Name: mapping genome-wide accessible chromatin in primary human t lymphocytes by atac-seq
Uploaded: 2017-11-13T13:00:00
Description: Watch this Scientific Journal Video about Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq at JoVE.com

Dette arbejde støttes af Israel Science Foundation (grant 748/14), Marie Curie-Integration yde (CIG) - RP7-folk-20013-CIG-618763 og CORE Program af planlægning og budgettering udvalg og The Israel Science Foundation give nr. 41/11.

alle procedurerne, der blev godkendt af institutionelle review board Bar Ilan Universitet og protokollen følger retningslinjer fastsat af udvalget godkender eksperimenterne.
 1. rensning af naive menneskers CD4 + celler og polarisering T hjælper 1 (Th1) og Th2 celler Note: her vi beskriver den procedure, der starter fra frosne humant perifert blod mononukleære celler (PBMC). Det første trin består af isolere CD4 + celler ved hjælp af microbeads og kolonner der...

<ol>
	<li>Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., Greenleaf, W. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transposition+of+native+chromatin+for+fast+and+sensitive+epigenomic+profiling+of+open+chromatin,+DNA-binding+proteins+and+nucleosome+position.">Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.</a> Nat Methods. 10 (12), 1213-1218 (2013).</li><li>Buenrostro, J. D., Wu, B., Chang, H. Y., Greenleaf, W. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ATAC-seq:+A+method+for+assaying+chromatin+accessibility+genome-wide.">ATAC-seq: A method for assaying chromatin accessibility genome-wide.</a> Curr Protoc Mol Biol. , 21.29.1-21.29.9 (2015).</li><li>Thurman, R. E., Rynes, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+accessible+chromatin+landscape+of+the+human+genome.">The accessible chromatin landscape of the human genome.</a> Nature. 489 (7414), 75-82 (2012).</li><li>Song, L., Crawford, G. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNase-seq:+a+high-resolution+technique+for+mapping+active+gene+regulatory+elements+across+the+genome+from+mammalian+cells.">DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.</a> Cold Spring Harb Protoc. (2), (2010).</li><li>Simon, J. M., Giresi, P. G., Davis, I. J., Lieb, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+formaldehyde-assisted+isolation+of+regulatory+elements+(FAIRE)+to+isolate+active+regulatory+DNA.">Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.</a> Nat Protoc. 7 (2), 256-267 (2012).</li><li>Cui, K., Zhao, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-Wide+Approaches+to+Determining+Nucleosome+Occupancy+in+Metazoans+Using+MNase-Seq.">Genome-Wide Approaches to Determining Nucleosome Occupancy in Metazoans Using MNase-Seq.</a> Methods Mol Biol. 833, 413-419 (2012).</li><li>Qu, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Individuality+and+Variation+of+Personal+Regulomes+in+Primary+Human+T+Cells.">Individuality and Variation of Personal Regulomes in Primary Human T Cells.</a> Cell Syst. 1 (1), 51-61 (2015).</li><li>Scharer, C. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ATAC-seq+on+biobanked+specimens+defines+a+unique+chromatin+accessibility+structure+in+na&#239;ve+SLE+B+cells.">ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in na&#239;ve SLE B cells.</a> Sci Rep. 6, 27030 (2016).</li><li>Seb&#233;-Pedr&#243;s, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Dynamic+Regulatory+Genome+of+Capsaspora+and+the+Origin+of+Animal+Multicellularity.">The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity.</a> Cell. 165 (5), 1224-1237 (2016).</li><li>Lu, Z., Hofmeister, B. T., Vollmers, C., DuBois, R. M., Schmitz, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Combining+ATAC-seq+with+nuclei+sorting+for+discovery+of+cis-regulatory+regions+in+plant+genomes.">Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes.</a> Nucleic Acids Res. 45 (6), e41 (2016).</li><li>Davie, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Discovery+of+Transcription+Factors+and+Regulatory+Regions+Driving+In+Vivo+Tumor+Development+by+ATAC-seq+and+FAIRE-seq+Open+Chromatin+Profiling.">Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling.</a> PLOS Genet. 11 (2), (2015).</li><li>Villar, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhancer+Evolution+across+20+Mammalian+Species.">Enhancer Evolution across 20 Mammalian Species.</a> Cell. 160 (3), 554-566 (2015).</li><li>Lara-Astiaso, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromatin+state+dynamics+during+blood+formation.">Chromatin state dynamics during blood formation.</a> Science. 345 (6199), 943-949 (2014).</li><li>Prescott, S. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhancer+Divergence+and+cis-Regulatory+Evolution+in+the+Human+and+Chimp+Neural+Crest.">Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest.</a> Cell. 163 (1), 68-83 (2015).</li><li>Wu, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+landscape+of+accessible+chromatin+in+mammalian+preimplantation+embryos.">The landscape of accessible chromatin in mammalian preimplantation embryos.</a> Nature. 534 (7609), 652-657 (2016).</li><li>Buenrostro, J. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+chromatin+accessibility+reveals+principles+of+regulatory+variation.">Single-cell chromatin accessibility reveals principles of regulatory variation.</a> Nature. 523 (7561), 486-490 (2015).</li><li>Corces, M. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lineage-specific+and+single-cell+chromatin+accessibility+charts+human+hematopoiesis+and+leukemia+evolution.">Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution.</a> Nat Genet. 48 (10), 1193-1203 (2016).</li><li>Jenner, R. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+transcription+factors+T-bet+and+GATA-3+control+alternative+pathways+of+T-cell+differentiation+through+a+shared+set+of+target+genes.">The transcription factors T-bet and GATA-3 control alternative pathways of T-cell differentiation through a shared set of target genes.</a> Proc Natl Acad Sci USA. 106 (42), 17876-17881 (2009).</li><li>DeAngelis, M. M., Wang, D. G., Hawkins, T. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Solid-phase+reversible+immobilization+for+the+isolation+of+PCR+products.">Solid-phase reversible immobilization for the isolation of PCR products.</a> Nucleic Acids Res. 23 (22), 4742-4743 (1995).</li><li>Aird, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analyzing+and+minimizing+PCR+amplification+bias+in+Illumina+sequencing+libraries.">Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.</a> Genome Biol. 12 (2), R18 (2011).</li><li>Langmead, B., Trapnell, C., Pop, M., Salzberg, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultrafast+and+memory-efficient+alignment+of+short+DNA+sequences+to+the+human+genome.">Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.</a> Genome Biol. 10 (3), R25 (2009).</li><li>Li, H., Handsaker, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Sequence+Alignment/Map+format+and+SAMtools.">The Sequence Alignment/Map format and SAMtools.</a> Bioinformatics. 25 (16), 2078-2079 (2009).</li><li>Quinlan, A. R., Hall, I. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BEDTools:+a+flexible+suite+of+utilities+for+comparing+genomic+features.">BEDTools: a flexible suite of utilities for comparing genomic features.</a> Bioinformatics. 26 (6), 841-842 (2010).</li><li>Zhang, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Model-based+Analysis+of+ChIP-Seq+(MACS).">Model-based Analysis of ChIP-Seq (MACS).</a> Genome Biol. 9 (9), R137 (2008).</li><li>Meyer, C. A., Shirley Liu, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identifying+and+mitigating+bias+in+next-generation+sequencing+methods+for+chromatin+biology.">Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.</a> Nat Rev Genet. 15 (11), 709-721 (2014).</li><li>He, H. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Refined+DNase-seq+protocol+and+data+analysis+reveals+intrinsic+bias+in+transcription+factor+footprint+identification.">Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.</a> Nat Methods. 11 (1), 73-78 (2013).</li><li>Madrigal, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+Accounting+for+Sequence-Specific+Bias+in+Genome-Wide+Chromatin+Accessibility+Experiments:+Recent+Advances+and+Contradictions.">On Accounting for Sequence-Specific Bias in Genome-Wide Chromatin Accessibility Experiments: Recent Advances and Contradictions.</a> Front Bioeng Biotechnol. 3, 1-4 (2015).</li><li>Qin, Q., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ChiLin:+a+comprehensive+ChIP-seq+and+DNase-seq+quality+control+and+analysis+pipeline.">ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.</a> BMC Bioinformatics. 17 (1), (2016).</li><li>Bao, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+ATAC-seq+approach+reveals+lineage-specific+reinforcement+of+the+open+chromatin+landscape+via+cooperation+between+BAF+and+p63.">A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63.</a> Genome Biol. 16 (1), 284 (2015).</li><li>Maurano, M. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Systematic+localization+of+common+disease-associated+variation+in+regulatory+DNA.">Systematic localization of common disease-associated variation in regulatory DNA.</a> Science. 337 (6099), 1190-1195 (2012).</li></ol>

ATAC-seq protokollen beskrevet her har været med succes ansat til analyse af tilgængelige kromatin i primærelementer (menneskelige Th1, Th2 celler og B-celler) samt kulturperler cellelinjer (MCF10A humane brystkræftceller og U261 glioblastom celler). Anvende ATAC-seq til andre celletyper kan kræve nogle protokol optimering, især i trinnet lysering. Hvis koncentrationen af nonionisk detergent er for højt, kan der være en højere procentdel af mitokondriel DNA forurening. Dette kan reduceres ved at mindske koncentr...

ATAC-seq1,2 er en robust metode, der muliggør identifikation af regulerende3 åbne kromatin regioner og nucleosome placering. Disse oplysninger anvendes til at udlede placering, identitet og aktivitet af transkriptionsfaktorer. Metodens følsomhed for måling af de kvantitative variationer i kromatin struktur giver mulighed for undersøgelse af kromatin faktorer, herunder kromatin remodelers samt modificeringer og RNA polymerase II1transcriptional aktivitet aktivitet. Dermed giver ATAC-seq en kraftfuld og fordomsfri tilgang til decifrere mekanismer, der styrer transkriptionel regulering i enhver celletype af interesse. Vi beskriver tilpasningen af ATAC-seq til primære menneskelige Th1 og Th2 celler.
I ATAC-FF., hyperaktiv Tn5 transposase fyldt med adaptere til næste generation sequencing (NGS) par DNA opsplitning med mærkning af DNA med adaptere (dvs., at "tagmentation")1. Efter PCR-amplifikation er de resulterende DNA biblioteker klar til næste generation sequencing (figur 1). Den privilegerede tagmentation af tilgængelige kromatin registreres af analysen af lokale berigelse af ATAC-seq sekventering læser.
Kort eksperimentel procedure og krav om mindre råvaren, i forhold til andre metoder til måling af kromatin tilgængelighed og nucleosomal positionering som DNase-seq4, FAIRE-seq5og MNase-seq6, har fremmet brugen af ATAC-seq i flere biologiske systemer, herunder menneskelige primærelementer1,7 kliniske prøver8, samt og encellede organismer9, planter10, bananfluer11 , og forskellige pattedyr12.
Identiteten af transskription faktorer, der er bundet til tilgængelige loci kan blive afsløret ved at analysere berigelsen af deres bindende sekvens motiver eller kombinere ATAC-seq med kromatin immunoprecipitation (ChIP) efterfulgt af høj overførselshastighed DNA-sekventering ( ChIP-seq). Denne tilgang aktiveret identifikation af afstamning-specifikke transkriptionsfaktorer vigtigt for bloddannelsen i mus13. ATAC-seq saglig og globale natur giver mulighed for at studere RIBOREGULATION i organismer som reagenser som antistoffer for ChIP analyse ikke er tilgængelige. For eksempel evolutionære variationer i cis-regulerende regioner er blevet identificeret ved at studere kraniel neurale crest celler fra mennesker og chimpanser14, udviklingsmæssige variationer i regulerende elementer under tidlige mus embryogenese15, ændringer i den lovgivningslandskab i løbet af en livscyklus af encellede C. owzarzaki9, og udviklingen af initiativtagerne og smagsforstærkere i hele 20 pattedyr arter12.
ATAC-seq har også været medvirkende til at måle kromatin tilgængelighed i enkelt celler, således afslørende variation inden for cellepopulationer, som normalt undviger genome-wide undersøgelser7,16. Derudover kan ATAC-seq bruges til at studere forandringer, der sker i DNA regulerende regioner i sygdomstilstande, hvor prøverne er sjældne. For eksempel, ATAC-seq kan bruges til at studere ændringer på den reguleringsmæssige landskab under udbruddet af akut myeloid leukæmi (AML)17 eller Ras-drevet oncogenesis11.

mapping genome-wide accessible chromatin in primary human t lymphocytes by atac-seq

Assay for Transposase-tilgængelige kromatin med høj overførselshastighed sekventering (ATAC-FF.) er en metode, der anvendes til identifikation af åbne (tilgængelige) regioner af kromatin. Disse områder repræsenterer regulerende DNA elementer (f.eks.promotorer, smagsforstærkere, locus kontrol regioner, isolatorer) til hvilke transskription faktorer binde. Kortlægning af de tilgængelige kromatin landskab er en kraftfuld tilgang til afsløring aktive regulerende elementer på tværs af genomet. Disse oplysninger tjener som en fordomsfri tilgang for at opdage netværket af relevante transkriptionsfaktorer og mekanismer af kromatin struktur, der styrer gen expression programmer. ATAC-seq er en robust og følsom alternativ til DNase jeg overfølsomhed analyse kombineret med næste generation sequencing (DNase-seq) og formaldehyd-assisteret isolation af regulerende elementer (FAIRE-seq) for genome-wide analyse af kromatin tilgængelighed og til sekvensering af micrococcal nukleasen-følsomme steder (MNase-seq) til at bestemme nucleosome placering. Vi præsenterer en detaljeret ATAC-seq protokol optimeret nemlig menneskelige primære immun celler dvs CD4 + lymfocytter (T hjælper 1 (Th1) og Th2 celler). Denne omfattende protokol begynder med celle høst, så beskriver den molekylære procedure af kromatin tagmentation, prøveforberedelse til næste generations sekvensering, og også omfatter metoder og overvejelser i forbindelse med de beregningsmæssige analyser bruges til at fortolke resultaterne. Desuden, for at spare tid og penge, vi indført kvalitetskontrolforanstaltninger til at vurdere ATAC-seq biblioteket før sekvensering. Vigtigere, tillader de principper, der er præsenteret i denne protokol dets tilpasning til andre menneskers immunforsvar og ikke-immune primærelementer og cellelinjer. Disse retningslinjer vil også være nyttigt for laboratorier, der ikke er dygtige med næste generations sekventering metoder.

Det endelige resultat af denne protokol er en ATAC-seq bibliotek af typisk 3-20 ng/µL. Når kører på et system for DNA integritet analyse (Se Tabel af materialer/udstyr), de viser stigen-lignende udseende2 (figur 3A). Den gennemsnitlige størrelse af DNA-fragmenter er typisk ~ 450-530 bp.
Ordentlig kvalitetsstyring ATAC-seq biblioteker før du udfører næ...

Watch this Scientific Journal Video about Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq at JoVE.com

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq (Video) | JoVE

Assay for Transposase-tilgængelige kromatin kombineret med høj overførselshastighed sekventering (ATAC-FF.) er en genome-wide metode til at afdække tilgængelige kromatin. Dette er en trinvis ATAC-seq-protokollen fra molekylære til den endelige beregningsmæssige analyse, optimeret til humane lymfocytter (Th1/Th2). Denne protokol kan vedtages af forskere uden forudgående erfaring i næste generations sekventering metoder.

Kortlægning Genome-wide tilgængelige kromatin i primære humane T lymfocytter af ATAC-Seq

Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions ...

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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

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