Discovery of active enhancers through bidirectional expression of short transcripts

In this study, we developed an in silico approach to model the previously reported phenomenon of transcriptional pausing, accompanied by divergent transcription, at active promoters. We then used this model for large-scale prediction of non-promoter-associated bidirectional expression of short transcripts. Our predictions were significantly enriched for DNase hypersensitive sites, histone H3 lysine 27 acetylation (H3K27ac), and other chromatin marks associated with active rather than poised or repressed enhancers. We also detected modest bidirectional expression at binding sites of the CCCTC-factor (CTCF) genome-wide, particularly those that overlap H3K27ac.Our findings indicate that the signature of bidirectional expression of short transcripts, learned from promoter-proximal transcriptional pausing, can be used to predict active long-range regulatory elements genome-wide, likely due in part to specific association of RNA polymerase with enhancer regions.Cellular identity and function are defined in large part by regulatory networks that determine gene expression profiles. Control of gene expression is complex, multi-faceted, and coordinated [1,2]. Over the past decade, with the advent of high-throughput genomic technologies, many systems-level biological approaches have been developed to help resolve these complexities, although substantive questions remain [3,4]. Recent large-scale human genetic studies have revealed that most complex disease-associated variants map to within non-coding genomic regions [5-7], providing additional impetus to expand current catalogs of gene regulatory elements and better understand cellular control of gene expression.The first step in gene expression is the recruitment to gene promoters of a multi-protein transcription initiation complex [8], which includes RNA polymerase (RNAP). Once RNAP is stably bound to the template DNA, it becomes transcriptionally engaged, and commences elongation. It was noted over two decades ago that RNAP