Abstract
Genome‐wide transcription studies are revealing an increasing number of “dispersed promoters” that, unlike “focused promoters”, lack well‐conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well‐defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters. Here, we have analyzed regions of transcription initiation in the eukaryotic parasite Trypanosoma brucei, in which RNA polymerase II transcription initiation occurs over broad regions without distinct promoter motifs and lacks regulation. Using a combination of site‐specific and genome‐wide assays, we identified GT‐rich promoters that can drive transcription and promote the targeted deposition of the histone variant H2A.Z in a genomic context‐dependent manner. In addition, upon mapping nucleosome occupancy at high resolution, we find nucleosome positioning to correlate with RNA pol II enrichment and gene expression, pointing to a role in RNA maturation. Nucleosome positioning may thus represent a previously unrecognized layer of gene regulation in trypanosomes. Our findings show that even highly dispersed, unregulated promoters contain specific DNA elements that are able to induce transcription and changes in chromatin structure.
Highlights
Transcription initiation involves the assembly of an elaborate complex of transcription factors to target the polymerase to the correct genomic locus
We use the term transcription start regions (TSRs) rather than transcription start site (TSS) and define TSRs as regions enriched in H2A.Z compared to the rest of the genome
In an effort to identify RNA polymerase (RNA pol) II promoter elements, we decided to determine the sites of RNA pol II transcription initiation more precisely following a two-pronged approach
Summary
Transcription initiation involves the assembly of an elaborate complex of transcription factors to target the polymerase to the correct genomic locus. Two key features of this process are a core promoter, which functions as a platform on which the transcription machinery assembles, and a chromatin structure that allows the transcription machinery to access the promoter DNA (Kadonaga, 2012). The core promoter is defined as the minimal DNA sequence necessary and sufficient to direct the accurate initiation of transcription by an RNA polymerase (RNA pol) (Roeder, 1996). Core promoters commonly comprise specific DNA elements that confer distinct properties to the promoter; for example, they serve as binding sites for transcription factors (Roeder, 1996) or are involved in defining a specific chromatin structures that leave the DNA depleted of nucleosomes (Raisner et al, 2005; Yuan et al, 2005; Mavrich et al, 2008a). Some studies report an activating role for H2A.Z on transcription, while others describe a repressive influence (reviewed in Marques et al, 2010)
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