Role and regulation of convergent antisense transcription by RNA polymerase II

RNA聚合酶II(POL II)的基因转录不是一个单向的过程。正义方向的转录通常伴随着相反方向的反义转录。反义转录是调控正义基因表达的一个新层次。我们最近开发了本地延长转录本测序(NET-SEQ)，作为一种定量的全基因组方法，用于研究人类细胞中核苷酸精确的正义和反义转录的全谱(Mayer等人，Cell，2015；Mayer等人，NAT协议，2016)。应用这种高分辨率的方法揭示了POL II在一大组编码蛋白质和长的非编码RNA基因的启动子近端的新的反义转录活性，称为收敛反义转录。聚合的反义转录主要发生在低表达的基因上，与正义转录呈负相关，提示存在潜在的调控联系。然而，汇聚性反义转录的关键方面仍未确定。在这里，我们提出了两个基本问题：(1)是什么分子机制驱动了这种反义转录活动？(2)汇聚的反义转录在控制细胞转录输出方面的功能是什么？为了了解人类细胞中聚合反义转录的决定因素和功能，我们将使用高分辨率全基因组方法、基因组编辑工具和单分子显微镜的跨学科组合。

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.