期刊
MOLECULAR SYSTEMS BIOLOGY
卷 11, 期 1, 页码 -出版社
WILEY-BLACKWELL
DOI: 10.15252/msb.20145794
关键词
modeling; mRNA decay; RNAP elongation; RNA-seq; transcription
资金
- NIH [GM096450]
- Japanese Society for the Promotion of Science
- Uehara Memorial Foundation
- NSFC [10901040, 21373021]
- Foundation for the Author of National Excellent Doctoral Dissertation of China [201119]
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.
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