosome The degradosome is a multiprotein complex present in most bacteria that is involved in the processing of ribosomal RNA and the degradation of messenger RNA and is regulated by Non-coding RNA. It contains the proteins RNA helicase B, RNase E and Polynucleotide phosphorylase. The store of
Degradosome
7197516
mRNA decay and sometimes the mRNA can exit the P-bodies and re-initiate translation, the question remains of what controls this switch. Another ambiguous point to be addressed is whether the proteins that localize to P-bodies are actively functioning in the miRNA gene silencing process or whether they are merely on standby. In 2017, a new method to purify processing bodies was published. Hubstenberger et al. used fluorescence-activated particle sorting (a method based on the ideas of fluorescence-activated cell sorting) to purify processing bodies from human epithelial cells. From these purified processing bodies they were able to use mass spectrometry and
P-bodies
15639479
cells except gametes. The role of the protein domain SWAP is to control sex-independent pre-mRNA processing in somatic cells, that is, in every cell except the sex cells This includes autoregulation, whereby it regulates the splicing of its own pre-mRNA. The mammalian homologue of SWAP acts as a thyroid hormone regulated gene. This mean it is controlled by the thyroid. SWAP proteins share a colinearly arrayed series of novel sequence motifs. This means that they have been conserved over time. The SWAP protein in different organisms share some similarity in terms of sequence and may have been related at some
SWAP protein domain
4187256
types of encoded messages that lead to translation of various types of products. Furthermore, primary transcript processing provides a control for gene expression as well as a regulatory mechanism for the degradation rates of mRNAs. The processing of pre-mRNA in eukaryotic cells includes 5' capping, 3' Polyadenylation, and alternative splicing. Shortly after transcription is initiated in eukaryotes, a pre-mRNA's 5' end is modified by the addition of a 7-methylguanosine cap, also known as a 5' cap. The 5' capping modification is initiated by the addition of a GTP to the 5' terminal nucleotide of the pre-mRNA in reverse orientation followed
Primary transcript
13367113
necrosis of parenchymal cells, activation and proliferation of PaSCs take place. Inflammation and parenchymal necrosis precede PaSC activation. Activated PaSCs are located in areas of major necrosis and inflammation that harbour cytokines, growth factors and reactive oxygen species. Inflammatory processes are essential in contributing towards the activation of stellate cells. Therefore, both autocrine and paracrine mediators are involved pancreatic stellate cell activation. Copious amounts of α- SMA-expressing cells are present in fibrotic areas of pancreatic tissue sections in patients with chronic pancreatitis. α-SMA-expressing cells in fibrotic areas yield MRNA encoding pro-collagen α1I, indicating that activated PaSCs are the predominant source
Pancreatic stellate cell
12033064
more likely source of cellular plasticity is through the Regulation of gene expression, such that while two cells may have near identical DNA, the differential expression of certain genes results in variation. Research has shown that cells are capable of regulating gene expression at several stages: mRNA transcription, processing and transportation as well as in protein translation, post-translational processing and degradation. Regulatory proteins that bind to DNA, RNA, and/or proteins are key effectors in these processes and function by positively or negatively regulating specific protein level and function in a cell. And, while DNA binding transcription factors provide a mechanism
Epigenomics
269931
enzymes during transcription so that processing can proceed quickly after the start of transcription. The short-lived, unprocessed or partially processed product is termed "precursor mRNA", or "pre-mRNA"; once completely processed, it is termed "mature mRNA". Processing of mRNA differs greatly among eukaryotes, bacteria, and archea. Non-eukaryotic mRNA is, in essence, mature upon transcription and requires no processing, except in rare cases. Eukaryotic pre-mRNA, however, requires extensive processing. A "5' cap" (also termed an RNA cap, an RNA 7-methylguanosine cap, or an RNA mG cap) is a modified guanine nucleotide that has been added to the "front" or 5' end of
Messenger RNA
91971
Such vectors allow for self-replication, inside the cells, and potentially integration in the host DNA. They typically also contain a strong promoter to drive transcription of the target cDNA into mRNA, which is then translated into protein. On June 13, 2013, the United States Supreme Court ruled in the case of "Association for Molecular Pathology v. Myriad Genetics" that while naturally occurring human genes cannot be patented, cDNA is patent eligible because it does not occur naturally. Some viruses also use cDNA to turn their viral RNA into mRNA (viral RNA → cDNA → mRNA). The mRNA is used to
Complementary DNA
1729036
cleavage occurs with only the synthesis and mitosis phases of the cell cycle. The addition of the two growth phases into the cell cycle allows for the cells to increase in size, as up to this point the blastomeres undergo reductive divisions in which the overall size of the embryo does not increase, but more cells are created. This transition begins the growth in size of the organism. The mid-blastula transition is also characterised by a marked increase in transcription of new, non-maternal mRNA transcribed from the genome of the organism. Large amounts of the maternal mRNA are destroyed at
Blastula
9757992
injury site; they are selective and will salvage certain factors. Macrophages produce apolipoprotien E which is involved in rescuing cholesterol in damaged nerves. In the same investigation, temporal levels of apolipoprotein E mRNA expression in the three models for demylenation and nerve damage were consistent with respect to models for cholesterol salvage in nerve injury. Macrophages play a role in salvaging cholesterol during nerve injury. Macrophages also play a role in inducing the proliferation of Schwann cells that occurs during Wallerian degeneration. Supernatant has been collected from medium in which macrophages are active in myelin phagocytosis where lysosomal processing of
Nerve injury
4187260
that code for rRNA, whereas endolytic cleavage corresponds to tRNA precursors. A study by Cindy L. Wills and Bruce J. Dolnick from the Department of Experimental Therapeutics at the Roswell Park Memorial Institute in Buffalo, New York and from the Cell and Molecular Biology Program at University of Wisconsin in Madison, Wisconsin was made to understand cellular processes involving primary transcripts. Researchers wanted to understand whether 5-Fluorouracil (FUra), a drug known for use in cancer treatment, inhibits or shuts down dihydrofolate reductase (DHFR) pre-mRNA processing and/or nuclear mRNA stability in methotrexate-resistant KB cells. Long-term exposure to FUra had no effect
Primary transcript
6255926
IFN-γ, natural T reg, Tr1, CD8+ T reg, and B reg. All of these lymphocytes act, at least in part, by secreting IL-10 and other suppressive cytokines. CD4+ T regs are present at increased frequency in the bone marrow of VL patients, are one source of IL-10, and proliferate in response to leishmania antigen. Levels of FoxP3 mRNA were also up-regulated in lesional tissue from PKDL patients. However, T regs are not elevated in spleen cells from VL patients nor does depletion of T regs increase leishmania antigen specific IFN-γ secretion The highest levels of IL-10 mRNA in spleen cells
Visceral leishmaniasis
11354079
data reveal that THOC5 is an essential element in the maintenance of stem cells and growth factor/cytokine-mediated differentiation/proliferation. Furthermore, depletion of THOC5 influences less than 1% of total mRNA export in the steady state, however it influences more than 90% of growth factor/cytokine induced genes. THOC5, thereby contributes to the 3′ processing and/or export of immediate-early genes induced by extracellular stimuli. These studies bring new insight into the link between the mRNA export complex and immediate-early gene response. The data from these studies also suggest that THOC5 may be a useful tool for studying stem cell biology, for modifying the
THOC5
7629372
deaminase activity. Mbisa et al. saw that APOBEC3G interferes with the processing and removal of primer tRNA from the DNA minus strand, thus leading to aberrant viral 3’ long terminal repeat (LTR) DNA ends. These viral DNA ends are inefficient substrates for integration and plus-strand DNA transfer. As a result, HIV-1 provirus formation is inhibited. APOBEC3G mRNA is expressed in certain cells, referred to as non-permissive cells, in which HIV-1 cannot properly infect and replicate in the absence of Vif. Such cells include physiologically relevant primary CD4 T lymphocytes and macrophages. The encapsidation of APOBEC3G into HIV-1 virions is very
APOBEC3G
3030452
5′ exonucleases is prevented (as mentioned above) by functionally looking like a 3′ end. Second, the CBC and eIF4E/eIF4G block the access of decapping enzymes to the cap. This increases the half-life of the mRNA, essential in eukaryotes as the export and translation processes take significant time. Decapping of a 7-methylguanylate-capped mRNA is catalyzed by the decapping complex made up of at least Dcp1 and Dcp2, which must compete with eIF4E to bind the cap. Thus the 7-methylguanylate cap is a marker of an actively translating mRNA and is used by cells to regulate mRNA half-lives in response to new
Five-prime cap
11324220
the RNA post-transcriptional to cooperate with the splicing-mRNA processing. Human embryonic stem cells are able to undergo the process of differentiation into specific and relevant cells. To maintain the pluripotency of the embryonic stem cells, transcription factors and epigenetic modifiers play an important role despite the fact that little is known about the regulation of pluripotency throughout the process of splicing. The factor SON is identified as essential for the maintenance of this pluripotency. It is confirmed that SON regulates the splicing process of transcripts (RNAm) that will encode the gens that are going to regulate the pluripotency of the
SON (gene)
11329196
to alleviate proteotoxic stress. AGR2 may help regulate the protein and mRNA levels in a cell overall as well. During late pregnancy and lactation, AGR2 levels peak when milk proteins are produced, and mammary-specific "Agr2" knockout mice had downregulated milk protein mRNA expression. AGR2 is expressed in relatively high levels for prostate cancer patients. Urine sediment tests determined "Agr2" transcript levels to be elevated. AGR2 expression was increased in metastatic prostate cancer cells cultured in a bone marrow microenvironment, where intense levels of "Agr2" mRNA were detected, suggesting AGR2 is required for bone metastasis of prostate cancer cells. AGR2 transcript
AGR2
20702534
Spatial transcriptomics Spatial transcriptomics is a technology used to spatially resolve RNA-seq data, and thereby all mRNAs, in individual tissue sections. The ordered attachment of spatially barcoded reverse transcription oligo(dT) primers to the surface of microscope slides enables the encoding and maintenance of positional information throughout mRNA sample processing and subsequent sequencing.This contrasts with RNA-sequencing of single cells, or the sequencing of bulk RNA extracted from tissue volumes, where precise spatial information is lost When a tissue cryosection is attached to a spatial transcriptomic slide the barcoded primers bind and capture adjacent mRNAs from the tissue. While the tissue section
Spatial transcriptomics
3030385
In eukaryotic somatic cells, the poly(A) tail of most mRNAs in the cytoplasm gradually get shorter, and mRNAs with shorter poly(A) tail are translated less and degraded sooner. However, it can take many hours before an mRNA is degraded. This deadenylation and degradation process can be accelerated by microRNAs complementary to the 3' untranslated region of an mRNA. In immature egg cells, mRNAs with shortened poly(A) tails are not degraded, but are instead stored without being translated. They are then activated by cytoplasmic polyadenylation after fertilisation, during egg activation. In animals, poly(A) ribonuclease (PARN) can bind to the 5' cap
Polyadenylation
11092730
different sequences common to all genes. In the group A rotaviruses, the 3'-end consensus sequence UGACC is highly conserved among the 11 genes. Rotavirus NSP3 presents several similarities to PABP; in rotavirus-infected cells, NSP3 can be cross-linked to the 3' end of rotavirus mRNAs and is coimmunoprecipitated with eIF4G. The binding of NSP3A to eIF4G and its specific interaction with the 3' end of viral mRNA brings the viral mRNA and the translation initiation machinery into contact, thus favoring efficient translation of the viral mRNA. NSP3 interacts with the same region of eIF4G as PABP does. As a consequence, during
Rotavirus translation
242918
the lysogenic pathway, whereas if cII is degraded the phage will go into the lytic pathway. Low temperature, starvation of the cells and high multiplicity of infection (MOI) are known to favor lysogeny (see later discussion). This occurs without the N protein interacting with the DNA; the protein instead binds to the freshly transcribed mRNA. Nut sites contain 3 conserved "boxes," of which only BoxB is essential. This is the lifecycle that the phage follows following most infections, where the cII protein does not reach a high enough concentration due to degradation, so does not activate its promoters. Rightward transcription
Lambda phage
267433
causes a significantly longer delay before output, which has caused MP3 to be considered unsuitable for studio applications where editing or other processing needs to take place. MP3 does not benefit from the 32 sub-band polyphased filter bank, instead just using an 18-point MDCT transformation on each output to split the data into 576 frequency components, and processing it in the frequency domain. This extra granularity allows MP3 to have a much finer psychoacoustic model, and more carefully apply appropriate quantization to each band, providing much better low-bitrate performance. Frequency-domain processing imposes some limitations as well, causing a factor of
MPEG-1
14567392
processing technique with one-step processing that achieves microstructural refinement densification and homogeneity”(MA) FSW helps modify materials so that metaling down or changing the material drastically does not have to take place. FSP, for example, can easily change the form of a piece of material as sheets of metal, where before it may have had to be melted down before and put into a mold for it to cool and form. (Smith,Mishra) “The microstructure and mechanical properties of the processed zone can be accurately controlled by optimizing the tool design, FSP parameters an active cooling/heating.”(MA) The same sheet of metal can
Friction stir processing
269930
begins with transcription, and ultimately ends in degradation. During its life, an mRNA molecule may also be processed, edited, and transported prior to translation. Eukaryotic mRNA molecules often require extensive processing and transport, while prokaryotic mRNA molecules do not. A molecule of eukaryotic mRNA and the proteins surrounding it are together called a messenger RNP. Transcription is when RNA is made from DNA. During transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as needed. This process is similar in eukaryotes and prokaryotes. One notable difference, however, is that eukaryotic RNA polymerase associates with mRNA-processing
Messenger RNA
17890310
reflect expression of a heterogeneous mix of cell populations. Even in the same cell type, tissue measurements, where a population of cells is obtained, mask both low-level mRNA expression in single cells and variation in expression between cells. The photoactivatable TIVA tag is engineered to capture the mRNA of a single cell in complex tissues. TIVA tags are created initially via solid-phase synthesis with the cell-penetrating peptide conjugated afterwards. The functional components of the tag can be summarized as following: Tissue fixation is performed by chemical fixation using formalin. This prevents the postmortem degeneration of the tissue and hardens soft
Transcriptome in vivo analysis tag
8008632
induction and inhibited by insulin. Conversely, intestinal proglucagon gene expression is reduced during fasting and stimulated upon food consumption. In mammals, the transcription gives rise to identical mRNA in all three cell types, which is further translated to the 180 amino acid precursor called proglucagon. However, as a result of tissue-specific posttranslational processing mechanisms, different peptides are produced in the different cells. In the pancreas (α-cells of the islets of Langerhans), proglucagon is cleaved by prohormone convertase (PC) 2 producing glicentin-related pancreatic peptide (GRPP), glucagon, intervening peptide-1 (IP-1) and major proglucagon fragment (MPGF). In the gut and brain, proglucagon is
Glucagon-like peptide-1
3038215
other processes such as transcription, neural physiology, and glucose homeostasis. Cyclin-dependent kinase Cyclin-dependent kinases (CDKs) are a family of protein kinases first discovered for their role in regulating the cell cycle. They are also involved in regulating transcription, mRNA processing, and the differentiation of nerve cells. They are present in all known eukaryotes, and their regulatory function in the cell cycle has been evolutionarily conserved. In fact, yeast cells can proliferate normally when their CDK gene has been replaced with the homologous human gene. CDKs are relatively small proteins, with molecular weights ranging from 34 to 40 kDa, and contain
Cyclin-dependent kinase
3038201
Cyclin-dependent kinase Cyclin-dependent kinases (CDKs) are a family of protein kinases first discovered for their role in regulating the cell cycle. They are also involved in regulating transcription, mRNA processing, and the differentiation of nerve cells. They are present in all known eukaryotes, and their regulatory function in the cell cycle has been evolutionarily conserved. In fact, yeast cells can proliferate normally when their CDK gene has been replaced with the homologous human gene. CDKs are relatively small proteins, with molecular weights ranging from 34 to 40 kDa, and contain little more than the kinase domain. By definition, a CDK
Cyclin-dependent kinase
11123253
invasion. Quondamatteo et al. immunohistochemically stained MMP7, and localized MMP7 in early human liver development. They reported that MMP7 was presented in some hepatocytes and endothelial cells in the 6th gestational week, and only hematopoietic cells remained after that time. In order for MMPs to escape TIMP inhibition, active MMP7s are recruited to the plasma membrane of epithelium inducing membrane-associated growth factors processing for epithelial repair and proliferation. In human endometrium, the expression of MMP7 mRNA increases at menstruation and remains high during the proliferative phase. Also, MMP-7 binds to the plasma membrane of epithelium containing cholesterol-rich domain. The bounded
MMP7
13224326
MRNA surveillance mRNA surveillance mechanisms are pathways utilized by organisms to ensure fidelity and quality of messenger RNA (mRNA) molecules. There are a number of surveillance mechanisms present within cells. These mechanisms function at various steps of the mRNA biogenesis pathway to detect and degrade transcripts that have not properly been processed. The translation of messenger RNA transcripts into proteins is a vital part of the central dogma of molecular biology. mRNA molecules are, however, prone to a host of fidelity errors which can cause errors in translation of mRNA into quality proteins. RNA surveillance mechanisms are methods cells use
MRNA surveillance
6436939
rapid cell cleavages give different cells various combinations of mRNA which can then lead to drastically different cell fates. RBPs are critical in the localization of this mRNA that insures proteins are only transcribed in their intended regions. One of these proteins is ZBP1. ZBP1 binds to beta-actin mRNA at the site of transcription and moves with mRNA into the cytoplasm. It then localizes this mRNA to the lamella region of several asymmetric cell types where it can then be translated. FMRP is another RBP involved in RNA localization. It was shown that in addition to other functions for FMRP
RNA-binding protein
17223341
identified that all express the core clock genes. However, the mRNAs appear to be expressed in a circadian and neuron-specific manner, which his lab has taken interest in determining whether this provides a link to the distinct functions of certain neuronal groups. He has also researched the effects of light on certain neuronal groups and has found that one subgroup is light-sensitive to lights on (dawn) and another is light-sensitive to lights off (dusk). The dawn cells have been shown to promote arousal while the dusk cells promote sleep. Today, Rosbash continues to research mRNA processing and the genetic mechanisms
Michael Rosbash
10764801
such as "Escherichia coli" and "Pseudoalteromonas haloplanktis". The multi-protein complex also serves as a machine for processing structured RNA precursors in the course of their maturation. RNA helicase is considered to help in the process of degradation to develop the double helix structure in RNA stem-loops. Occasionally, copurification of rRNA with degradosome is appreciated, which suggests that the complex may take part in rRNA and mRNA degradation. There is very few clear information about the role of degradosome. Looking into the steps of the degradation of a transcript in "E. coli", what is known is that in the first place
Degradosome
18635660
of the M23 family of metalloendopeptidases. Unlike this family of peptidases, however, LECT2 has not been found to possess enzymatic activity and does not appear to share any functions with M23 metalloendopeptidases. It is widely expressed in vascular tissues, smooth muscle cells, adipocytes, cerebral neurons, apical squamous epithelia, parathyroid tissues, the epithelial cells of sweat and sebaceous glands, Hassall bodies, and monocytes. The liver hepatocyte is considered to be the source of the LECT2 circulating in blood. However, its expression in these cells is extremely low or undetectable even though these cells express very high levels of LECT2 mRNA. This
LECT2 amyloidosis
6683387
contains 17 exons in humans. P-selectin is constitutively expressed in megakaryocytes (the precursor of platelets) and endothelial cells. P-selectin expression is induced by two distinct mechanisms. First, P-selectin is synthesized by megakaryocytes and endothelial cells, where it is sorted into the membranes of secretory granules. When megakaryocytes and endothelial cells are activated by agonists such as thrombin, P-selectin is rapidly translocated to the plasma membrane from granules. Secondly, increased levels of P-selectin mRNA and protein are induced by inflammatory mediators such as tumor necrosis factor-a (TNF-a), LPS, and interleukin-4 (IL-4). Although TNF-a and LPS increase levels of both mRNA and
P-selectin
10894982
It has been suggested that if a failure of caspase activation under stress conditions were to occur, necroptosis would take place. Overactivation of PARPs has led to a necrotic cell death regulated by the tumor necrosis factor protein. Though the mechanism is not yet understood, PARP inhibitors have been shown to affect necroptosis. ADP-ribosylation can affect gene expression at nearly every level of regulation, including chromatin organization, transcription factor recruitment and binding, and mRNA processing. The organization of nucleosomes is key to regulation of gene expression: the spacing and organization of nucleosomes changes what regions of DNA are available for
ADP-ribosylation
13082369
washed out. All the processes after lysis - isolation, purification, fragmentation and labelling of target rRNA's - are stable chemical reactions Fragments <500 bp easily hybridize to the gel matrix. The total number of eluted off the chip is determined by UV spectrophotometer. The process from sample preparation to identification of organisms based on automated algorithms take place in 2 hours. cDNAs obtained from reverse transcription of mRNA population extracted from the cells in varying physiological and experimental conditions are used as immobilized probes. These arrays are widely used to study gene expression. The potential obstacle in using cDNAs is
MAGIChip
348382
of peripheral functional importance. This was confirmed with the deciphering of the 3-dimensional structure of the ribosome in 2001. Specifically, peptide bond formation, the reaction that binds amino acids together into proteins, is now known to be catalyzed by an adenine residue in the rRNA. RNAs are known to play roles in other cellular catalytic processes, specifically in the targeting of enzymes to specific RNA sequences. In eukaryotes, the processing of pre-mRNA and RNA editing take place at sites determined by the base pairing between the target RNA and RNA constituents of small nuclear ribonucleoproteins (snRNPs). Such enzyme targeting is
RNA world
12993761
are shaded by pigment cells forming a cup. The photoreceptor cells do not synapse directly onto ciliated cells or muscle cells but onto inter-neurons of a processing center. This way the information of all four eye cups can be compared and a low resolution image of four pixels can be created telling the larvae where the light is coming from. This way the larva does not need to scan its environment by rotating. This is an adaption for living on the bottom of the sea the life style of the nectochaete larva while scanning rotation is more suited for living
Phototaxis
10309290
be linked to cell growth, and its mRNA content is linked to changes in the cell cycle. Hamster BHK "ts11" cells produce an inactive asparagine synthetase enzyme, and this loss of asparagine synthetase activity directly led to cell cycle arrest in the cells as a consequence of a depletion of cellular asparagine. Upregulation of asparagine synthetase mRNA was observed as well in these hamster cells. Other experiments demonstrated that quiescent rat thyroid cells entering S phase as a result of thyroid-stimulating hormone treatment was matched with a concurrent increase in asparagine synthetase mRNA content. There seem to be two major
Asparagine synthetase
11219877
on these issues. GPR31 receptor mRNA is highly expressed in the PC-3 prostate cancer cell line and to a lesser extent the DU145 prostate cancer cell line and to human umbilical vein endothelial cells (HUVEC), human umbilical vein endothelial cells (HUVEC), human brain microvascular endothelial cells (HBMEC), and human pulmonary aortic endothelial cells (HPAC). Its mRNA is also express but at rather low levels in several other human cell lines including: K562 cells (human myelogenous leukemia cells); Jurkat cells (T lymphocye cells); Hut78 cells (T cell lymphoma cells), HEK 293 cells (primary embryonic kidney cells), MCF-7 cells (mammary adenocarcinoma cellss),
GPR31
11234863
to more than one of these families. It is thought that each family has a specific role in RNA metabolism, for example both DEAD box and DEAH box proteins NTPase activities become stimulated by RNA, but DEAD box proteins use ATP and DEAH does not. DEAD box proteins are considered to be RNA helicases and many have been found to be required in cellular processes such as pre-mRNA processing and rearranging of ribonucleoproteins (RNP) complexes. Pre-mRNA splicing requires rearrangements of five large RNP complexes, which are snRNPs U1, U2, U4, U5, and U6. DEAD box proteins are helicases that perform
DEAD box
269946
end (called kissing stem loops), circularizing the mRNA without any proteins involved. RNA virus genomes (the + strands of which are translated as mRNA) are also commonly circularized. During genome replication the circularization acts to enhance genome replication speeds, cycling viral RNA-dependent RNA polymerase much the same as the ribosome is hypothesized to cycle. Different mRNAs within the same cell have distinct lifetimes (stabilities). In bacterial cells, individual mRNAs can survive from seconds to more than an hour. However, the lifetime averages between 1 and 3 minutes, making bacterial mRNA much less stable than eukaryotic mRNA. In mammalian cells, mRNA
Messenger RNA
20060281
many (microarray, RNA-Seq) genes. These techniques generally measure relative mRNA levels and employ normalization methods that assume only a small number of genes show altered expression. Instead, single cell or cell count normalized absolute measurements of mRNA abundance are required to reveal transcriptional amplification. Additionally, global measurements of mRNA or total mRNA per cell can also uncover evidence for transcriptional amplification. Cells in which transcription has been amplified have additional suggestive hallmarks that amplification has occurred. Cells with increased mRNA levels may be larger, consistent with an increased abundance of gene products. This increase in the amount of gene product
Transcriptional amplification
8243245
thought that the 3′-flanking DNA was not transcribed at all, but it was discovered to be transcribed into RNA and quickly removed during processing of the primary transcript to form the mature mRNA. The 3′-flanking region often contains sequences that affect the formation of the 3′-end of the message. It may also contain enhancers or other sites to which proteins may bind. The 3′-"untranslated" region (3′-UTR) is a region of the DNA which "is" transcribed into mRNA and becomes the 3′-end of the message, but which does not contain protein coding sequence. Everything between the stop codon and the polyA
Directionality (molecular biology)
9606266
replication of cells. At this stage, the zygote starts producing its own mRNAs that are made from its own DNA, and no longer uses the maternal mRNA. This can also be called the maternal to zygotic transition. The maternal mRNAs are then degraded. Since the cells are now transcribing their own DNA, this stage is where expression of paternal genes is first observed. When the zygote begins to produce its own mRNA, the cell cycle begins to slow down and the G1 and G2 phases are added to the cell cycle. The addition of these phases allows the cell to
Midblastula
16492637
"in cis". An interaction between the maternal and paternal homolgous regions of these genes was in fact observed in human and mouse cells during interphase. One mechanism to explain "in trans" silencing includes an interaction between the paternal "Ube3a-ATS" RNA and the maternal "Ube3a" mRNA. It is possible that the maternal "Ube3a" mRNA interacts with the paternal "Ube3a-ATS" RNA and decreases the stability of both of these transcripts. When only "Ube3a-ATS" is made without "Ube3a", the "Ube3a-ATS" becomes more stable. Another study has suggested that "Ube3a-ATS" expression does not occur in imprinted regions. "In situ" hybridizations did not reveal "Ube3a-ATS"
Ube3a-ATS
1669831
the bacterial ribosome, interfering with the binding of formyl-methionyl-tRNA to the 30S subunit. This leads to codon misreading, eventual inhibition of protein synthesis and ultimately death of microbial cells through mechanisms that are still not understood. Speculation on this mechanism indicates that the binding of the molecule to the 30S subunit interferes with 50S subunit association with the mRNA strand. This results in an unstable ribosomal-mRNA complex, leading to a frameshift mutation and defective protein synthesis; leading to cell death. Humans have ribosomes which are structurally different from those in bacteria, so the drug does not have this effect in
Streptomycin
1670272
6 encodes the membrane-bound form of the Fas receptor, which promotes apoptosis, or programmed cell death. Increased expression of Fas receptor in skin cells chronically exposed to the sun, and absence of expression in skin cancer cells, suggests that this mechanism may be important in elimination of pre-cancerous cells in humans. If exon 6 is skipped, the resulting mRNA encodes a soluble Fas protein that does not promote apoptosis. The inclusion or skipping of the exon depends on two antagonistic proteins, TIA-1 and polypyrimidine tract-binding protein (PTB). This mechanism is an example of exon definition in splicing. A spliceosome assembles
Alternative splicing
6573463
of males with autonomous P elements (P Strain/P cytotype) and females that lack P elements (M Strain/M cytotype). The hybrid dysgenesis syndrome is marked by temperature-dependent sterility, elevated mutation rates, and increased chromosome rearrangement and recombination. The hybrid dysgenesis phenotype is affected by the transposition of P elements within the germ-line cells of offspring of "P strain" males with "M strain" females. Transposition only occurs in germ-line cells, because a splicing event needed to make transposase mRNA does not occur in somatic cells. Hybrid dysgenesis manifests when crossing P strain males with M strain females and not when crossing P
P element
3305831
Hyperkalemia may only become apparent when a person's platelet concentration is more than 500,000/microL in a clotted blood sample (serum blood sample). Potassium leaks out of platelets after clotting has occurred. On the other hand, processing of heparinised, unclot blood does not cause falsely elevated potassium. In addition to that, high white cell count (greater than 120,000/microL) in patient with chronic lymphocytic leukemia increases red blood cells fragility, thus causing pseudohyperkalemia during blood processing. This problem can be avoided by processing serum samples, because formation of clot protect the cells from haemolysis during processing. A familial form of pseudohyperkalemia may
Hyperkalemia
18258022
where epithelial cells, which have been shown to be the only cell type give rise to cancer, only consist 10% of the cell count. This led to development of laser capture microdissection (LCM), a technique that can isolate individual cell types individual cells, which gave rise to cDNA libraries of specific cell types. The sequencing of cDNA will produce the entire mRNA transcript that generated it. Practically, only part of the sequence is required to uniquely identify the mRNA or protein associated. The resultant part of the sequence was termed the expressed sequence tag (EST) and is always at the
Cancer Genome Anatomy Project
7110967
need for the protein coded by the mRNA, perhaps indicating a homeostatic response or a pathological condition. For example, higher levels of mRNA coding for alcohol dehydrogenase suggest that the cells or tissues under study are responding to increased levels of ethanol in their environment. Similarly, if breast cancer cells express higher levels of mRNA associated with a particular transmembrane receptor than normal cells do, it might be that this receptor plays a role in breast cancer. A drug that interferes with this receptor may prevent or treat breast cancer. In developing a drug, one may perform gene expression profiling
Gene expression profiling
4220376
dsRNA added. To test whether their observation of decreased mRNA levels was a result of mRNA being targeted directly (as suggested by data from other systems), "Drosophila" S2 cells were transfected with either "Drosophila" cyclin E dsRNAs or "lacZ" dsRNAs and then incubated with synthetic mRNAs for cyclin E or "lacZ". Cells transfected with cyclin E dsRNAs only showed degradation in cyclin E transcripts — the "lacZ" transcripts were stable. Conversely, cells transfected with "lacZ" dsRNAs only showed degradation in "lacZ" transcripts and not cyclin E transcripts. Their results led Hannon and his colleagues to suggest RNAi degrades target mRNA
RNA-induced silencing complex
3036283
in muscle stem cells. miRNA sequestration of mRNA within ribonucleoprotein complexes allows quiescent cells to store the mRNA necessary for quick entry into the G1 phase. Stem cells that have been quiescent for a long time often face various environmental stressors, such as oxidative stress. However, several mechanisms allow these cells to respond to such stressors. For example, the FOXO transcription factors respond to the presence of reactive oxygen species (ROS) while HIF1A and LKB1 respond to hypoxic conditions. In hematopoietic stem cells, autophagy is induced to respond to metabolic stress. Stem cells are cells with the unique ability to
G0 phase
9279522
thus implying resveratrol’s inhibitory action at the transcriptional level. To further see whether survivin played a key role in sensitization of the cancer cells to cytotoxic drugs, survivin antisense oligonucleotides were used to knock down any survivin mRNA, and, thus, its possibility to be translated is also eliminated. siRNAs for survivin are complements in sequence to the mRNA sequence encoding survivin. When these siRNAs for survivin are introduced into cells, they will bind to the respective complementary mRNA and, thus, prevent its translation since the mRNA is now impeded from proper physical interaction with the translational machinery. In this way,
Survivin
17484660
James L. Manley James Manley is Julian Clarence Levi Professor of Life Sciences at Columbia University, where his laboratory studies gene expression in mammalian cells. Manley and colleagues identified and characterized the key factors responsible for polyadenylation of mRNA precursors, and elucidated how this remarkably complex machinery functions in gene regulation, for example during cell growth and differentiation. He has also studied the mechanism and regulation of the process by which introns are removed from mRNA precursors, mRNA splicing. Manley and his coworkers codiscovered the first alternative splicing factor (SR protein), characterized how this and other splicing regulatory proteins function
James L. Manley
9757990
increase in MCP-1 mRNA expression followed by an increase in macrophage recruitment occurred. In addition varying levels of MCP-1 mRNA expression also had an effect. Increased MCP-1 mRNA levels correlated positively with an increase in macrophage recruitment. Furthermore, in situ hybridation determined that the cellular source of MCP-1 was Schwann cells. Schwann cells play an important role in not only producing neurotrophic factors such as nerve growth factor (NGF) and ciliary neurotrophic factor (CNTF), which promote growth, of both the damaged nerve and supporting Schwann cells, but also producing neurite promoting factors, which guide the growing axon, both of which
Nerve injury
15392763
Bioelectrochemical reactor Bioelectrochemical reactors are a type of bioreactor where bioelectrochemical processes can take place. They are used in bioelectrochemical syntheses, environmental remediation and electrochemical energy conversion. Examples of bioelectrochemical reactors include microbial electrolysis cells, microbial fuel cells and enzymatic biofuel cells and electrolysis cells, microbial electrosynthesis cells, and biobatteries. This bioreactor is divided in two parts: The anode, where the oxidation reaction takes place; And the cathode, where the reduction occurs. In 1911 M. Potter described how microbial conversions could create reducing power, and thus electric current. Twenty years later Cohen (1931) investigated the capacity of bacteria to produce
Bioelectrochemical reactor
11330549
PABPC4 Polyadenylate-binding protein 4 (PABPC4) is a protein that in humans is encoded by the "PABPC4" gene. Poly(A)-binding proteins (PABPs) bind to the poly(A) tail present at the 3-prime ends of most eukaryotic mRNAs. PABPC4 or IPABP (inducible PABP) was isolated as an activation-induced T-cell mRNA encoding a protein. Activation of T cells increased PABPC4 mRNA levels in T cells approximately 5-fold. PABPC4 contains 4 RNA-binding domains and proline-rich C terminus. PABPC4 is localized primarily to the cytoplasm. It is suggested that PABPC4 might be necessary for regulation of stability of labile mRNA species in activated T cells. PABPC4 was
PABPC4
9279509
the dose-dependent effect of 4003 on the down-regulation of survivin mRNA levels. It was found that a concentration of 400 nM resulted in a maximum down-regulation of 70% of the initial survivin mRNA present. Another experiment on 4003 involved assessing any biological or cytotoxic effect 4003 down-regulation of survivin mRNA has on A549 cells using the MTT assay. The numbers of A549 cells transfected with 4003 significantly decreased with increasing concentration of 4003 compared to cells transfected either with a mismatch form of the 4003 or lipofectin control. Many physical observations that confirmed the induction of apoptosis by 4003 were
Survivin
894183
presence of cell-associated PCA3 mRNA in fluid obtained from the prostate and first-void urine sample has also been under investigation. PCA3 mRNA is expressed almost exclusively by prostate cells and has been shown to be highly over-expressed in prostate cancer cells. The test result is currently reported as a specimen ratio of PCA3 mRNA to PSA mRNA. Although not a replacement for serum PSA level, the PCA3 test is an additional tool to help decide whether, in men suspected of having prostate cancer (especially if an initial biopsy fails to explain the elevated serum PSA), a biopsy/rebiopsy is really needed.
Prostate cancer
8121944
Splice site mutation A splice site mutation is a genetic mutation that inserts, deletes or changes a number of nucleotides in the specific site at which splicing takes place during the processing of precursor messenger RNA into mature messenger RNA. Splice site consensus sequences that drive exon recognition are located at the very termini of introns. The deletion of the splicing site results in one or more introns remaining in mature mRNA and may lead to the production of abnormal proteins. When a splice site mutation occurs, the mRNA transcript possesses information from these introns that normally should not be
Splice site mutation
6534963
Post-transcriptional modification Post-transcriptional modification or Co-transcriptional modification is the process in eukaryotic cells where primary transcript RNA is converted into mature RNA. A notable example is the conversion of precursor messenger RNA into mature messenger RNA (mRNA) that occurs prior to protein translation. The process includes three major steps: addition of a 5' cap, addition of a 3' poly-adenylation tail, and splicing. This process is vital for the correct translation of the genomes of eukaryotes because the initial precursor mRNA produced during transcription contains both exons (coding or important sequences involved in translation), and introns (non-coding sequences). The pre-mRNA molecule
Post-transcriptional modification
5520572
(ODC) and Prostate Specific Antigen (PSA) however, M, C4, and C5 sublines express 5-10X more PSA mRNA. M, C4, C5 and C4-2 also expressed reduced human androgen receptor mRNA as expected in AI cells. Androgen Insensitivity All sublines were treated with dihydrotestosterone (DHT), a high-affinity ligand for AR. DHT treatment elicited markedly reduced growth in C4 and C5 cells and no growth in C4-2 cells when compared to the high rate of growth seen in LNCaP cells, suggesting reduced androgen sensitivity in C4 and C5 and AI in C4-2 cells. Whole-cell AR assay also indicated that LNCaP cells have a
LNCaP
10266548
got disproved by the late 1950s. It is involved on mRNA processing and degradation in bacteria, plants, and in humans. In humans, the enzyme is encoded by the gene. In its active form, the protein forms a ring structure consisting of three PNPase molecules. Each PNPase molecule consists of two RNase PH domains, an S1 RNA binding domain and a K-homology domain. The protein is present in bacteria and in the chloroplasts and mitochondria of some eukaryotic cells. In eukaryotes and archaea, a structurally and evolutionary related complex exists, called the "exosome complex". The same abbreviation ("PNPase") is also used
Polynucleotide phosphorylase
11324219
the progression of the cell cycle and it has remained largely unexplored, it’s certain that this splicing-associated protein is necessary for the maintenance of the embryonic stem cells because it influences the splicing of pluripotency regulators. SON plays an important role in the mRNA processing. Nevertheless, this process is still a little uncertain and this is why in a future it will be interesting to understand how exactly this protein interacts with the spliceosomal complex, its exact molecular function in the context of splicing. Not only the SON protein interferes in the splicing but also makes complex mechanisms such as
SON (gene)
9838911
larger role must be derived from the function of its protein components (PSP1, p54nrb, PSP2 and possibly CFI(m)68 and PSF). The function of PSP1, the protein whose localization pattern led to the discovery of the paraspeckle, is not well understood. Myojin et al. speculated that PSP1, which is highly concentrated in the testis, may regulate the germ cells' early mRNA processing and assist in chromatin remodeling and nuclear shaping during spermatogenesis. PSP1 also forms a dimer with the second protein component: p54nrb. P54nrb has reported involvement in numerous nuclear events including "transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited
Paraspeckle
5040306
extremely small because of limited transcription due to an inefficient promoter in addition to altered processing of the mRNA transcript. The 2 human protamines are denoted and . Examples of protamines from fish are: The primary structure of protamine P1, the protamine used for packaging DNA in sperm cells, in placental mammals is usually 49 or 50 amino acids long. This sequence is divided into three separate domains: an arginine-rich domain for DNA binding flanked by shorter peptide sequences containing mostly cysteine residues. The arginine-rich domain consists of 3-11 arginine residues and is conserved between fish protamine and mammalian protamine
Protamine
7436775
granules, suggesting that stress granules only influence a minority of mRNAs in the cell and may not be as important for mRNA processing as previously thought. The stress proteins that are the main component of stress granules in plant cells are molecular chaperones that sequester, protect, and possibly repair proteins that unfold during heat and other types of stress. Therefore, any association of mRNAs with stress granules may simply be a side effect of the association of partially unfolded RNA-binding proteins with stress granules, similar to the association of mRNAs with proteasomes. Environmental stressors trigger cellular signaling which eventually leads
Stress granule
11821145
the repeats, although these positions are not equivalent. The phosphorylation state changes as RNAPII progresses through the transcription cycle: The initiating RNAPII is form IIA, and the elongating enzyme is form II0. While RNAPII0 does consist of RNAPs with hyperphosphorylated CTDs, the pattern of phosphorylation on individual CTDs can vary due to differential phosphorylation of Ser2 versus Ser5 residues and/or to differential phosphorylation of repeats along the length of the CTD. The PCTD (phosphoCTD of an RNAPII0) physically links pre-mRNA processing to transcription by tethering processing factors to elongating RNAPII, e.g., 5′-end capping, 3′-end cleavage, and polyadenylation. Ser5 phosphorylation (Ser5PO)
RNA polymerase II holoenzyme
7324920
to induction of genes associated with apoptosis and cell death, but repression of genes was not limited to proteins associated with a specific pathway. When T84 intestinal epithelial cells are exposed to hypoxic conditions for 24 hours a significant increase in perlecan mRNA and protein production occurs. They relate this to the fact that many genes elevated in response to hypoxia contain a cAMP response element (CRE) in their promoter, as does pln. This difference between endothelial cells from the study in 2007 and the epithelial cell studied in these experiments is indicative of how varied the regulatory mechanisms of
Perlecan
10430312
responsible for the shut-off of cellular protein synthesis. Rotavirus mRNAs terminate a 3’ GACC motif that is recognized by the viral protein NSP3. This is the location where NSP3 competes with poly(A)-binding protein for eIF4G binding. Once rotavirus infection occurs viral GACC-tailed mRNAs are translated while the poly(A)-tailed mRNA is severely impaired. In infected cells, there have been high magnitudes of both translation induction (GACC-tailed mRNA) and reduction (poly(A)-tailed mRNA) both dependent on the rotavirus strain. These data suggest that NSP3 is a translational surrogate of the PABP-poly(A) complex; therefore, it cannot by itself be responsible for inhibiting the translation
Poly(A)-binding protein
20980821
combination of the TIS proteins and the endoplasmic reticulum creates a distinct place in which mRNA and proteins collect, interact, and grow. The striped pattern of the TIS granules that are interweaving with the endoplasmic reticuum also resemble the orange and black stripes of a tiger. The TIGER domain has been found in all types of cells scientists have looked at so far. TIGER domain The TIGER domain is a minor membraneless organelle in which messenger RNA (mRNA) encodes certain types of proteins to find the appropriate environment for growth. It is closely associated with the endoplasmic reticulum during protein
TIGER domain
2228330
The first way is called preformistic and involves that the cells destined to become germ cells inherit the specific germ cell determinants present in the germ plasm (specific area of the cytoplasm) of the egg (ovum). The unfertilized egg of most animals is asymmetrical: different regions of the cytoplasm contain different amounts of mRNA and proteins. The second way is found in birds and mammals, where germ cells are not specified by such determinants but by signals controlled by zygotic genes. In mammals, a few cells of the early embryo are induced by signals of neighboring cells to become primordial
Germ cell
3873517
Place cell function changes with age. Pharmaceuticals that target pathways involved in protein synthesis increase place cell functioning in senescence. Frequency of protein translation changes as animals age. A factor that aids in transcription, known as zif268 mRNA, is shown to decrease with age, thereby affecting memory consolidation. This form of mRNA is decreased in both the CA1 and CA2 hippocampal regions, these reduced levels causing spatial learning deficits. Senile rats' performance on the Morris water maze does not differ from young rats' performance when the trials are repeated shortly after one another. However, when time has elapsed between trials,
Place cell
4220378
levels of transcript available to be translated by ribosomes. There are two main requirements for mRNA degradation to take place: mRNA degradation is localised in cytoplasmic bodies called P-bodies. RISC can modulate the loading of ribosome and accessory factors in translation to repress expression of the bound mRNA transcript. Translational repression only requires a partial sequence match between the guide strand and target mRNA. Translation can be regulated at the initiation step by: Translation can be regulated at post-initiation steps by: There is still speculation on whether translational repression via initiation and post-initiation is mutually exclusive. Some RISCs are able
RNA-induced silencing complex
8464578
an indication that depth processing occurs at a very early stage, aiding recognition of 3D objects. Later, many other cells with specific functions have been discovered: (a) end-stopped cells which are thought to detect singularities like line and edge crossings, vertices and line endings; (b) bar and grating cells. The latter are not linear operators because a bar cell does not respond when seeing a bar which is part of a periodic grating, and a grating cell does not respond when seeing an isolated bar. Using the mathematical Gabor model with sine and cosine components (phases), complex cells are then
Simple cell