Atlas of 5'P mRNA decay in bacteria

Regulation of mRNA stability is a central process in gene expression. Here, report an atlas of 5´ monophosphorylated mRNA decay intermediates (5´P) in 96 species. We use those data to demonstrate that in species with 5´-3´exonuclease activity, the exoribonuclease RNase J follows the trailing ribosome, producing an in vivo single-nucleotide toeprint of its 5´ position. While in other species, ribosome position alters endonucleolytic cleavage sites. Our work demonstrates the universal connection between RNA decay and translation and paves the way for use of metadegradome sequencing to investigate post-transcriptional regulation of unculturable species present and complex microbial communities.

Data was analyzed using our fivepseq software.  Improved computational analysis of ribosome dynamics from 5′P degradome data using fivepseq. Lilit Nersisyan, Maria Ropat & Vicent Pelechano. NAR Genomics and Bioinformatics, Volume 2, Issue 4, December 2020, lqaa099, https://doi.org/10.1093/nargab/lqaa099

mRNA稳定性调控是基因表达的核心过程。本研究构建了涵盖96个物种的5′单磷酸化mRNA降解中间产物（5´P）图谱。我们利用这些数据证实：在携带5′-3′核酸外切酶活性的物种中，外切核糖核酸酶RNase J会尾随核糖体行进，并在其5′端位置生成体内单核苷酸分辨率的足迹信号；而在其他物种中，核糖体的位置会改变核酸内切酶的切割位点。本研究证实了RNA降解与翻译之间的普遍关联，并为利用宏降解组测序（metadegradome sequencing）探究现存未培养物种及复杂微生物群落的转录后调控机制铺平了道路。

本研究采用fivepseq软件对数据进行分析。《基于5′P降解组数据优化的核糖体动态计算分析方法》。作者：Lilit Nersisyan、Maria Ropat与Vicent Pelechano。刊载于《NAR基因组学与生物信息学》，2020年12月，第2卷第4期，文章编号lqaa099，DOI：10.1093/nargab/lqaa099。