Role and regulation of convergent antisense transcription by RNA polymerase II

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Gene transcription by RNA polymerase II (Pol II) is not a unidirectional process. Transcription in the sense direction is usually accompanied by antisense transcription in the opposite orientation. Antisense transcription is emerging as a new layer in regulating the expression of the sense gene. We have recently developed native elongating transcript sequencing (NET-seq) as a quantitative genome-wide approach for studying the full spectrum of sense and antisense transcription with nucleotide precision in human cells (Mayer et al., Cell, 2015; Mayer et al., Nat Protocols, 2016). Application of this high-resolution method has revealed a new antisense transcriptional activity of Pol II in the promoter-proximal region of a large set of protein-coding and long non-coding RNA genes, called convergent antisense transcription. Convergent antisense transcription predominantly occurs at lower expressed genes and inversely correlates with sense transcription suggesting a potential regulatory link. However, key aspects of convergent antisense transcription remain undefined. Here, we propose to address two fundamental questions: (1) What molecular mechanisms drive this antisense transcriptional activity? (2) What is the functional role of convergent antisense transcription in controlling the transcriptional output of cells? To understand the determinants and functions of convergent antisense transcription in human cells, we will employ an interdisciplinary combination of high-resolution genome-wide approaches, genome editing tools and single-molecule microscopy.