ChIP-Seq: Library Preparation and Sequencing

  • Karyn L. Sheaffer
  • Jonathan SchugEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1402)


Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-Seq) has been used extensively to determine the genome-wide location of DNA-binding factors, such as transcription factors, posttranscriptionally modified histones, and members of the transcription complex, to assess regulatory input, epigenetic modifications, and transcriptional activity, respectively. Here we describe methods to isolate chromatin from tissues, immunoprecipitate DNA bound to a protein of interest, and perform next-generation sequencing to identify a genome-wide DNA-binding pattern.

Key words

Chromatin immunoprecipitation Next-generation sequencing DNA binding 


  1. 1.
    Hahn S, Young ET (2011) Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics 189(3):705–736. doi: 10.1534/genetics.111.127019 CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Farnham PJ (2009) Insights from genomic profiling of transcription factors. Nat Rev Genet 10(9):605–616. doi: 10.1038/nrg2636 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Rothbart SB, Strahl BD (2014) Interpreting the language of histone and DNA modifications. Biochim Biophys Acta 1839(8):627–643. doi: 10.1016/j.bbagrm.2014.03.001 CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Rodriguez R, Miller KM (2014) Unravelling the genomic targets of small molecules using high-throughput sequencing. Nat Rev Genet 15(12):783–796. doi: 10.1038/nrg3796 CrossRefPubMedGoogle Scholar
  5. 5.
    Mundade R, Ozer HG, Wei H, Prabhu L, Lu T (2014) Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond. Cell Cycle 13(18):2847–2852. doi: 10.4161/15384101.2014.949201 CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 13(12):840–852. doi: 10.1038/nrg3306 CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Zhang Z, Pugh BF (2011) High-resolution genome-wide mapping of the primary structure of chromatin. Cell 144(2):175–186. doi: 10.1016/j.cell.2011.01.003 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grontved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R (2013) Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 155(7):1507–1520. doi: 10.1016/j.cell.2013.11.039 CrossRefPubMedGoogle Scholar
  9. 9.
    Van Nostrand EL, Kim SK (2013) Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions. Genome Res 23(6):941–953. doi: 10.1101/gr.152876.112 CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli 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, Stamatoyannopoulos 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. doi: 10.1101/gr.136184.111 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Derrien T, Estelle J, Marco Sola S, Knowles DG, Raineri E, Guigo R, Ribeca P (2012) Fast computation and applications of genome mappability. PLoS One 7(1):e30377. doi: 10.1371/journal.pone.0030377 CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Tian B, Yang J, Brasier AR (2012) Two-step cross-linking for analysis of protein-chromatin interactions. Methods Mol Biol 809:105–120. doi: 10.1007/978-1-61779-376-9_7 CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Wal M, Pugh BF (2012) Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq. Methods Enzymol 513:233–250. doi: 10.1016/B978-0-12-391938-0.00010-0 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of Genetics, and Institute for Diabetes, Obesity and Metabolism, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaUSA

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