The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures

Abstract

RNA polymerase transcription initiation sites are largely unknown in Caenorhabditis elegans. The initial 59 end of most protein-coding transcripts is removed by trans-splicing, and noncoding initiation sites have not been investigated. We characterized the landscape of RNA Pol II transcription initiation, identifying 73,500 distinct clusters of initiation. Bidirectional transcription is frequent, with a peak of transcriptional pairing at 120 bp. We assign transcription initiation sites to 7691 protein-coding genes and find that they display features typical of eukaryotic promoters. Strikingly, the majority of initiation events occur in regions with enhancer-like chromatin signatures. Based on the overlap of transcription initiation clusters with mapped transcription factor binding sites, we define 2361 transcribed intergenic enhancers. Remarkably, productive transcription elongation across these enhancers is predominantly in the same orientation as that of the nearest downstream gene. Directed elongation from an upstream enhancer toward a downstream gene could potentially deliver RNA polymerase II to a proximal promoter, or alternatively might function directly as a distal promoter. Our results provide a new resource to investigate transcription regulation in metazoans.

DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome

“…Eukaryotic nucleosome organization is most distinct near the 5 ′ ends of genes, where regularly spaced nucleosomes lie downstream from a nucleosome-depleted region (Yuan et al 2005;Lee et al 2007;Mavrich et al 2008b;Lantermann et al 2010;Chang et al 2012;Chen et al 2013b). We find that this pattern is conserved in both Tetrahymena and yeast (Fig.…”

“…The stereotypical nucleosome array that has been previously observed near transcription start sites in aggregate plots remains somewhat of a mystery. This organization has been observed in diverse eukaryotes (Yuan et al 2005;Mavrich et al 2008b;Lantermann et al 2010;Ponts et al 2010;Chen et al 2013b;Zhang et al 2014), suggesting that it is established by a widely conserved mechanism. However, the functional relationship between the stereotypical nucleosome array and gene transcription is unclear, since even highly expressed genes exhibit this nucleosome organization (Shivaswamy et al 2008;Lantermann et al 2010).…”

“…Genome-wide nucleosome maps in major model organisms have revealed strikingly similar nucleosome patterns near gene starts, where a nucleosome-depleted region upstream of the TSS is followed by a stereotypical array of nucleosomes inside the gene (Yuan et al 2005;Lee et al 2007;Mavrich et al 2008b;Lantermann et al 2010;Chang et al 2012;Chen et al 2013b;Zhang et al 2014). Recent studies have used Saccharomyces cerevisiae as a model to understand nucleosome positioning mechanisms underlying the stereotypical nucleosome pattern near eukaryotic TSSs.…”

RNA Polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation

“…146 Because trans-splicing occurs on the majority of genes, the TSS for many Pol II genes cannot be mapped from the 5′ sequence of mature mRNA as is commonly done in other organisms. 147,148 Thus, although the TSS has been mapped for individual genes in C. elegans, 149 genomewide approaches for TSS identification have only recently been performed. 145,147,148,150 These recent results have, for the first time, allowed scientists to analyze the regulation of early steps of Pol II transcription on a global scale.…”

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

“…They are often bidirectionally transcribed (Kim et al 2010;Melgar et al 2011;Hah et al 2013;Kaikkonen et al 2013;Andersson et al 2014a), although some unidirectional transcription has also been reported (Ho et al 2006;Kim et al 2007;De Santa et al 2010;Koch et al 2011). In Caenorhabditis elegans, putative enhancers (intergenic TF-bound regions) have bidirectional eRNA transcription but form longer transcripts in the direction of the closest downstream gene (Chen et al 2013). This resembles some intragenic mammalian enhancers, which also transcribe long noncoding RNA (lncRNA) transcripts in the direction of the gene's transcription (Kowalczyk et al 2012).…”