Mapping and analysis of chromatin state dynamics in nine human cell types

Nature

Volumn 473, Issue 7345, 2011, Pages 43-49

  Ernst, Jason ^a,b   Kheradpour, Pouya ^a,b   Mikkelsen, Tarjei S ^a   Shoresh, Noam ^a   Ward, Lucas D ^a,b   Epstein, Charles B ^a   Zhang, Xiaolan ^a   Wang, Li ^a   Issner, Robbyn ^a   Coyne, Michael ^a   Ku, Manching ^a,c   Durham, Timothy ^a   Kellis, Manolis ^a,b   Bernstein, Bradley E ^a,c  

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

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

CELL ORGANELLE; GENE EXPRESSION; GENOME; PHENOTYPE;

AMINO ACID SEQUENCE; ARTICLE; CELL SPECIFICITY; CHROMATIN; ENHANCER REGION; GENE CONTROL; GENE EXPRESSION; GENE MAPPING; GENE REPRESSION; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; NUCLEOSOME; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DEPLETION; SINGLE NUCLEOTIDE POLYMORPHISM;

BINDING SITES; CELL LINE; CELL LINE, TUMOR; CELL PHYSIOLOGICAL PHENOMENA; CELLS, CULTURED; CHROMATIN; CHROMOSOME MAPPING; GENE EXPRESSION REGULATION; GENOME, HUMAN; HEP G2 CELLS; HUMANS; PROMOTER REGIONS, GENETIC; REPRODUCIBILITY OF RESULTS; TRANSCRIPTION FACTORS;

EID: 79955583542     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature09906     Document Type: Article

References (65)

1. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816 (2007). (Pubitemid 46920138)
2. Kim, H. D., Shay, T., O'Shea, E. K. & Regev, A. Transcriptional regulatory circuits: predicting numbers from alphabets. Science 325, 429-432 (2009).
3. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837 (2007). (Pubitemid 46802390)
4. Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007). (Pubitemid 47206934)
5. Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. & Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77-88 (2007). (Pubitemid 47031323)
6. Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the humangenome. NatureGenet.39, 311-318 (2007). (Pubitemid 46328487)
7. Hon, G., Wang, W. & Ren, B. Discovery and annotation of functional chromatin signatures in the human genome. PLOS Comput. Biol. 5, e1000566 (2009).
8. Ernst, J.& Kellis,M. Discoveryandcharacterizationofchromatinstatesforsystematic annotation of the human genome. Nature Biotechnol. 28, 817-825 (2010).
9. Bernstein, B. E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169-181 (2005). (Pubitemid 40174761)
10. Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108-112 (2009).
11. Phillips, J. E. & Corces, V. G. CTCF: master weaver of the genome. Cell 137, 1194-1211 (2009).
12. Hansen, R. S. et al. Sequencing newly replicatedDNA reveals widespread plasticity in human replication timing. Proc. Natl Acad. Sci. USA 107, 139-144 (2010).
13. Raha, D. et al. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc. Natl Acad. Sci. USA 107, 3639-3644 (2010).
14. Kasowski, M. et al. Variation in transcription factor binding among humans. Science 328, 232-235 (2010).
15. Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948-951 (2008). (Pubitemid 351832561)
16. Jaenisch, R. & Young, R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132, 567-582 (2008). (Pubitemid 351253686)
17. DeSanta, F. et al. A large fraction of extragenicRNA pol II transcription sites overlap enhancers. PLoS Biol. 8, e1000384 (2010).
18. Kim, T. K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
19. Talbert, P. B. & Henikoff, S. Histone variants-ancient wrap artists of the epigenome. Nature Rev. Mol. Cell Biol. 11, 264-275 (2010).
20. Schadt, E. E. et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 6, e107 (2008).
21. Pickrell, J. K. et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768-772 (2010).
22. Montgomery, S. B. et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773-777 (2010).
23. Veyrieras, J. B. et al. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 4, e1000214 (2008).
24. Kunarso, G. et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nature Genet. 42, 631-634 (2010).
25. Fujiwara, T. et al. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol. Cell 36, 667-681 (2009).
26. Lemaigre, F. & Zaret, K. S. Liver development update: new embryo models, cell lineage control, and morphogenesis. Curr. Opin. Genet. Dev. 14, 582-590 (2004). (Pubitemid 39360307)
27. Sabourin, L. A. & Rudnicki, M. A. The molecular regulation of myogenesis. Clin. Genet. 57, 16-25 (2000). (Pubitemid 30105556)
28. Bartel, F. O., Higuchi, T. & Spyropoulos, D. D. Mouse models in the study of the Ets family of transcription factors. Oncogene 19, 6443-6454 (2000). (Pubitemid 32108434)
29. Law, J. C., Ritke, M. K., Yalowich, J. C., Leder, G. H. & Ferrell, R. E. Mutational inactivation of the p53 gene in the human erythroid leukemic K562 cell line. Leuk. Res. 17, 1045-1050 (1993). (Pubitemid 23358335)
30. Forte, E. & Luftig, M. A.MDM2-dependent inhibition of p53 is required for Epstein-Barr virus B-cell growth transformation and infected-cell survival. J. Virol. 83, 2491-2499 (2009).
31. Solozobova, V., Rolletschek, A. & Blattner, C. Nuclear accumulation and activation of p53 in embryonic stem cells after DNA damage. BMC Cell Biol. 10, 46 (2009).
32. Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499-509 (2004). (Pubitemid 38264428)
33. Wei, C. L. et al. A global mapof p53 transcription-factor binding sites in the human genome. Cell 124, 207-219 (2006).
34. Hoshino, H. et al. Co-repressor SMRT and class II histone deacetylases promote Bach2nuclear retentionand formation ofnuclear foci that are responsible for local transcriptional repression. J. Biochem. 141, 719-727 (2007). (Pubitemid 47014020)
35. Vassen, L., Fiolka, K. & Moroy, T. Gfi1b alters histone methylation at target gene promoters and sites of gamma-satellite containing heterochromatin. EMBO J. 25, 2409-2419 (2006). (Pubitemid 44012224)
36. He, H. H. et al. Nucleosome dynamics define transcriptional enhancers. Nature Genet. 42, 343-347 (2010).
37. Hindorff, L. A. et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA 106, 9362-9367 (2009).
38. Ganesh, S. K. et al. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. Nature Genet. 41, 1191-1198 (2009).
39. Han, J. W. et al. Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nature Genet. 41, 1234-1237 (2009).
40. Kathiresan, S. et al. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.Nature Genet. 40, 189-197 (2008). (Pubitemid 351171402)
41. Teslovich, T. M. et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466, 707-713 (2010).
42. Houlston, R. S. et al. Meta-analysis of genome-wide association data identifies four newsusceptibility loci for colorectal cancer. Nature Genet. 40, 1426-1435 (2008).
43. Newton-Cheh, C. et al. Genome-wide association study identifies eight loci associated with blood pressure. Nature Genet. 41, 666-676 (2009).
44. Stahl, E. A. et al. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nature Genet. 42, 508-514 (2010).
45. Liu, X. et al. Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis. Nature Genet. 42, 658-660 (2010).
46. Kamatani, Y. et al. Genome-wide association study of hematological and biochemical traits in a Japanese population. Nature Genet. 42, 210-215 (2010).
47. Soranzo, N. et al. A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nature Genet. 41, 1182-1190 (2009).
48. Papaemmanuil, E. et al. Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia. Nature Genet. 41, 1006-1010 (2009).
49. Visel, A., Rubin, E. M. & Pennacchio, L. A. Genomic views of distant-acting enhancers. Nature 461, 199-205 (2009).
50. Naumova, N. & Dekker, J. Integrating one-dimensional and three-dimensional maps of genomes. J. Cell Sci. 123, 1979-1988 (2010).
51. Ludwig, T. E. et al. Feeder-independent culture of human embryonic stem cells. Nature Methods 3, 637-646 (2006). (Pubitemid 44123431)
52. Geiss, G. K. et al. Direct multiplexed measurement of gene expression with colorcoded probe pairs. Nature Biotechnol. 26, 317-325 (2008). (Pubitemid 351355126)
53. Reich, M. et al. GenePattern 2.0. Nature Genet. 38, 500-501 (2006).
54. Kent, W. J. et al. The human genomebrowser at UCSC. Genome Res. 12, 996-1006 (2002).
55. Pruitt, K. D., Tatusova, T. & Maglott, D. R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61-D65 (2007). (Pubitemid 46056171)
56. Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005). (Pubitemid 41126859)
57. Ernst, J. & Bar-Joseph, Z. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics 7, 191 (2006).
58. Ashburner, M. et al. Gene Ontology: tool for the unification of biology. Nature Genet. 25, 25-29 (2000). (Pubitemid 30257031)
59. Matys, V. et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378 (2003). (Pubitemid 36150406)
60. Sandelin, A., Alkema,W., Engstrom, P.,Wasserman, W. W. & Lenhard, B.JASPAR:an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32, D91-D94 (2004). (Pubitemid 38081611)
61. Berger, M. F. et al. Variation in homeodomain DNA binding revealed by highresolution analysis of sequence preferences. Cell 133, 1266-1276 (2008). (Pubitemid 351852913)
62. Badis, G. et al. Diversity andcomplexity inDNArecognition by transcriptionfactors. Science 324, 1720-1723 (2009).
63. Berger, M. F. et al. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnol. 24, 1429-1435 (2006). (Pubitemid 44722107)
64. Touzet, H. & Varre, J. S. Efficient and accurate P-value computation for Position Weight Matrices. Algorithms Mol. Biol. 2, 15 (2007).
65. Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326 (2006).