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

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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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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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.

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

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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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