[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

A unique chromatin signature uncovers early developmental enhancers in humans

Nature volume 470, pages 279–283 (2011)Cite this article

Subjects

Abstract

Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment1,2. However, identification of genomic sequences that control human embryonic development represents a formidable challenge3. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term ‘poised enhancers’, are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Unique chromatin signatures distinguish two classes of regulatory elements in hESCs.
Figure 2: Functional and molecular characterization of class I and II elements.
Figure 3: A subset of class II elements acquires active enhancer chromatin signature upon neuroectodermal differentiation.
Figure 4: Class II elements have developmental enhancer activity in vivo.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

All sequencing data have been deposited in Gene Expression Omnibus (GEO) data repository under accession number GSE24447.

References

  1. Bulger, M. & Groudine, M. Enhancers: the abundance and function of regulatory sequences beyond promoters. Dev. Biol. 339, 250–257 (2010)

    Article  CAS  PubMed  Google Scholar 

  2. Hallikas, O. et al. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124, 47–59 (2006)

    Article  CAS  PubMed  Google Scholar 

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

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  4. Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854–858 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  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)

    Article  CAS  PubMed  Google Scholar 

  7. Chan, K. K. et al. KLF4 and PBX1 directly regulate NANOG expression in human embryonic stem cells. Stem Cells 27, 2114–2125 (2009)

    Article  CAS  PubMed  Google Scholar 

  8. Yeom, Y. I. et al. Germline regulatory element of Oct-4 specific for the totipotent cycle of embryonal cells. Development 122, 881–894 (1996)

    CAS  PubMed  Google Scholar 

  9. Kerppola, T. K. Polycomb group complexes–many combinations, many functions. Trends Cell Biol. 19, 692–704 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Cockerill, P. N. et al. Human granulocyte-macrophage colony-stimulating factor enhancer function is associated with cooperative interactions between AP-1 and NFATp/c. Mol. Cell. Biol. 15, 2071–2079 (1995)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Nakabayashi, H. et al. Functional mapping of tissue-specific elements of the human α-fetoprotein gene enhancer. Biochem. Biophys. Res. Commun. 318, 773–785 (2004)

    Article  CAS  PubMed  Google Scholar 

  12. Itani, H. A., Liu, X., Pratt, J. H. & Sigmund, C. D. Functional characterization of polymorphisms in the kidney enhancer of the human renin gene. Endocrinology 148, 1424–1430 (2007)

    Article  CAS  PubMed  Google Scholar 

  13. Segawa, K. et al. Identification of a novel distal enhancer in human adiponectin gene. J. Endocrinol. 200, 107–116 (2009)

    Article  CAS  PubMed  Google Scholar 

  14. Mito, Y., Henikoff, J. G. & Henikoff, S. Histone replacement marks the boundaries of cis-regulatory domains. Science 315, 1408–1411 (2007)

    Article  ADS  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  16. 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)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Harris, R. A. et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnol. 28, 1097–1105 (2010)

    Article  CAS  Google Scholar 

  18. McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnol. 28, 495–501 (2010)

    Article  CAS  Google Scholar 

  19. Bajpai, R. et al. Molecular stages of rapid and uniform neuralization of human embryonic stem cells. Cell Death Differ. 16, 807–825 (2009)

    Article  CAS  PubMed  Google Scholar 

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

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  21. Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L. A. VISTA Enhancer Browser–a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88–D92 (2007)

    Article  CAS  PubMed  Google Scholar 

  22. Fisher, S. et al. Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish. Nature Protocols 1, 1297–1305 (2006)

    Article  CAS  PubMed  Google Scholar 

  23. Navratilova, P. et al. Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev. Biol. 327, 526–540 (2009)

    Article  CAS  PubMed  Google Scholar 

  24. Sprague, J. et al. The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res. 34, D581–D585 (2006)

    Article  CAS  PubMed  Google Scholar 

  25. Hancock, S. N., Agulnik, S. I., Silver, L. M. & Papaioannou, V. E. Mapping and expression analysis of the mouse ortholog of Xenopus Eomesodermin . Mech. Dev. 81, 205–208 (1999)

    Article  CAS  PubMed  Google Scholar 

  26. Ryan, K., Garrett, N., Mitchell, A. & Gurdon, J. B. Eomesodermin, a key early gene in Xenopus mesoderm differentiation. Cell 87, 989–1000 (1996)

    Article  CAS  PubMed  Google Scholar 

  27. Danielian, P. S. & McMahon, A. P. Engrailed-1 as a target of the Wnt-1 signalling pathway in vertebrate midbrain development. Nature 383, 332–334 (1996)

    Article  ADS  CAS  PubMed  Google Scholar 

  28. Marin, O., Baker, J., Puelles, L. & Rubenstein, J. L. Patterning of the basal telencephalon and hypothalamus is essential for guidance of cortical projections. Development 129, 761–773 (2002)

    CAS  PubMed  Google Scholar 

  29. Robb, L. et al. Cloning, expression analysis, and chromosomal localization of murine and human homologues of a Xenopus mix gene. Dev. Dyn. 219, 497–504 (2000)

    Article  CAS  PubMed  Google Scholar 

  30. Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods 5, 829–834 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Furlan-Magaril, M., Rincon-Arano, H. & Recillas-Targa, F. Sequential chromatin immunoprecipitation protocol: ChIP-reChIP. Methods Mol. Biol. 543, 253–266 (2009)

    Article  CAS  PubMed  Google Scholar 

  33. Ho, L. et al. An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc. Natl Acad. Sci. USA 106, 5187–5191 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  34. Ieda, M. et al. Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. Cell 142, 375–386 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Peng, J. C. et al. Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell 139, 1290–1302 (2009)

    Article  PubMed  PubMed Central  Google Scholar 

  36. 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)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Rahl, P. B. et al. c-Myc regulates transcriptional pause release. Cell 141, 432–445 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Hargreaves, D. C., Horng, T. & Medzhitov, R. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 138, 129–145 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Blechinger, S. R. et al. The heat-inducible zebrafish hsp70 gene is expressed during normal lens development under non-stress conditions. Mech. Dev. 112, 213–215 (2002)

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank Wysocka laboratory members for ideas and manuscript comments; I. A. Shestopalov and J. K. Chen for sharing zebrafish resources, equipment and knowledge; T. Howes and D. M. Kingsley for the pT2HE vector; Z. Weng and A. Sidow for Illumina sequencing; and A. Valouev for discussion on ChIP-seq data analysis. This work was supported by WM Keck Foundation Distinguished Young Scholar in Biomedical Research Award and CIRM RN1 00579-1 grant to J.W. A.R.-I. was supported by an EMBO long-term fellowship.

Author information

Authors and Affiliations

  1. Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, 94305, California, USA

    Alvaro Rada-Iglesias, Ruchi Bajpai, Tomek Swigut, Samantha A. Brugmann, Ryan A. Flynn & Joanna Wysocka

  2. Department of Developmental Biology, Stanford University School of Medicine, Stanford, 94305, California, USA

    Joanna Wysocka

Authors
  1. Alvaro Rada-Iglesias
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ruchi Bajpai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tomek Swigut
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Samantha A. Brugmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ryan A. Flynn
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Joanna Wysocka
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

A.R.-I. conceived the project, performed and interpreted most experiments, including all genomic data analyses. R.B. established hESC culture and differentiation and performed most zebrafish imaging. T.S. generated enhancer reporter constructs, and together with S.A.B. and A.R-I. participated in the in vivo enhancer screening. R.A.F. performed the RT-qPCR analysis of enhancer RNAs. J.W. contributed ideas and interpreted results. A.R-I. and J.W. wrote the manuscript with input from all authors.

Corresponding author

Correspondence to Joanna Wysocka.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-22 with legends and Supplementary Tables 1-4. (PDF 6621 kb)

Supplementary Data 1

This file contains genomic coordinates for all Class I, Class II and class II→I elements identified in this work. (XLS 472 kb)

Supplementary Data 2

This file contains the complete GREAT analysis list of overrepresented categories and statistical tests for Class I elements. (XLS 55 kb)

Supplementary Data 3

This file contains the complete GREAT analysis list of overrepresented categories and statistical tests for Class II elements. (XLS 61 kb)

Supplementary Data 4

This file contains the Complete GREAT analysis list of overrepresented categories and statistical tests for class II→I elements. (XLS 55 kb)

Supplementary Data 5

This file contains a list of primers used for ChIP-qPCR and RT-qPCR analysis. (XLS 57 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rada-Iglesias, A., Bajpai, R., Swigut, T. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2011). https://doi.org/10.1038/nature09692

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature09692

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing