In our latest pre-print a talented PhD student (Martin Larke) developed a new method, scaRNA-seq, to examine the role of enhancers in regulating transcription initation and pausing.
biorxiv.org/content/10.110…
biorxiv.org/content/10.110…
scaRNAseq (Think Simba's uncle) enriches for single short (<300nt) capped RNA molecules. Using it you can simultaneously identify transcription start and pause sites. 
scaRNAseq gives base pair resolution mapping of transcripts. Revealing focused initiation (TSS ±5bp), pausing (+46bp) and termination coincident with the +1 nucleosome.
Using erythropoiesis as a model, we found that changes in expression level throughout differentiation were associated with changes in initiation rather than pausing.
Using genetically engineered mouse models lacking the major transcriptional enhancers in the locus conrol regions of the alpha and beta globin genes, we show enhancers regulate transcriptional initiation and/or recruitment of Pol2 but not pausing.
We conclude that, in vivo, enhancers predominantly control the transcription cycle via initiation, and that pausing occurs as a result of the kinetic bottleneck imposed by the +1 nucleosome.
@threadreaderapp unroll
