Enhancers predominantly control transcription initiation [Capture-C]

Gene transcription occurs via a cycle of linked events including initiation, promoter proximal pausing and elongation of RNA polymerase II (Pol 2). 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). When analysed in parallel with nascent RNA-seq, these data show that differential gene expression is achieved predominantly via changes in transcription initiation rather than Pol 2 pausing or elongation. Using genetically engineered mouse models deleted for specific enhancers we show that these elements control gene expression via Pol 2 recruitment and/or initiation rather than via promoter proximal pause release. Using genome-wide analysis we show that enhancers, in general, control gene expression at the stage of Pol 2 recruitment and initiation rather than via pausing. NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments; in this case haemoglobin alpha (hba-a1) haemoglobin beta (Hbb-b1) and mitoferrin (slc25a37), were used as viewpoints. The method was applied to primary mouse fetal liver erythroid cells in which the HS2 and HS3 enhancers of beta globin are homozygously deleted in combination. Wildtype and R1R2 KO have been published and data were deposited under GSE78803.