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

Article metrics


Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cellular phenotypes yet remain largely uncharted. Here we map nine chromatin marks across nine cell types to systematically characterize regulatory elements, their cell-type specificities and their functional interactions. Focusing on cell-type-specific patterns of promoters and enhancers, we define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. We use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them. The resulting annotations and regulatory predictions have implications for the interpretation of genome-wide association studies. Top-scoring disease single nucleotide polymorphisms are frequently positioned within enhancer elements specifically active in relevant cell types, and in some cases affect a motif instance for a predicted regulator, thus suggesting a mechanism for the association. Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Chromatin state discovery and characterization.
Figure 2: Cell-type-specific promoter and enhancer states and associated functional enrichments.
Figure 3: Correlations in activity patterns link enhancers to gene targets and upstream regulators.
Figure 4: Validation of regulatory predictions by nucleosome depletions and enhancer activity.
Figure 5: Disease variants annotated by chromatin dynamics and regulatory predictions.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

Sequencing and expression data has been deposited into the Gene Expression Omnibus under accession number GSE26386.


  1. 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)

  2. 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. 3

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

  4. 4

    Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007)

  5. 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)

  6. 6

    Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genet. 39, 311–318 (2007)

  7. 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. 8

    Ernst, J. & Kellis, M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature Biotechnol. 28, 817–825 (2010)

  9. 9

    Bernstein, B. E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169–181 (2005)

  10. 10

    Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009)

  11. 11

    Phillips, J. E. & Corces, V. G. CTCF: master weaver of the genome. Cell 137, 1194–1211 (2009)

  12. 12

    Hansen, R. S. et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc. Natl Acad. Sci. USA 107, 139–144 (2010)

  13. 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. 14

    Kasowski, M. et al. Variation in transcription factor binding among humans. Science 328, 232–235 (2010)

  15. 15

    Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948–951 (2008)

  16. 16

    Jaenisch, R. & Young, R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132, 567–582 (2008)

  17. 17

    De Santa, F. et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 8, e1000384 (2010)

  18. 18

    Kim, T. K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182–187 (2010)

  19. 19

    Talbert, P. B. & Henikoff, S. Histone variants — ancient wrap artists of the epigenome. Nature Rev. Mol. Cell Biol. 11, 264–275 (2010)

  20. 20

    Schadt, E. E. et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 6, e107 (2008)

  21. 21

    Pickrell, J. K. et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768–772 (2010)

  22. 22

    Montgomery, S. B. et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773–777 (2010)

  23. 23

    Veyrieras, J. B. et al. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 4, e1000214 (2008)

  24. 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. 25

    Fujiwara, T. et al. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol. Cell 36, 667–681 (2009)

  26. 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)

  27. 27

    Sabourin, L. A. & Rudnicki, M. A. The molecular regulation of myogenesis. Clin. Genet. 57, 16–25 (2000)

  28. 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)

  29. 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)

  30. 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. 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. 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)

  33. 33

    Wei, C. L. et al. A global map of p53 transcription-factor binding sites in the human genome. Cell 124, 207–219 (2006)

  34. 34

    Hoshino, H. et al. Co-repressor SMRT and class II histone deacetylases promote Bach2 nuclear retention and formation of nuclear foci that are responsible for local transcriptional repression. J. Biochem. 141, 719–727 (2007)

  35. 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)

  36. 36

    He, H. H. et al. Nucleosome dynamics define transcriptional enhancers. Nature Genet. 42, 343–347 (2010)

  37. 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. 38

    Ganesh, S. K. et al. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. Nature Genet. 41, 1191–1198 (2009)

  39. 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. 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)

  41. 41

    Teslovich, T. M. et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466, 707–713 (2010)

  42. 42

    Houlston, R. S. et al. Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nature Genet. 40, 1426–1435 (2008)

  43. 43

    Newton-Cheh, C. et al. Genome-wide association study identifies eight loci associated with blood pressure. Nature Genet. 41, 666–676 (2009)

  44. 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. 45

    Liu, X. et al. Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis. Nature Genet. 42, 658–660 (2010)

  46. 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. 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. 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. 49

    Visel, A., Rubin, E. M. & Pennacchio, L. A. Genomic views of distant-acting enhancers. Nature 461, 199–205 (2009)

  50. 50

    Naumova, N. & Dekker, J. Integrating one-dimensional and three-dimensional maps of genomes. J. Cell Sci. 123, 1979–1988 (2010)

  51. 51

    Ludwig, T. E. et al. Feeder-independent culture of human embryonic stem cells. Nature Methods 3, 637–646 (2006)

  52. 52

    Geiss, G. K. et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nature Biotechnol. 26, 317–325 (2008)

  53. 53

    Reich, M. et al. GenePattern 2.0. Nature Genet. 38, 500–501 (2006)

  54. 54

    Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002)

  55. 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)

  56. 56

    Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005)

  57. 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. 58

    Ashburner, M. et al. Gene Ontology: tool for the unification of biology. Nature Genet. 25, 25–29 (2000)

  59. 59

    Matys, V. et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374–378 (2003)

  60. 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)

  61. 61

    Berger, M. F. et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133, 1266–1276 (2008)

  62. 62

    Badis, G. et al. Diversity and complexity in DNA recognition by transcription factors. Science 324, 1720–1723 (2009)

  63. 63

    Berger, M. F. et al. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature Biotechnol. 24, 1429–1435 (2006)

  64. 64

    Touzet, H. & Varre, J. S. Efficient and accurate P-value computation for Position Weight Matrices. Algorithms Mol. Biol. 2, 15 (2007)

  65. 65

    Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006)

Download references


We thank members of the epigenomics community at the Broad Institute and the Bernstein and Kellis laboratories, and M. Daly, D. Altshuler and E. Lander for discussions and criticisms. We also thank M. Suva, E. Mendenhall and S. Gillespie for assistance with experiments, and L. Goff and A. Chess for critical reading of the manuscript. We acknowledge the Broad Institute Genome Sequencing Platform for their expertise and assistance with data production. This research was supported by the National Human Genome Research Institute under an ENCODE grant (U54 HG004570; B.E.B.), R01 HG004037 (M. Kellis), RC1 HG005334 (M. Kellis), the Howard Hughes Medical Institute (B.E.B.), the National Science Foundation (awards 0644282 (M. Kellis) and 0905968 (J.E.)) and the Sloan Foundation (M. Kellis).

Author information

J.E. conducted chromatin state analysis. J.E. and P.K. conducted regulatory motif analysis. J.E. and L.W. conducted GWAS SNP analysis. T.S.M., N.S. and T.D. implemented the ChIP-seq data processing pipeline. C.B.E., X.Z., L.W., R.I., M.C. and M. Ku developed the experimental pipeline and conducted experiments. M. Kellis designed and directed the computational analysis. B.E.B. designed the experimental approach and oversaw the work. J.E., M. Kellis and B.E.B. wrote the paper.

Correspondence to Manolis Kellis.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-19 with legends and additional references. (PDF 2664 kb)

Supplementary Data 1

This file contains the data for the Experimental Primers and Constructs. (XLS 35 kb)

PowerPoint slides

PowerPoint slide for Fig. 1

PowerPoint slide for Fig. 2

PowerPoint slide for Fig. 3

PowerPoint slide for Fig. 4

PowerPoint slide for Fig. 5

Rights and permissions

Reprints and Permissions

About this article

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.