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


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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

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.

Accession codes


Gene Expression Omnibus


  1. 1

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

    CAS  Article  Google Scholar 

  2. 2

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

    CAS  Article  Google Scholar 

  3. 3

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

    CAS  Article  Google Scholar 

  4. 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).

    CAS  Article  Google Scholar 

  5. 5

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

    CAS  Article  Google Scholar 

  6. 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).

    CAS  Article  Google Scholar 

  7. 7

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

    CAS  Article  Google Scholar 

  8. 8

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

    CAS  Article  Google Scholar 

  9. 9

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

    CAS  Article  Google Scholar 

  10. 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. 11

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

    CAS  Article  Google Scholar 

  12. 12

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

    CAS  Article  Google Scholar 

  13. 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).

    CAS  Article  Google Scholar 

  14. 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. 15

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

    CAS  Article  Google Scholar 

  16. 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).

    CAS  Article  Google Scholar 

  17. 17

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

    CAS  Article  Google Scholar 

  18. 18

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

    CAS  Article  Google Scholar 

  19. 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).

    CAS  Article  Google Scholar 

  20. 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).

    CAS  Article  Google Scholar 

  21. 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).

    CAS  Article  Google Scholar 

  22. 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).

    CAS  Article  Google Scholar 

  23. 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).

    CAS  Article  Google Scholar 

  24. 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).

    CAS  Article  Google Scholar 

  25. 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).

    CAS  Article  Google Scholar 

  26. 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).

    CAS  Article  Google Scholar 

  27. 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).

    CAS  Article  Google Scholar 

  28. 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. 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).

    CAS  Article  Google Scholar 

  30. 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).

    CAS  Article  Google Scholar 

  31. 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).

    CAS  Article  Google Scholar 

  32. 32

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

    CAS  Article  Google Scholar 

  33. 33

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

    CAS  Article  Google Scholar 

  34. 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).

    CAS  Article  Google Scholar 

  35. 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).

    CAS  Article  Google Scholar 

  36. 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).

    CAS  Article  Google Scholar 

  37. 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).

    CAS  Article  Google Scholar 

  38. 38

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

    CAS  Article  Google Scholar 

  39. 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. 40

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

    CAS  Article  Google Scholar 

  41. 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).

    CAS  Article  Google Scholar 

  42. 42

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

    CAS  Article  Google Scholar 

  43. 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. 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. 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).

    CAS  Article  Google Scholar 

  46. 46

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

    CAS  Article  Google Scholar 

Download references


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.

Author information




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 or Pierre Ferrier or Jean-Christophe Andrau.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

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

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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).

Download citation

Further reading