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Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

Nature Structural & Molecular Biology volume 18, pages 956–963 (2011)Cite this article

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Abstract

Recent work has shown that RNA polymerase (Pol) II can be recruited to and transcribe distal regulatory regions. Here we analyzed transcription initiation and elongation through genome-wide localization of Pol II, general transcription factors (GTFs) and active chromatin in developing T cells. We show that Pol II and GTFs are recruited to known T cell–specific enhancers. We extend this observation to many new putative enhancers, a majority of which can be transcribed with or without polyadenylation. Importantly, we also identify genomic features called transcriptional initiation platforms (TIPs) that are characterized by large areas of Pol II and GTF recruitment at promoters, intergenic and intragenic regions. TIPs show variable widths (0.4–10 kb) and correlate with high CpG content and increased tissue specificity at promoters. Finally, we also report differential recruitment of TFIID and other GTFs at promoters and enhancers. Overall, we propose that TIPs represent important new regulatory hallmarks of the genome.

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Figure 1: Pol II and GTF recruitment to T-cell stage-specific enhancers of active loci or genes poised for activation.
Figure 2: Epigenetic or transcriptional features and tissue-specific expression of putative enhancers recruiting Ser5P and TBP.
Figure 3: TBP and Ser5P enhancers are transcribed with or without polyadenylation.
Figure 4: Poly(A) and non-poly(A) IGR subpopulations show distinct chromatin signatures between each other and genes.
Figure 5: Pol II and GTFs transcription initiation platforms.
Figure 6: TIPs correlate with CpG content and tissue-specific expression at promoters.
Figure 7: Average profiles of TIPs and model summarizing their features at distinct genomic locations.

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References

  1. Sikorski, T.W. & Buratowski, S. The basal initiation machinery: beyond the general transcription factors. Curr. Opin. Cell Biol. 21, 344–351 (2009).

    Article  CAS  Google Scholar 

  2. Buratowski, S. Progression through the RNA polymerase II CTD cycle. Mol. Cell 36, 541–546 (2009).

    Article  CAS  Google Scholar 

  3. Carninci, P. et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38, 626–635 (2006).

    Article  CAS  Google Scholar 

  4. Koch, F., Jourquin, F., Ferrier, P. & Andrau, J.C. Genome-wide RNA polymerase II: not genes only!. Trends Biochem. Sci. 33, 265–273 (2008).

    Article  CAS  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  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40, 897–903 (2008).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  10. Xi, H. et al. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 3, e136 (2007).

    Article  Google Scholar 

  11. Higgs, D.R., Vernimmen, D. & Wood, B. Long-range regulation of alpha-globin gene expression. Adv. Genet. 61, 143–173 (2008).

    Article  CAS  Google Scholar 

  12. Fromm, G. & Bulger, M. A spectrum of gene regulatory phenomena at mammalian beta-globin gene loci. Biochem. Cell Biol. 87, 781–790 (2009).

    Article  CAS  Google Scholar 

  13. Szutorisz, H., Dillon, N. & Tora, L. The role of enhancers as centres for general transcription factor recruitment. Trends Biochem. Sci. 30, 593–599 (2005).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  16. Giresi, P.G., Kim, J., McDaniell, R.M., Iyer, V.R. & Lieb, J.D. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 17, 877–885 (2007).

    Article  CAS  Google Scholar 

  17. Bosselut, R. CD4/CD8-lineage differentiation in the thymus: from nuclear effectors to membrane signals. Nat. Rev. Immunol. 4, 529–540 (2004).

    Article  CAS  Google Scholar 

  18. Anderson, M.K. At the crossroads: diverse roles of early thymocyte transcriptional regulators. Immunol. Rev. 209, 191–211 (2006).

    Article  CAS  Google Scholar 

  19. Sawada, S. & Littman, D.R. Identification and characterization of a T-cell-specific enhancer adjacent to the murine CD4 gene. Mol. Cell Biol. 11, 5506–5515 (1991).

    Article  CAS  Google Scholar 

  20. Cherrier, M., D'Andon, M.F., Rougeon, F. & Doyen, N. Identification of a new cis-regulatory element of the terminal deoxynucleotidyl transferase gene in the 5′ region of the murine locus. Mol. Immunol. 45, 1009–1017 (2008).

    Article  CAS  Google Scholar 

  21. Kaufmann, C. et al. A complex network of regulatory elements in Ikaros and their activity during hemo-lymphopoiesis. EMBO J. 22, 2211–2223 (2003).

    Article  CAS  Google Scholar 

  22. Georgopoulos, K., van den Elsen, P., Bier, E., Maxam, A. & Terhorst, C.A. T cell-specific enhancer is located in a DNase I-hypersensitive area at the 3′ end of the CD3-delta gene. EMBO J. 7, 2401–2407 (1988).

    Article  CAS  Google Scholar 

  23. Yannoutsos, N. et al. A cis element in the recombination activating gene locus regulates gene expression by counteracting a distant silencer. Nat. Immunol. 5, 443–450 (2004).

    Article  CAS  Google Scholar 

  24. Hostert, A. et al. Hierarchical interactions of control elements determine CD8alpha gene expression in subsets of thymocytes and peripheral T cells. Immunity 9, 497–508 (1998).

    Article  CAS  Google Scholar 

  25. Ellmeier, W., Sunshine, M.J., Losos, K. & Littman, D.R. Multiple developmental stage-specific enhancers regulate CD8 expression in developing thymocytes and in thymus-independent T cells. Immunity 9, 485–496 (1998).

    Article  CAS  Google Scholar 

  26. Schmidl, C. et al. Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. Genome Res. 19, 1165–1174 (2009).

    Article  CAS  Google Scholar 

  27. Schorle, H., Holtschke, T., Hunig, T., Schimpl, A. & Horak, I. Development and function of T cells in mice rendered interleukin-2 deficient by gene targeting. Nature 352, 621–624 (1991).

    Article  CAS  Google Scholar 

  28. Shi, W. & Zhou, W. Frequency distribution of TATA Box and extension sequences on human promoters. BMC Bioinformatics 7 (suppl. 4), S2 (2006).

    Article  Google Scholar 

  29. Eyquem, S., Chemin, K., Fasseu, M. & Bories, J.C. The Ets-1 transcription factor is required for complete pre-T cell receptor function and allelic exclusion at the T cell receptor beta locus. Proc. Natl. Acad. Sci. USA 101, 15712–15717 (2004).

    Article  CAS  Google Scholar 

  30. Xie, X. et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434, 338–345 (2005).

    Article  CAS  Google Scholar 

  31. Saxonov, S., Berg, P. & Brutlag, D.L. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl. Acad. Sci. USA 103, 1412–1417 (2006).

    Article  CAS  Google Scholar 

  32. Blackledge, N.P. et al. CpG islands recruit a histone H3 lysine 36 demethylase. Mol. Cell 38, 179–190 (2010).

    Article  CAS  Google Scholar 

  33. Spicuglia, S. et al. Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes. Mol. Cell 10, 1479–1487 (2002).

    Article  CAS  Google Scholar 

  34. Ho, Y., Elefant, F., Cooke, N. & Liebhaber, S. A defined locus control region determinant links chromatin domain acetylation with long-range gene activation. Mol. Cell 9, 291–302 (2002).

    Article  CAS  Google Scholar 

  35. Andrau, J.C. et al. Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA. Mol. Cell 22, 179–192 (2006).

    Article  CAS  Google Scholar 

  36. Radonjic, M. et al. Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol. Cell 18, 171–183 (2005).

    Article  CAS  Google Scholar 

  37. Core, L.J., Waterfall, J.J. & Lis, J.T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845–1848 (2008).

    Article  CAS  Google Scholar 

  38. Seila, A.C. et al. Divergent transcription from active promoters. Science 322, 1849–1851 (2008).

    Article  CAS  Google Scholar 

  39. Ørom, U.A. et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46–58 (2010).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  41. Nicol, J.W., Helt, G.A., Blanchard, S.G. Jr., Raja, A. & Loraine, A.E. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25, 2730–2731 (2009).

    Article  CAS  Google Scholar 

  42. Benoukraf, T. et al. CoCAS: a ChIP-on-chip analysis suite. Bioinformatics 25, 954–955 (2009).

    Article  CAS  Google Scholar 

  43. Wu, C . et al. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol. 10, R130 (2009).

    Article  Google Scholar 

  44. Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36 (1994).

    CAS  PubMed  Google Scholar 

  45. 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).

    Article  CAS  Google Scholar 

  46. Thomas-Chollier, M. et al. RSAT: regulatory sequence analysis tools. Nucleic Acids Res. 36, W119–W127 (2008).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Work in the P.F. laboratory is supported by institutional grants from Institut National de la Santé et de la Recherche Médicale and the Centre National de la Recherche Scientifique (CNRS), and by specific grants from the Fondation Princesse Grace de Monaco, the Agence Nationale de la Recherche (ANR), the Institut National du Cancer (INCa) and the Commission of the European Communities. F.K. was supported by grants from Chromatin Plasticity, Marie Curie Research Training Network and Association pour la Recherche sur le Cancer, R.F. by Genopole and CNRS, and P.C. by grants from INCa and Fondation pour la Recherche Médicale. The work was also supported by a Regulome grant from the ANR. D.E. was supported by Deutsche Forschungsgemeinschaft, Transregio-5. We are grateful to B. Escaliere for useful advice on the statistical analyses, to J.J. Waterfall and J.L. Core from the Lis lab (Cornell University, Ithaca, USA) for help in the generation of the mappability track, to G. Natoli (European Institute of Oncology) for the gift of plasmids used in preliminary experiments for reporter assays, to E. Soucie and V. Cauchy for critical reading of the manuscript, to J. Blanc for technical assistance, to Y. Duffourd from the Centre National de Génotypage-Commissariat à l'Energie Atomique lab for sequencing quality controls and to members of the P.F. lab for help and advice. We dedicate this work to the memory of distinguished colleague Vanessa Ranc-Rongere, who left us too early.

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Author notes

  1. Frederic Koch, Romain Fenouil and Marta Gut: These authors contributed equally to this work.

Authors and Affiliations

  1. Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, Campus de Luminy, Marseille, France

    Frederic Koch, Romain Fenouil, Pierre Cauchy, Joaquin Zacarias-Cabeza, Salvatore Spicuglia, Albane Lamy de la Chapelle, Pierre Ferrier & Jean-Christophe Andrau

  2. Centre National de la Recherche Scientifique, UMR6102, Marseille, France

    Frederic Koch, Romain Fenouil, Pierre Cauchy, Joaquin Zacarias-Cabeza, Salvatore Spicuglia, Albane Lamy de la Chapelle, Pierre Ferrier & Jean-Christophe Andrau

  3. Institut National de la Santé et de la Recherche Médicale, Marseille, U631, France

    Frederic Koch, Romain Fenouil, Pierre Cauchy, Joaquin Zacarias-Cabeza, Salvatore Spicuglia, Albane Lamy de la Chapelle, Pierre Ferrier & Jean-Christophe Andrau

  4. Centre National de Génotypage, Commissariat à l'Energie Atomique, Evry, France

    Marta Gut & Ivo Gut

  5. Fondation Jean Dausset—Centre d'Etude du Polymorphisme Humain, Paris, France

    Marta Gut

  6. Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac, Barcelona, Spain.,

    Marta Gut & Ivo Gut

  7. Techniques Avancées pour le Génome et la Clinique, Marseille, France

    Pierre Cauchy

  8. Institute of Molecular Tumor Biology, Medical Faculty of the Westfälische Wilhelms-Universität, Münster, Germany

    Thomas K Albert

  9. Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany

    Martin Heidemann, Corinna Hintermair & Dirk Eick

Authors
  1. Frederic Koch
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Contributions

J.-C.A., F.K., T.K.A., P.F. and I.G. conceived the framework of the study. J.-C.A. and F.K. designed the experiments. R.F., P.C. and F.K. carried out the bioinformatic analyses and data treatment. D.E., C.H. and M.H. produced and provided the Ser2P and Ser5P antibodies as well as other antibodies that were not presented in this study. All ChIP-seq and RNA-seq materials were prepared by F.K. with the exception of ETS1 ChIP-seq, which was prepared by P.C., M.G. and I.G. conducted all ChIP-seq and RNA sequencing experiments. J.Z.-C. and S.S. did the FAIRE experiment. F.K. did the cloning and luciferase experiments and A.L.d.l.C. participated and provided technical assistance. J.-C.A. wrote the manuscript, and F.K., R.F. and P.C. participated in its preparation. All authors reviewed the manuscript.

Corresponding authors

Correspondence to Ivo Gut, Pierre Ferrier or Jean-Christophe Andrau.

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The authors declare no competing financial interests.

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Supplementary Figures 1–12, Supplementary Tables 1 and 2, and Supplementary Methods (PDF 10137 kb)

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Koch, F., Fenouil, R., Gut, M. et al. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol 18, 956–963 (2011). https://doi.org/10.1038/nsmb.2085

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