Chen, HuiyiShiroguchi, KatsuyukiGe, HaoXie, Xiaoliang2015-01-282015Chen, Huiyi, Katsuyuki Shiroguchi, Hao Ge, and Xiaoliang Sunney Xie. 2015. “Genome-Wide Study of mRNA Degradation and Transcript Elongation in Escherichia coli.” Molecular Systems Biology 11 (1): 781.1744-4292http://nrs.harvard.edu/urn-3:HUL.InstRepos:13849011An 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.en-USmodelingmRNA decayRNAP elongationRNA-seqtranscriptionJournal Article2014-12-16Huiyi Chen,Katsuyuki Shiroguchi, Hao Ge, X. Sunney Xie2015-01-2810.15252/msb.20145794