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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Sikorski, T.W. & Buratowski, S. The basal initiation machinery: beyond the general transcription factors. Curr. Opin. Cell Biol. 21, 344–351 (2009).
Buratowski, S. Progression through the RNA polymerase II CTD cycle. Mol. Cell 36, 541–546 (2009).
Carninci, P. et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38, 626–635 (2006).
Koch, F., Jourquin, F., Ferrier, P. & Andrau, J.C. Genome-wide RNA polymerase II: not genes only!. Trends Biochem. Sci. 33, 265–273 (2008).
Heintzman, N.D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).
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).
Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40, 897–903 (2008).
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854–858 (2009).
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).
Higgs, D.R., Vernimmen, D. & Wood, B. Long-range regulation of alpha-globin gene expression. Adv. Genet. 61, 143–173 (2008).
Fromm, G. & Bulger, M. A spectrum of gene regulatory phenomena at mammalian beta-globin gene loci. Biochem. Cell Biol. 87, 781–790 (2009).
Szutorisz, H., Dillon, N. & Tora, L. The role of enhancers as centres for general transcription factor recruitment. Trends Biochem. Sci. 30, 593–599 (2005).
De Santa, F. et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 8, e1000384 (2010).
Kim, T.K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182–187 (2010).
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).
Bosselut, R. CD4/CD8-lineage differentiation in the thymus: from nuclear effectors to membrane signals. Nat. Rev. Immunol. 4, 529–540 (2004).
Anderson, M.K. At the crossroads: diverse roles of early thymocyte transcriptional regulators. Immunol. Rev. 209, 191–211 (2006).
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).
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).
Kaufmann, C. et al. A complex network of regulatory elements in Ikaros and their activity during hemo-lymphopoiesis. EMBO J. 22, 2211–2223 (2003).
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).
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).
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).
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).
Schmidl, C. et al. Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. Genome Res. 19, 1165–1174 (2009).
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).
Shi, W. & Zhou, W. Frequency distribution of TATA Box and extension sequences on human promoters. BMC Bioinformatics 7 (suppl. 4), S2 (2006).
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).
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).
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).
Blackledge, N.P. et al. CpG islands recruit a histone H3 lysine 36 demethylase. Mol. Cell 38, 179–190 (2010).
Spicuglia, S. et al. Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes. Mol. Cell 10, 1479–1487 (2002).
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).
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).
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).
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).
Seila, A.C. et al. Divergent transcription from active promoters. Science 322, 1849–1851 (2008).
Ørom, U.A. et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46–58 (2010).
Boyer, L.A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005).
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).
Benoukraf, T. et al. CoCAS: a ChIP-on-chip analysis suite. Bioinformatics 25, 954–955 (2009).
Wu, C . et al. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol. 10, R130 (2009).
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).
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).
Thomas-Chollier, M. et al. RSAT: regulatory sequence analysis tools. Nucleic Acids Res. 36, W119–W127 (2008).
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.
The authors declare no competing financial interests.
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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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