Widespread transcriptional pausing and elongation control at enhancers

Regulation by gene-distal enhancers is critical for cell-type and condition-specific patterns of gene expression. Thus, to understand the fundamental basis of gene activity in a given cell type or tissue, we must be able to identify the precise locations of enhancers, and to functionally characterize their behaviors. Herein, we demonstrate that transcription is nearly universal feature of enhancers in Drosophila and mammalian cells, and that nascent RNA-sequencing strategies are optimal for identification of both enhancers and super-enhancers. We dissect the mechanisms governing enhancer transcription and discover remarkable similarities with transcription at protein-coding genes. We show that RNA polymerase II (RNAPII) undergoes regulated pausing and release at enhancers. However, as compared to mRNA genes, RNAPII at enhancers is less stable and more prone to early termination. Further, we find that the level of histone H3 Lysine 4 (H3K4) methylation at enhancers corresponds to transcriptional activity, such that highly-active enhancers display H3K4 tri-methylation rather than H3K4 mono-methylation considered a hallmark of enhancers. Finally, our work provides insights into the unique characteristics of super-enhancers, which stimulate high-level gene expression through rapid pause release; interestingly, this property renders associated genes resistant to loss of factors that stabilize paused RNAPII. 4sU experiments: 5 biological replicates were generated for Control (B-galactosidade treated) and Spt5-depletion (treated with double stranded RNA for Spt5) in S2 cells. 2 biological replicates were generated for Control and NELF-KO (4OHT treated) mouse embryonic stem cells. Start-seq: 2 biological replicates were generated for Control (B-galactosidase treated) and Spt5-depleted (treated with double stranded RNA targeting Spt5) S2 cells. 4 additional replicates of untreated samples were generated. ChIP-seq: 2 biological replicates using untreated cells were generated for all ChIP-seq datasets, with the exception of Pol II ChIP-seq for Control (B-galactosidade treated) and Spt5-dep. (Spt5 treated) S2 cells. Please note that [1] the 'processed_data_files.tar.gz' contains the processed data files for GSM2259961-GSM2259991; [2] the other Series supplementary files are associated with GSM2866861-GSM2866870; [3] the associated files are indicated in the corresponding sample description field.