High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

Nature Protocols

Volumn 8, Issue 3, 2013, Pages 539-554

  Blecher Gonen, Ronnie ^a   Barnett Itzhaki, Zohar ^a   Jaitin, Diego ^a   Amann Zalcenstein, Daniela ^a   Lara Astiaso, David ^a   Amit, Ido ^a,b  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING AFFINITY; BINDING SITE; CELL ISOLATION; CELL STIMULATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; CROSS LINKING; EPIGENETICS; HIGH THROUGHPUT SEQUENCING; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; SEQUENCE ANALYSIS;

BINDING SITES, ANTIBODY; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME MAPPING; DNA-BINDING PROTEINS; EPIGENESIS, GENETIC; GENOMIC LIBRARY; INTERFERON REGULATORY FACTORS;

EID: 84875207585     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2013.023     Document Type: Article

References (47)

1. Graf, T. & Enver, T. Forcing cells to change lineages. Nature 462, 587-594 (2009).
2. Struhl, K. Gene regulation. A paradigm for precision. Science 293, 1054-1055 (2001).
3. Weintraub, H. et al. Activation of muscle-specific genes in pigment, nerve, fat, liver, and fibroblast cell lines by forced expression of MyoD. Proc. Natl. Acad. Sci. USA 86, 5434-5438 (1989).
4. Zhou, Q., Brown, J., Kanarek, A., Rajagopal, J. & Melton, D.A. In vivo reprogramming of adult pancreatic exocrine cells to beta-cells. Nature 455, 627-632 (2008).
5. Davidson, E.H. Emerging properties of animal gene regulatory networks. Nature 468, 911-920 (2010).
6. Capaldi, A.P. et al. Structure and function of a transcriptional network activated by the MAPK Hog1. Nat. Genet. 40, 1300-1306 (2008).
7. Harbison, C.T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).
8. Ramirez-Carrozzi, V.R. et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138, 114-128 (2009).
9. Bossard, P. & Zaret, K.S. GATA transcription factors as potentiators of gut endoderm differentiation. Development 125, 4909-4917 (1998).
10. Thanos, D. & Maniatis, T. The high mobility group protein HMG I(Y) is required for NF-κB-dependent virus induction of the human IFN-β gene. Cell 71, 777-789 (1992).
11. Berger, M.F. et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133, 1266-1276 (2008).
12. Segal, E. et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34, 166-176 (2003).
13. Amit, I. et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326, 257-263 (2009).
14. Solomon, M.J. & Varshavsky, A. Formaldehyde-mediated DNA-protein cross-linking: a probe for in vivo chromatin structures. Proc. Natl. Acad. Sci. USA 82, 6470-6474 (1985).
15. Aparicio, O., Geisberg, J.V. & Struhl, K. Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr. Protoc. Cell Biol 17, 17 (2004).
16. Buck, M.J. & Lieb, J.D. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83, 349-360 (2004).
17. Collas, P. A chromatin immunoprecipitation protocol for small cell numbers. Methods Mol. Biol. 791, 179-193 (2011).
18. O'Neill, L.P., VerMilyea, M.D. & Turner, B.M. Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat. Genet. 38, 835-841 (2006).
19. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837 (2007).
20. Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007).
21. Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007).
22. Adli, M., Zhu, J. & Bernstein, B.E. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat. Methods 7, 615-618 (2010).
23. Blahnik, K.R. et al. Characterization of the contradictory chromatin signatures at the 3′ exons of zinc finger genes. PLoS ONE 6, e17121 (2011).
24. Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
25. Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012).
26. Bernstein, B.E. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
27. Abdel-Wahab, O. et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell 22, 180-193 (2012).
28. Garber, M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012).
29. Hawkins, T.L., O'Connor-Morin, T., Roy, A. & Santillan, C. DNA purification and isolation using a solid-phase. Nucleic Acids Res. 22, 4543-4544 (1994).
30. Lundin, S., Stranneheim, H., Pettersson, E., Klevebring, D. & Lundeberg, J. Increased throughput by parallelization of library preparation for massive sequencing. PLoS ONE 5, e10029 (2010).
31. Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).
32. Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
33. Natoli, G. Maintaining cell identity through global control of genomic organization. Immunity 33, 12-24 (2010).
34. Bonn, S. et al. Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat. Protoc. 7, 978-994 (2012).
35. Schmidt, D. et al. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148, 335-348 (2012).
36. Schmidt, D. et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328, 1036-1040 (2010).
37. Clarke, S.L. et al. Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet. 8, e1002852 (2012).
38. Junion, G. et al. A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell 148, 473-486 (2012).
39. Mullen, A.C. et al. Master transcription factors determine cell-type-specific responses to TGF-β signaling. Cell 147, 565-576 (2011).
40. Liu, C.L. et al. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 3, e328 (2005).
41. Weiner, A. et al. Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol. 10, e1001369 (2012).
42. Fanelli, M., Amatori, S., Barozzi, I. & Minucci, S. Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue. Nat. Protoc. 6, 1905-1919 (2011).
43. Shankaranarayanan, P., Mendoza-Parra, M.A., van Gool, W., Trindade, L.M. & Gronemeyer, H. Single-tube linear DNA amplification for genome-wide studies using a few thousand cells. Nat. Protoc. 7, 328-338 (2012).
44. Rhee, H.S. & Pugh, B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419 (2011).
45. Klockenbusch, C. & Kast, J. Optimization of formaldehyde cross-linking for protein interaction analysis of non-tagged integrin beta1. J Biomed. Biotechnol. 2010, 927585 (2010).
46. Nowak, D.E., Tian, B. & Brasier, A.R. Two-step cross-linking method for identification of NF-κB gene network by chromatin immunoprecipitation. BioTechniques 39, 715-725 (2005).
47. Landt, S.G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813-1831 (2012).