Atlas of nascent RNA transcripts reveals high confidence enhancer associated bidirectionals linked with genes across different tissue types
Gene transcription is controlled and modulated by enhancers and promoters. These regions are abundant in non-coding bidirectional RNA transcripts which have been used as a read-out of enhancer and promoter activity. Using nascent RNA transcription data across hundreds of samples, we identified 500,000 regions of bidirectional transcription and linked the transcripts to gene targets. The identified bidirectional and gene pairs are associated with diseases associated SNPs and these pairs are links in 3D genome space. We present these resources as an SQL database which allows for further investigation and understanding of how gene transcription is regulated. Overall design: WT or p53 -/- MCF10A cells were treated with 10uM nutlin3a and 0.01% DMSO (control) for 3 hours with a total of 2 biological replicates. Nuclei were isolated and PRO-seq libraries were constructed and sequenced.