Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [RNAPII_inhibitor CUT&RUN]

The RNA transcribed from enhancer regions, referred to as eRNA, has been suggested to directly activate transcription by helping to recruit transcription factors and co-activators. Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find the AT-hook of SWI/SNF alone binds preferentially RNA and as part of the esBAF complexes likely associates with eRNA that are transcribed from intronic and intergenic regions. SWI/SNF is globally recruited in cis by eRNA to cell-type specific enhancers at two distinct stages in early mammalian development and not at promoters or enhancers that are shared between the two stages. SWI/SNF recruited by eRNA facilitates recruitment and/or activation of MLL3/4, p300/CBP and Mediator co-activators to stage-specific super-enhancers that in the primed embryonic stage activate cell lineage priming related genes. We find a strong connection between ATP-dependent chromatin remodeling and eRNA in cell identity and super-enhancer activation. To understand the importance of RNA polymerase II trasnscripts in AT hook dependent Brg1 localization, we created Brg1 AT hook domain knock-out E14 cell lines. After then, 10µM Triptolide were treated for 2hr and 3µg/mL Actinomycin D was treated for 4hr to inhibit transcription initiation and elongation separately. DMSO was treated as a control. And then, we classified Brg1 peaks via transcription and/or AT hook dependency using Cleavage under targets and release using nuclease (CUT&RUN) sequencing for Brg1/SMARCA4 in mouse embryonic stem cells (E14). RNA polymerase II CUT&RUN samples were used to show the transcriptional defects in inhibitors.