Transcription-replication interactions reveal principles of bacterial genome regulation

作者：Andrew W. Pountain, Peien Jiang, Tianyou Yao, Ehsan Homaee, Yichao Guan, Magdalena Podkowik, Bo Shopsin, Victor J. Torres, Ido Golding, Itai Yanai · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2022 · DOI：10.1101/2022.10.22.513359 · 被引用次数：9 · 研究领域：Bacterial Genetics and Biotechnology、Genomics and Chromatin Dynamics、RNA and protein synthesis mechanisms

Abstract Organisms determine the transcription rates of thousands of genes through a few modes of regulation that recur across the genome. These modes interact with a changing cellular environment to yield highly dynamic expression patterns. In bacteria, the relationship between a gene’s regulatory architecture and its expression is well understood for individual model gene circuits. However, a broader perspective of these dynamics at the genome-scale is lacking, in part because bacterial transcriptomics have hitherto captured only a static snapshot of expression averaged across millions of cells. As a result, the full diversity of gene expression dynamics and their relation to regulatory architecture remains unknown. Here we present a novel genome-wide classification of regulatory modes based on each gene’s transcriptional response to its own replication, which we term the Transcription-Replication Interaction Profile (TRIP). We found that the response to the universal perturbation of chromosomal replication integrates biological regulatory factors with biophysical molecular events on the chromosome to reveal a gene’s local regulatory context. While the TRIPs of many genes conform to a gene dosage-dependent pattern, others diverge in distinct ways, including altered timing or amplitude of expression, and this is shaped by factors such as intra-operon position, repression state, or presence on mobile genetic elements. Our transcriptome analysis also simultaneously captures gl...