Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

Abstract

Despite the conventional distinction between them, promoters and enhancers share many features in mammals, including divergent transcription and similar modes of transcription factor binding. Here, we examine the architecture of transcription initiation through comprehensive mapping of transcription start sites (TSSs) in human lymphoblastoid B-cell (GM12878) and chronic myelogenous leukemic (K562) tier 1, ENCODE cell lines. Using a nuclear run-on protocol called GRO-cap, which captures TSSs for both stable and unstable transcripts, we conduct detailed comparisons of thousands of promoters and enhancers in human cells. These analyses reveal a common architecture of initiation, including tightly spaced (110 bp) divergent initiation, similar frequencies of core-promoter sequence elements, highly positioned flanking nucleosomes, and two modes of transcription factor binding. Post-initiation transcript stability provides a more fundamental distinction between promoters and enhancers than patterns of histone modifications, transcription factors or co-activators. These results support a unified model of transcription initiation at promoters and enhancers.

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

“…To specifically measure transcription initiating at enhancers (eRNA) we used very deeply sequenced CAGE data, providing quantitative information on TSS usage at base-pair resolution (Shiraki et al 2003;Carninci et al 2006), and PRO-cap data (Mahat et al 2016), measuring 5 ′ ends of short nascent RNA that are still transcriptionally engaged with Pol II, including nascent unstable transcripts. The sensitivity and accuracy of both techniques to detect eRNA has been demonstrated in a number of studies in vertebrates (Andersson et al 2014a;Core et al 2014;Arner et al 2015). We performed strand-specific PRO-cap on tightly staged embryos at two embryonic time windows: 3-4 h after egg laying (AEL), corresponding mainly to blastoderm embryos when the majority of cells is multipotent (∼66 million mapped reads) (Supplemental Table S1), and 6-8 h AEL, mainly stages 10-11, when the major lineages within the mesoderm and neuronal primordia are specified (∼52 million mapped reads) (Supplemental Fig.…”

“…To assess these properties in Drosophila, we first estimated the relative abundance of eRNA using measurements of nascent transcription in both species: The levels of PRO-cap signal in Drosophila embryos (this study) was compared with published GRO-cap (a global run-on sequencing variant) signal in human K562 cells (Core et al 2014) and PROcap signal in Drosophila S2 cells (Kwak et al 2013). To make the analysis comparable between species, we sampled the transcription data so that the median counts at gene promoters (TSS-proximal regions) were similar (Materials and Methods; Supplemental Fig.…”

Promoter architectures and developmental gene regulation

“…To overcome these limitations, novel approaches for detecting nascent transcripts (GRO-seq) have been coupled with techniques for capturing the 5' cap structure, and have been recently used to map TSSs of nascent transcripts at single base-pair resolution [39]. By mapping both stable and unstable RNAs, the GRO-cap approach has revealed the precise architecture of pervasive divergent transcription initiation in human genome, as well as its underlying sequence and chromatin features [39]. which are arranged as a linear array along the DNA polymer creating a "beads on a string" structure.…”

Insights in human epigenomic dynamics through comparative primate analysis

“…These data also support the architectural commonality that is becoming increasingly recognised between promoter and enhancers, with operative interchangeability and role switching between tissues or time-course [55] (see Figure 1). Both functional units share many features, including core promoter sequence elements, similar transcription factor binding and divergent RNA transcription [56]. Chromosome conformation capture data identified interaction between two peaks within DPP10, a gene previously associated with disorders such as autism [57] and bipolar disorder [58].…”