Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Nature Methods - Tập 10 Số 12 - Trang 1213-1218 - 2013
Jason D. Buenrostro1, Paul G. Giresi2, Lisa C. Zaba2, Howard Y. Chang2, William J. Greenleaf1
1Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
2Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA

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Kornberg, R.D. Chromatin structure: a repeating unit of histones and DNA. Science 184, 868–871 (1974).

Kornberg, R.D. & Lorch, Y. Chromatin structure and transcription. Annu. Rev. Cell Biol. 8, 563–587 (1992).

Mellor, J. The dynamics of chromatin remodeling at promoters. Mol. Cell 19, 147–157 (2005).

Boyle, A.P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008).

Thurman, R.E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75–82 (2012).

Schones, D.E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 132, 887–898 (2008).

Valouev, A. et al. Determinants of nucleosome organization in primary human cells. Nature 474, 516–520 (2011).

Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).

Gerstein, M.B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91–100 (2012).

Goryshin, I.Y. & Reznikoff, W.S. Tn5 in vitro transposition. J. Biol. Chem. 273, 7367–7374 (1998).

Adey, A. et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol. 11, R119 (2010).

Gangadharan, S., Mularoni, L., Fain-Thornton, J., Wheelan, S.J. & Craig, N.L. DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo. Proc. Natl. Acad. Sci. USA 107, 21966–21972 (2010).

Song, L. & Crawford, G.E. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb. Protoc. 2010 pdb.prot5384 (2010).

Simon, J.M., Giresi, P.G., Davis, I.J. & Lieb, J.D. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nat. Protoc. 7, 256–267 (2012).

The ENCODE Project Consortium. A user's guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol. 9, e1001046 (2011).

Giresi, P.G. & Lieb, J.D. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48, 233–239 (2009).

Hoffman, M.M. et al. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 41, 827–841 (2013).

Prioleau, M.-N., Nony, P., Simpson, M. & Felsenfeld, G. An insulator element and condensed chromatin region separate the chicken β-globin locus from an independently regulated erythroid-specific folate receptor gene. EMBO J. 18, 4035–4048 (1999).

Ghirlando, R., Litt, M.D., Prioleau, M.-N., Recillas-Targa, F. & Felsenfeld, G. Physical properties of a genomic condensed chromatin fragment. J. Mol. Biol. 336, 597–605 (2004).

Kornberg, R.D. & Lorch, Y. Chromatin and transcription: where do we go from here. Curr. Opin. Genet. Dev. 12, 249–251 (2002).

Zhou, J., Fan, J.Y., Rangasamy, D. & Tremethick, D.J. The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression. Nat. Struct. Mol. Biol. 14, 1070–1076 (2007).

Chen, K. et al. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 23, 341–351 (2013).

Kundaje, A. et al. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res. 22, 1735–1747 (2012).

Hesselberth, J.R. et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat. Methods 6, 283–289 (2009).

Boyle, A.P. et al. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res. 21, 456–464 (2011).

Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83–90 (2012).

Pique-Regi, R. et al. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 21, 447–455 (2011).

Fraser, J.D., Irving, B.A., Crabtree, G.R. & Weiss, A. Regulation of interleukin-2 gene enhancer activity by the T cell accessory molecule CD28. Science 251, 313–316 (1991).

Flanagan, W.M., Corthésy, B., Bram, R.J. & Crabtree, G.R. Nuclear association of a T-cell transcription factor blocked by FK-506 and cyclosporin A. Nature 352, 803–807 (1991).

Lopez-Girona, A. et al. Lenalidomide downregulates the cell survival factor, interferon regulatory factor-4, providing a potential mechanistic link for predicting response. Br. J. Haematol. 154, 325–336 (2011).

Verstovsek, S. et al. Safety and efficacy of INCB018424, a JAK1 and JAK2 inhibitor, in myelofibrosis. N. Engl. J. Med. 363, 1117–1127 (2010).

Maurano, M.T. et al. Systematic localization of common disease-associated variation in regulatory. Science 337, 1190–1195 (2012).

Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377–382 (2009).

Shalek, A.K. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236–240 (2013).

Jolma, A. et al. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 20, 861–873 (2010).

Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

Guo, Y., Mahony, S. & Gifford, D.K. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput. Biol. 8, e1002638 (2012).

Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863–14868 (1998).