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Chromatin Immunoprecipitation and High-Throughput Sequencing (ChIP-Seq): Tips and Tricks Regarding the Laboratory Protocol and Initial Downstream Data Analysis

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Epigenome Editing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1767))

Abstract

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become an essential tool for epigenetic scientists. ChIP-seq is used to map protein-DNA interactions and epigenetic marks such as histone modifications at the genome-wide level. Here we describe a complete ChIP-seq laboratory protocol (tailored toward processing tissue samples as well as cell lines) and the bioinformatic pipelines utilized for handling raw sequencing files through to peak calling.

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References

  1. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669–680

    Article  CAS  Google Scholar 

  2. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459(7243):108–112

    Article  CAS  Google Scholar 

  3. Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ (2009) Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res 19(6):967–977

    Article  CAS  Google Scholar 

  4. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA (2000) Genome-wide location and function of DNA binding proteins. Science (New York, NY) 290(5500):2306–2309

    Article  CAS  Google Scholar 

  5. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409(6819):533–538

    Article  CAS  Google Scholar 

  6. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28(4):327–334

    Article  CAS  Google Scholar 

  7. Horak CE, Snyder M (2002) ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol 350:469–483

    Article  CAS  Google Scholar 

  8. Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ (2002) Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev 16(2):235–244

    Article  CAS  Google Scholar 

  9. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4(8):651–657

    Article  CAS  Google Scholar 

  10. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science (New York, NY) 316(5830):1497–1502

    Article  CAS  Google Scholar 

  11. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human genome. Cell 129(4):823–837

    Article  CAS  Google Scholar 

  12. Landt SG, Marinov GK, Kundaje A, Kheradpour P, PaμLi F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, StamatoyannopoμLos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22(9):1813–1831

    Article  CAS  Google Scholar 

  13. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48(3):240–248

    Article  CAS  Google Scholar 

  14. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767–1771

    Article  Google Scholar 

  15. Fabbro CD, Scalabrin S, Morgante M, Giorgi FM (2013) An extensive evaluation of read trimming effects on illumina NGS data analysis. PLoS One 8(12):e85024

    Article  Google Scholar 

  16. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  Google Scholar 

  17. Zhao H, Sun Z, Wang J, Huang H, Kocher J-P, Wang L (2013) CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics 30:1006–1007

    Article  Google Scholar 

  18. Li H, Homer N (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11:473–483

    Article  CAS  Google Scholar 

  19. Langmead B (2010) Aligning short sequencing reads with bowtie. Curr Protoc Bioinformatics. Chapter 11:Unit 11.7

    Google Scholar 

  20. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  CAS  Google Scholar 

  21. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    Article  Google Scholar 

  22. Wilbanks EG, Facciotti MT (2010) Evaluation of algorithm performance in ChIP-Seq peak detection. PLoS One 5(7):e11471

    Article  Google Scholar 

  23. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9(9):R137

    Article  Google Scholar 

  24. Feng J, Liu T, Qin B, Zhang Y, Liu XS (2012) Identifying ChIP-seq enrichment using MACS. Nat Protoc 7:1728–1740

    Article  CAS  Google Scholar 

  25. Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Gonzalez JN, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, Lee CM, Nejad P, Raney BJ, Rosenbloom KR, Speir ML, Villarreal C, Vivian J, Zweig AS, Haussler D, Kuhn RM, Kent WJ (2017) The UCSC Genome Browser database: 2017 update. Nucleic Acids Res 45(D1):D626–D634

    CAS  PubMed  Google Scholar 

  26. Thorvaldsdottir H, Robinson JT, Mesirov JP (2012) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178–192

    Article  Google Scholar 

  27. Steinhauser S, Kurzawa N, Eils R, Herrmann C (2016) A comprehensive comparison of tools for differential ChIP-seq analysis. Brief Bioinform 17(6):953–966

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842

    Article  CAS  Google Scholar 

  29. Jee J, Rozowsky J, Yip KY, Lochovsky L, Bjornson R, Zhong G, Zhang Z, Fu Y, Wang J, Weng Z, Gerstein M (2011) ACT: aggregation and correlation toolbox for analyses of genome tracks. Bioinformatics 27:1152–1154

    Article  CAS  Google Scholar 

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Acknowledgement

This work was supported by the European Union Horizon 2020 research and innovation programme (642691).

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Authors and Affiliations

  1. Department of Surgery and Cancer, Imperial College London, London, UK

    Darren K. Patten, Giacomo Corleone & Luca Magnani

  2. Department of Bariatric and Emergency General Surgery, Homerton University Hospital, London, UK

    Darren K. Patten

Authors
  1. Darren K. Patten
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  2. Giacomo Corleone
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  3. Luca Magnani
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Corresponding author

Correspondence to Luca Magnani .

Editor information

Editors and Affiliations

  1. Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart, Germany

    Albert Jeltsch

  2. Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands

    Marianne G. Rots

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Patten, D.K., Corleone, G., Magnani, L. (2018). Chromatin Immunoprecipitation and High-Throughput Sequencing (ChIP-Seq): Tips and Tricks Regarding the Laboratory Protocol and Initial Downstream Data Analysis. In: Jeltsch, A., Rots, M. (eds) Epigenome Editing. Methods in Molecular Biology, vol 1767. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7774-1_15

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  • DOI: https://doi.org/10.1007/978-1-4939-7774-1_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7773-4

  • Online ISBN: 978-1-4939-7774-1

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