Methods to investigate chromatin thumb|Microscopy of heterochromatic versus euchromatic nuclei (H&E stain). thumb|Granular "salt-and-pepper chromatin", seen on H&E, Pap stain and comparison to actual salt and pepper. Its finding on microscopy indicates mainly medullary thyroid carcinoma, neuroendocrine tumours or pheochromocytoma. thumb|Schematic karyogram of a human, showing an overview of the human genome using G banding, which is a method that includes Giemsa staining, wherein the lighter staining regions are generally more euchromatic (and more transcriptionally active), whereas darker regions generally are more heterochromatic. ChIP-seq (Chromatin immunoprecipitation sequencing) is recognized as the vastly utilized chromatin identification method it has been using the antibodies that actively selected, identify and combine with proteins including "histones, histone restructuring, transaction factors and cofactors". This has been providing data about the state of chromatin and the transaction of a gene by trimming "oligonucleotides" that are unbound. Chromatin immunoprecipitation sequencing aimed against different histone modifications, can be used to identify chromatin states throughout the genome. Different modifications have been linked to various states of chromatin. DNase-seq (DNase I hypersensitive sites Sequencing) uses the sensitivity of accessible regions in the genome to the DNase I enzyme to map open or accessible regions in the genome. FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements sequencing) uses the chemical properties of protein-bound DNA in a two-phase separation method to extract nucleosome depleted regions from the genome. ATAC-seq (Assay for Transposable Accessible Chromatin sequencing) uses the Tn5 transposase to integrate (synthetic) transposons into accessible regions of the genome consequentially highlighting the localisation of nucleosomes and transcription factors across the genome. DNA footprinting is a method aimed at identifying protein-bound DNA. It uses labeling and fragmentation coupled to gel electrophoresis to identify areas of the genome that have been bound by proteins. MNase-seq (Micrococcal Nuclease sequencing) uses the micrococcal nuclease enzyme to identify nucleosome positioning throughout the genome. Chromosome conformation capture determines the spatial organization of chromatin in the nucleus, by inferring genomic locations that physically interact. MACC profiling (Micrococcal nuclease ACCessibility profiling) uses titration series of chromatin digests with micrococcal nuclease to identify chromatin accessibility as well as to map nucleosomes and non-histone DNA-binding proteins in both open and closed regions of the genome.
methods to InVestIgate chrOMATin ThuMb|micRoscOpy of hETeRochRomatic VersuS euchrOmAtic nUclEI (h&e stAiN). thuMB|grAnULAR "salt-And-Pepper cHroMatin", seen on H&e, pap StaIn aND compariSoN to acTual sAlT and pepPer. its fIndINg ON MIcrOscopy inDiCates MAInlY MEdullaRY thyroid CarcInoMa, NEuRoEndocRiNE TumourS OR phEoChromoCyToMa. thUMb|schematiC kaRyOGram Of a hUmAN, showiNg an overview of The hUmaN GEnoMe usINg G bAndIng, Which is a mEthoD thAT inCludES giemsA staiNiNG, WhereiN the lightEr stAinIng RegIOns are generally more euchRomatic (aNd mOre trAnscrIptionALlY active), wHereaS darkeR regionS generAlLY are mORe hETerocHroMaTic chip-Seq (ChromatIN imMUnOpRECipiTatION sEquencinG) Is rECOgNIzeD as tHE vAsTlY UtiLIZed chromATiN identIFicaTIOn metHOd it has been usINg thE anTibODIes tHat activelY seleCteD, idenTIfY aNd comBiNe wiTH PRoTeInS IncLuDing "HisTones, HistOnE ReStrUctUrINg, tRanSActioN FactorS and cOfaCtors". tHis has beeN pRoVIding data ABOUt thE State OF cHrOmatin and tHe transactIon OF a gene By trImming "OligonuCLeoTides" tHat arE unBouNd. chrOmatin immUnopreCipItATioN sEquenCInG aImeD Against dIffErENt hisTone modificatIonS, cAn be USEd to iDentify chromAtin sTAtes tHRoUghOuT the genOme. difFEReNt mODificAtions havE BeeN lInked To vArious staTes OF chromatin. dnasE-sEq (dNASe i hyPErsensitivE sItes seqUenCinG) Uses The sEnsiTIvitY of AccesSibLe rEgions iN tHE GEnOMe to the dnase i enZymE to mAp OPeN or aCCessible reGiOnS iN tHe genome. fAIrE-seQ (fOrmalDeHYde-assisTeD isolatIoN Of REgulaTOry elemEntS SEQuenCINg) uSEs THe ChemIcaL propeRties Of prOtein-bound dna in a tWO-phasE sePaRAtiOn MetHoD tO extrAct nucleOsome depLEteD RegIoNs fRoM THe GEnome. ATAc-seq (asSay fOR transPoSaBle aCcesSIbLE chRomaTin sequencing) uses thE tn5 TraNsposasE to iNteGrAte (synThetic) traNSpoSons INto accESsiblE rEGIons oF ThE genOme conseQuEnTIally highLIgHTiNG thE LoCaliSatIOn oF nuClEosomeS aND TraNScRiptioN factorS acroSS the genome. Dna FoOtPriNtIng is A mETHod aimEd At iDeNtifyINg PrOteIn-bouNd dnA. It Uses labeLing And fragmentatIOn coUplEd to geL ElEctroPhOResiS to idENtIFY Areas of tHe GeNome thAt Have beeN BOunD BY ProtEins. MNaSe-sEq (microCoccAL nuclease sequeNciNg) uSEs The mICROCOCCal nuclease eNZyme to IdEnTify nucleosoMe pOsitiONing ThRoughoUt thE genome. chromosoME ConFORmAtion capture DeteRmines the spatial organiZation OF chrOMaTiN In The NUclEus, BY inFeRriNg GenoMIc lOcations tHAt PhySicalLY iNTERAct. macC profiliNG (microCoccal nucLeaSe accessiBiliTy pROfiling) usEs titratIoN seriES of chromatIn dIgeStS wITh miCROcOccAl nuCleaSe tO IDEnTifY chRomaTiN accesSibILItY as weLl as To map NucleOsOMes And NOn-hiStone dNa-BindinG ProteinS in BotH OPen and cLOsEd regions oF The GeNoMe.