School of Life Sciences, University of Warwick, Coventry, UK.
Mathematics Institute and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK.
Genome Biol. 2021 Feb 4;22(1):56. doi: 10.1186/s13059-020-02227-5.
Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. Several factors contributing to transcriptional bursting have been identified, usually classified as intrinsic, in other words local to single genes, or extrinsic, relating to the macroscopic state of the cell. However, some possible contributors have not been explored yet. Here, we focus on processes at the 3 and 5 ends of a gene that enable reinitiation of transcription upon termination.
Using Bayesian methodology, we measure the transcriptional bursting in inducible transgenes, showing that perturbation of polymerase shuttling typically reduces burst size, increases burst frequency, and thus limits transcriptional noise. Analysis based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide. The observed noise patterns are also reproduced by a generative model that captures major characteristics of the polymerase flux between the ends of a gene and a phase-separated compartment.
Interactions between the 3 and 5 ends of a gene, which facilitate polymerase recycling, are major contributors to transcriptional noise.
哺乳动物细胞中的转录是一个复杂的随机过程，涉及聚合酶在基因之间的穿梭和相分离的液体凝聚物。它以爆发的形式发生，导致同基因细胞群体中 mRNA 物种的数量差异极大。已经确定了几种导致转录爆发的因素，通常分为内在因素，即与单个基因有关，或外在因素，与细胞的宏观状态有关。然而，一些可能的贡献者尚未被探索。在这里，我们专注于基因 3 和 5 末端的过程，这些过程能够在转录终止后重新启动转录。
我们使用贝叶斯方法测量了可诱导转基因中的转录爆发，表明聚合酶穿梭的干扰通常会减小爆发大小，增加爆发频率，从而限制转录噪声。基于配对末端标签测序（PolII ChIA-PET）的分析表明，这种效应是全基因组范围的。观察到的噪声模式也可以通过一个生成模型来再现，该模型捕获了聚合酶在基因末端和相分离隔室之间流动的主要特征。
基因 3 和 5 末端促进聚合酶回收的相互作用是转录噪声的主要贡献者。
