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.

Transcriptional regulation of the Ikzf1 locus

“…Mapping of histone modification signatures and the preinitiation and elongation forms of RNApII at the Ikzf1 locus in thymocytes has provided further insight into the location of promoter and enhancer elements, residing in the vicinity of conserved lymphoid-specific DHS clusters. 23,24,[32][33][34] The promoter-demarcating H3K4me3 and H3K9Ac were highly enriched over the previously characterized Ikzf1 lympho-myeloid promoter B. On the other hand, a restricted enrichment of H3K4me2, H3K27Ac, and the preinitiation form of RNApII over the intronic Ikzf1 DHS clusters was consistent with previous reports of their marking active and poised enhancers.…”

“…On the other hand, a restricted enrichment of H3K4me2, H3K27Ac, and the preinitiation form of RNApII over the intronic Ikzf1 DHS clusters was consistent with previous reports of their marking active and poised enhancers. 23,24,[32][33][34] Because the ultimate proof of enhancer activity is the ability to stimulate expression from the gene's promoter, the ability of putative enhancers was tested on the Ikzf1 lympho-myeloid promoter in vivo. The Ikzf1 enhancer regions were evaluated for their ability to counteract transcriptionally repressive chromatin, to increase transcriptional rate, and to promote cell type-specific expression of a transgenic reporter during lymphoid and myeloid lineage differentiation.…”

Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells

“…Such a pattern is more consistent with SCC acting as a TF rather than as a repair complex randomly scanning the genome. One alternative explanation we considered was the possibility that RAD23B recruitment at regulatory regions might represent a byproduct of XPC interacting with TFIIH (39), the latter being an intrinsic component of transcription initiation platforms assembled at promoters and tissue-specific enhancers (40). Two lines of evidence suggest that TFIIH is not the driver: (i) truncated versions of XPC lacking putative TFIIH interaction domains (19,37) remain competent to interact with O/S (Fig.…”

Experimental assessment of the contribution of electrodynamic interactions to long-distance recruitment of biomolecular partners: Theoretical basis

“…Indeed, protein-protein and protein-nucleic acid interactions in vivo generally take place within complex structural scaffolds such as the membrane cytoskeleton or the chromatin envelope, which are themselves the subject of highly dynamical regulations (e.g., Refs. [40,41]); and may also possibly interfere with the spatiotemporal control of the given reactions (e.g., Refs. [42,43]).…”