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Home page > Research Groups > Jean-Christophe ANDRAU - Transcription & Epigenomics in Developing T-Cells

Jean-Christophe ANDRAU - Transcription & Epigenomics in Developing T-Cells

During the last years, the advent of high-throughput sequencing technologies has open wide gates for our understanding of the epigenetic and transcriptional processes guiding differentiation in its normal and pathological states. Our laboratory is interested by the epigenetic and transcriptional events involved in the outcome of T-cell differentiation, using mouse as a model organism. How a stem cell becomes a fully differentiated T-lymphocyte, transiting from the thymus to the periphery and during activation represents a paradigm that can now be envisioned at the epigenetic level and genomic scale. Using ChIPseq and RNAseq, we recently showed that active enhancer elements controlling the most critical stage- and tissue-specific genes, associated to differentiation in thymic CD4+CD8+ (DP) cells are transcribed by RNA polymerase (Pol) II, recruit general transcription factors (GTFs; such as TBP, TFIIB and TFIIH) and can be followed by the co-occurrence of specific epigenetic marks (Koch et al, NSMB 2011; Natoli and Andrau, An. Rev. Genet. 2012). We are now extending these genome-wide analyses to other differentiation stages and wish to understand how the dynamic of regulatory elements usage affects T-cell fate in normal and pathological states, essentially in type 2 diabetes and T-ALL cancer situations (Navarro et al, Nat. Com 2015). The role of noncoding RNAs in mouse and human differentiation is also part of our interest, as we could for example show that enhancers can be transcribed with or without polyadenylation of associated RNAs (Koch et al, NSMB 2011). We therefore developed several RNAseq protocol dedicated to the analysis of specific RNA populations (polyA-, total- and short-RNAseq see Spicuglia et al, Methods 2013).

Another aspect of our research project relies on deciphering the rules governing promoter and enhancer nucleosome positioning and depletion. We previously showed that CpG islands intrinsically deplete nucleosome at promoters, independently of transcriptional activity associated with these promoters (Fenouil et al, Gen. Res. 2012). We are now further investigating the determinants of both positioning and depletion of nucleosomes as well as the influence of the act of transcription, not only at promoters but also at regulatory regions that are associated with Pol II and GTFs.

Finally, in collaboration with group of D. Eick (Helmholtz institute, Munich), we are investigating post-translational modifications of the carboxy-terminal domain of Pol II. We showed that in vivo, Transcription Initiation Platforms (TIPs), hallmarked by Pol II phosphorylated on position 5 of CTD (Ser5P), are enriched at tissue specific promoters and enhancers in developing T-cells (Koch et al, NSMB 2011). We previously showed in human B cells that Threo4P of the CTD is involved in elongation/termination steps of transcription (Hintermair et al, EMBO J. 2012) and more recently that Tyr1P is associated with antisense transcription both at promoters and active enhancers (Descostes et al, Elife 2014). We are pursuing this work at several modifiable residue of the CTD to understand, based on mutant investigation combined to genome-wide analyses, the precise role of these modifications in the transcription cycle.

A- Model and summary of transcription initiation platforms (TIPs) at promoters and enhancers (see Koch et al, NSMB 2011). Both promoters and enhancers recruit Pol II and GTFs and display bidirectional transcription. The epigenetic marks H3K4me1 and H3K4me3 are present at the two types of elements even though the balance is higher for H3K4me1 at enhancer and for H3K4me3 at promoters. Promoters allow Pol II to enter the elongation stage, a property that is not shared with most enhancers.

B- CpG islands (CGIs) containing promoters intrinsically deplete nucleosomes, independently of transcription. Promoters are ranked by growing CpG content (left panel) and their nucleosome depletion trend follows that of the CGIs length (middle panels). This property is conserved in the presence of absence of transcription or Pol II recruitment (ChIPseq Pol II, right panel). See also Fenouil et al, Gen. Res. 2012.

C- Composite average profiling of Pol II and phospho-isoforms of the CTD at mammalian genes. Whereas Ser5P residues essentially accumulate around the TSS, consistent with their role in initiation, Ser2P and Thr4P accumulate at the 3’ end of the genes in agreement with their role in elongation and termination of transcription (Hintermair et al, EMBO J. 2012).

Selected recent publications :

CapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals Vanhille L, Griffon A, Maqbool MA, Zacarías-Cabeza J, Lan. T.M. Dao, Fernandez N, Ballester B, Andrau JC, Spicuglia S. Nature Communications 2015 in press

Transcription dependent generation of a specialized chromatin structure at the TCR locus. Zacarías-Cabeza J, Belhocine M, Vanhille L, Cauchy P, Koch F, Pekowska A, Fenouil R, Bergon A, Gut M, Gut I, Eick D, Imbert J, Ferrier P, Andrau JC, Spicuglia S. Journal of Immunology 2015 in press.

Site- and allele-specific de-silencing of Polycomb repressive activity by insertional oncogenesis: a new recurrent mechanism of TAL1 activation in T-ALL. Navarro JM, Touzart A, Pradel LC, Loosveld M, Koubi M, Fenouil R, Le Noir S, Maqbool MA, Morgado E, Gregoire C, Jaeger S, Mamessier E, Pignon C, Hacien-Bey-Abina S, Malissen B, Gut M, Gut I, Hevré D, Macintyre EA, Howe SJ, Gaspar HB, Trasher AJ, Ifrah N, Payet-Bornet D, Duprez E, Andrau JC, Asnafi V, Nadel B. Nature Communications 2015 Jan 23;6:6094. doi: 10.1038/ncomms7094.

Tyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells. Descostes N, Heidemann M, Spinelli L, Schüller R, Maqbool MA, Fenouil R, Koch F, Innocenti C, Gut M, Gut I, Eick D, Andrau JC. Elife 2014 May 9:e02105

Divergent transcription is associated with promoters of transcriptional regulators. Lepoivre C, Belhocine M, Bergon A, Griffon A, Yammine M, Vanhille L, Zacarias-Cabeza J, Garibal MA, Koch F, Maqbool MA, Fenouil R, Loriod B, Holota H, Gut M, Gut I, Imbert J, Andrau JC, Puthier D, Spicuglia S. BMC Genomics. 2013 Dec 23;14:914

An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function. Spicuglia S, Maqbool MA, Puthier D, Andrau JC. Methods 2013 Sep 1;63(1):3-17

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Fenouil R, Cauchy P, Koch F, Descostes N, Cabeza JZ, Innocenti C, Ferrier P, Spicuglia S, Gut M, Gut I, Andrau JC. Genome Res 2012 22, 2399-2408.

Noncoding transcription at enhancers: general principles and functional models. Natoli G, and Andrau JC. Annu Rev Genet 2012 46, 1-19.

Argonaute proteins couple chromatin silencing to alternative splicing. Ameyar-Zazoua M, Rachez C, Souidi M, Robin P, Fritsch L, Young R, Morozova N, Fenouil R, Descostes N, Andrau JC, Mathieu J, Hamiche A, Ait-Si-Ali S, Muchardt C, Batsché E, Harrel-Bellan A. Nat Struct Mol Biol 2012 19, 998-1004.

Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation. Hintermair C, Heidemann M, Koch F, Descostes N, Gut M, Gut I, Fenouil R, Ferrier P, Flatley A, Kremmer E, Chapman RD, Andrau JC, Eick D. EMBO J. 2012 31, 2784-2797.

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. de Almeida SF, Grosso AR, Koch F, Fenouil R, Carvalho S, Andrade J, Levezinho H, Gut M, Eick D, Gut I, Andrau JC, Ferrier P, Carmo-Fonseca M. Nat Struct Mol Biol. 2011 26;18(9):977-83.

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC. Nat Struct Mol Biol. 2011 17;18(8):956-63.

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