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.
Highlights
Descriptions of RNA synthesis and degradation are essential for understanding the dynamics of gene expression
For the 263 transcripts with a measured elongation rate in our dataset, we found that 88 (33%) in exponential phase have synthesis time that is longer than the lifetime of their 5’ end (Fig. 5a, Supplementary Table S9), suggesting that co-transcriptional degradation is potentially common
While our work does not comment on the specific mechanism of the decay pathway, it provides limits to the models of RNA degradation on a genome-wide scale, which has not yet been achieved in literature
Summary
Descriptions of RNA synthesis and degradation are essential for understanding the dynamics of gene expression. Like microarray, have increased the amount of information through genome-wide measurements, allowing researchers to observe the global behaviors for identifying the typical and the unusual in gene expression systems. The first microarray study of RNA lifetime in E.coli increased the number of measured RNA lifetimes from by two orders of magnitude (Bernstein et al, 2002) The availability of such data allowed researchers to perform systemwide analysis and modeling (Bon et al, 2006; Deneke et al, 2013). We apply RNAseq to the study of the kinetics of RNA dynamics to obtain high resolution data genome-wide so that we can further understand the interplay between degradation and synthesis. We obtained details of global RNA dynamics in exponentially-growing and stationary phase E. coli cells using RNA-seq, with sub-minute time resolution to allow observation of RNA synthesis and degradation. We revisited the meaning of the observed exponential decay of RNA and propose that co-transcriptional degradation is prevalent among RNAs, underscoring the interlinked nature of transcription, translation and RNA degradation
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