Determinants of Transcription Initiation Directionality in Metazoans

Abstract

Divergent transcription from promoters and enhancers is pervasive in many species, but it remains unclear if it is a general and passive feature of all eukaryotic cis regulatory elements. To address this, we define promoters and enhancers in C. elegans, D. melanogaster and H. sapiens using ATAC-Seq and investigate the determinants of their transcription initiation directionalities by analyzing genome-wide nascent, cap-selected, polymerase run-on assays. All three species initiate divergent transcription from separate core promoter sequences. Sequence asymmetry downstream of forward and reverse initiation sites, known to be important for . CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was . http://dx.doi.org/10.1101/224642 doi: bioRxiv preprint first posted online termination and stability in H. sapiens, is unique in each species. Chromatin states of divergent promoters are not entirely conserved, but in all three species, the levels of histone modifications on the +1 nucleosome are independent from those on the -1 nucleosome, arguing for independent initiation events. This is supported by an integrative model of H3K4me3 levels and core promoter sequence that is highly predictive of promoter directionality and of two types of promoters: those with balanced initiation directionality and those with skewed directionality. Lastly, D.melanogaster enhancers display variation in chromatin architecture depending on enhancer location, and D. melanogaster promoter regions with dual enhancer/promoter potential are enriched for divergent transcription. Our results point to a high degree of variation in regulatory element transcription initiation directionality within and between metazoans, and to non-passive regulatory mechanisms of transcription initiation directionality in those species.The application of deep sequencing assays led to the unanticipated observation that the promoters of many genes are transcribed in both directions, a phenomenon dubbed divergent transcription. In divergent promoters, transcripts made in the direction antisense to the annotated gene are non-protein-coding and highly unstable such that they can typically only be detected in assays enriching for nascent RNA.Divergent transcription is pervasive across many eukaryotes including yeast, C.elegans, M. musculus and H. sapiens [1][2][3][4][5] , though is highly depleted in D.In mammals, the asymmetric output of divergent promoters was suggested to be the result of a post-transcriptional competition model between the splicing machinery and the cleavage/polyadenylation machinery such that enriched splice site . CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/224642 doi: bioRxiv preprint first posted online sequences lead to transcript extension and stabilization in the forward direction, whereas ...