title: Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli.
abstract: An essential part of gene expression is the coordination of RNA synthesis and degradation, which occurs in the same cellular compartment in bacteria. Here, we report a genome-wide RNA degradation study in Escherichia coli using RNA-seq, and present evidence that the stereotypical exponential RNA decay curve obtained using initiation inhibitor, rifampicin, consists of two phases: residual RNA synthesis, a delay in the interruption of steady state that is dependent on distance relative to the mRNA's 5' end, and the exponential decay. This gives a more accurate RNA lifetime and RNA polymerase elongation rate simultaneously genome-wide. Transcripts typically have a single RNA decay constant along all positions, which is distinct between different operons, indicating that RNA stability is unlikely determined by local sequences. These measurements allowed us to establish a model for RNA processing involving co-transcriptional degradation, providing quantitative description of the macromolecular coordination in gene expression in bacteria on a system-wide level.
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
authors.forename: Huiyi
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
authors.forename: Katsuyuki
authors.initials: K
authors.lastname: Shiroguchi
authors.affiliation: Biodynamic Optical Imaging Center (BIOPIC), School of Life Science Peking University, Beijing, China Beijing International Center for Mathematical Research (BICMR) Peking University, Beijing, China haoge@pku.edu.cn xie@chemistry.harvard.edu.
authors.forename: Hao
authors.initials: H
authors.lastname: Ge
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA Biodynamic Optical Imaging Center (BIOPIC), School of Life Science Peking University, Beijing, China haoge@pku.edu.cn xie@chemistry.harvard.edu.
authors.forename: Xiaoliang Sunney
authors.initials: XS
authors.lastname: Xie
mesh_terms: D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D056726:Genetic Association Studies; D009876:Operon; D020871:RNA Stability / Q000235:genetics*; D012329:RNA, Bacterial / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D012329:RNA, Bacterial; D012333:RNA, Messenger
keywords: RNAP elongation; RNA‐seq; mRNA decay; modeling; transcription