Enhancers predominantly regulate gene expression in vivo via transcription initiation

Abstract

Gene transcription occurs via a cycle of linked events including initiation, promoter proximal pausing and elongation of RNA polymerase II (Pol II). A key question is how do transcriptional enhancers influence these events to control gene expression? Here we have used a new approach to quantify transcriptional initiation and pausing in vivo, while simultaneously identifying transcription start sites (TSSs) and pause-sites (TPSs) from single RNA molecules. When analyzed in parallel with nascent RNA-seq, these data show that differential gene expression is achieved predominantly via changes in transcription initiation rather than Pol II pausing. Using genetically engineered mouse models deleted for specific enhancers we show that these elements control gene expression via Pol II recruitment and/or initiation rather than via promoter proximal pause release. Together, our data show that enhancers, in general, control gene expression predominantly by Pol II recruitment and initiation rather than via pausing.

The regulatory landscapes of developmental genes

“…The assembly of these components is initiated by heritable and stable properties of the DNA sequence itself, generally referred to as regulatory elements. These are defined as cis -acting, generally non-coding DNA elements approximately 1 kb in size that can be found at various distances from their target promoters, and possibly – although not always – act through a proximity-dependent effect that modulates the probability of transcriptional initiation ( Alexander et al, 2019 ; Bartman et al, 2016 ; Benabdallah et al, 2019 ; Larke et al, 2019 preprint). Regulatory sequences acting at very long range are primarily found in vertebrate species and their discovery was associated with genes displaying complex developmental expression ( Grosveld et al, 1987 ; Lettice et al, 2003 ; Spitz et al, 2003 ).…”

The mouse alpha-globin cluster: a paradigm for studying genome regulation and organization

“…Previous work in cell lines [ 30 ] and more recently in primary erythroblasts [ 31 • ] has shown that the primary function of the enhancers is to increase the recruitment of the pre-initiation complex to the promoters of the α-globin genes. Whether the changes in chromatin structure actively facilitate this process or merely reflect the molecular interactions between enhancers and promoters remains an important open question.…”