Etude de la localisation à grande échelle de la machinerie de transcription de classe III, et de sa relation avec le facteur de transcription TFIIS dans les cellules souches embryonnaires de souris

摘要

In eukaryotes, RNA polymerase (RNAP) III transcribes the tRNAs, the 5S ribosomal RNA and a half a dozen known untranslated RNA. Mammalian genome contains several thousand of repeated elements, the Short interspersed repetitive elements (SINE). In vitro, they are transcribed by RNAP III. RNAP III transcription levels determine cell growth and proliferation and, importantly, its deregulation is associated with cancer. Looking at the genome-wide distribution of RNAP III and its transcription factors, TFIIIB and TFIIIC, we develop a highly specific tandem ChIP-sequencing method. We have determined the set of genes that are transcribed by RNAP III in mouse embryonic stem cells. We discovered that not all known class III genes were transcribed in ES cells. We also observed that RNAP III and its transcription factors were present at thirty unannotated sites on the mouse genome, only one of which was conserved in human. Only a couple of hundreds of SINEs out of more than half a million are associated with RNAP III in mouse ES cells. Our study reveals numerous ‘TFIIIC-only’ sites, called ETC for extra-TFIIIC loci in yeast. These sites are correlated with association of CTCF and the cohesin. Cohesin has been shown to occupy sites bound by CTCF and to contribute to DNA loop formation associated with gene repression or activation. This observation suggests that TFIIIC may play a role in chromosome organization in mouse. We also demonstrated that TCEA1, the ubiquitous isoform of TFIIS RNAP II elongation factor, is associated with active class III genes suggesting that TFIIS is a RNAP III transcription factor in mammals. Finally, the distribution of TFIIS on RNAP II-transcribed genes indicated that its recruitment does not control the transition of RNAP II paused at genes 5’ end into elongation.