Chromatin tandem affinity purification sequencing

Nature Protocols

Volumn 8, Issue 8, 2013, Pages 1525-1534

  Soleimani, Vahab D ^a,b   Palidwor, Gareth A ^a   Ramachandran, Parameswaran ^a,b   Perkins, Theodore J ^a,b   Rudnicki, Michael A ^a,b  

^a OTTAWA HOSPITAL RESEARCH INSTITUTE   (Canada)

^b UNIVERSITY OF OTTAWA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AFFINITY CHROMATOGRAPHY; ANALYTIC METHOD; ARTICLE; BINDING SITE; CELL TYPE; CHROMATIN; CHROMATIN TANDEM AFFINITY PURIFICATION; CLINICAL PROTOCOL; CROSS LINKING; CYTOLYSIS; DNA PURIFICATION; ELUTION; EXPERIMENTAL DESIGN; PHOTOLYSIS; PRIORITY JOURNAL; PROCESS DESIGN; PROTEIN DNA BINDING; PROTEIN EXPRESSION; ULTRASOUND; VALIDATION PROCESS;

BINDING SITES; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CHROMATOGRAPHY, AFFINITY; DNA-BINDING PROTEINS; HEK293 CELLS; HUMANS; SONICATION;

EID: 84880263451     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2013.088     Document Type: Article

References (27)

1. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000). (Pubitemid 32041573)
2. Horak, C.E. et al. GATA-1 binding sites mapped in the β-globin locus by using mammalian ChIP-chip analysis. Proc. Natl. Acad. Sci. USA 99, 2924-2929 (2002). (Pubitemid 34240562)
3. Blais, A. et al. An initial blueprint for myogenic differentiation. Genes Dev. 19, 553-569 (2005). (Pubitemid 40314988)
4. Mardis, E.R. ChIP-seq: welcome to the new frontier. Nat. Methods 4, 613-614 (2007). (Pubitemid 47202468)
5. Schmid, C.D. & Bucher, P. ChIP-seq data reveal nucleosome architecture of human promoters. Cell 131, 831-832 (2007). (Pubitemid 350138097)
6. Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-seq data. Nat. Methods 5, 829-834 (2008).
7. Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858 (2009).
8. Fullwood, M.J. et al. An oestrogen-receptor-α-bound human chromatin interactome. Nature 462, 58-64 (2009).
9. Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84-98 (2012).
10. Harada, R. & Nepveu, A. Chromatin affinity purification. Methods Mol. Biol. 809, 237-253 (2012).
11. Soleimani, V.D. et al. Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Dev. Cell 22, 1208-1220 (2012).
12. Soleimani, V.D. et al. Snail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis. Mol. Cell 47, 457-468 (2012).
13. Puig, O. et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218-229 (2001). (Pubitemid 32846428)
14. McKinnell, I.W. et al. Pax7 activates myogenic genes by recruitment of a histone methyltransferase complex. Nat. Cell Biol. 10, 77-84 (2008).
15. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030-1032 (1999). (Pubitemid 29474865)
16. Burckstummer, T. et al. An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells. Nat. Methods 3, 1013-1019 (2006). (Pubitemid 44782701)
17. Huh, W.K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686-691 (2003).
18. Ghaemmaghami, F. et al. First-line chemotherapy with 5-FU and platinum for advanced and recurrent cancer of the cervix: a phase II study. J. Obstet. Gynaecol. 23, 422-425 (2003). (Pubitemid 36918726)
19. Rohila, J.S., Chen, M., Cerny, R. & Fromm, M.E. Improved tandem affinity purification tag and methods for isolation of protein heterocomplexes from plants. Plant J. 38, 172-181 (2004). (Pubitemid 38448454)
20. Abe, M., Fujiwara, M., Kurotani, K., Yokoi, S. & Shimamoto, K. Identification of dynamin as an interactor of rice GIGANTEA by tandem affinity purification (TAP). Plant Cell Physiol. 49, 420-432 (2008). (Pubitemid 351398314)
21. Auerbach, R.K. et al. Mapping accessible chromatin regions using Sono-seq. Proc. Natl. Acad. Sci. USA 106, 14926-14931 (2009).
22. Vega, V.B., Cheung, E., Palanisamy, N. & Sung, W.K. Inherent signals in sequencing-based chromatin-immunoprecipitation control libraries. PLoS ONE 4, e5241 (2009).
23. Cao, Y. et al. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev. Cell 18, 662-674 (2010).
24. Mullen, A.C. et al. Master transcription factors determine cell-type-specific responses to TGF-β signaling. Cell 147, 565-576 (2011).
25. Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007). (Pubitemid 46906620)
26. Rozowsky, J. et al. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol. 27, 66-75 (2009).
27. Landt, S.G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813-1831 (2012).