title: Regulation of gene expression by small non-coding RNAs: a quantitative view.
abstract: The importance of post-transcriptional regulation by small non-coding RNAs has recently been recognized in both pro- and eukaryotes. Small RNAs (sRNAs) regulate gene expression post-transcriptionally by base pairing with the mRNA. Here we use dynamical simulations to characterize this regulation mode in comparison to transcriptional regulation mediated by protein-DNA interaction and to post-translational regulation achieved by protein-protein interaction. We show quantitatively that regulation by sRNA is advantageous when fast responses to external signals are needed, consistent with experimental data about its involvement in stress responses. Our analysis indicates that the half-life of the sRNA-mRNA complex and the ratio of their production rates determine the steady-state level of the target protein, suggesting that regulation by sRNA may provide fine-tuning of gene expression. We also describe the network of regulation by sRNA in Escherichia coli, and integrate it with the transcription regulation network, uncovering mixed regulatory circuits, such as mixed feed-forward loops. The integration of sRNAs in feed-forward loops provides tight repression, guaranteed by the combination of transcriptional and post-transcriptional regulations.
authors: Racah Institute of Physics, The Hebrew University, Jerusalem, Israel.
authors: Yishai
authors: Y
authors: Shimoni
authors: Gilgi
authors: G
authors: Friedlander
authors: Guy
authors: G
authors: Hetzroni
authors: Gali
authors: G
authors: Niv
authors: Shoshy
authors: S
authors: Altuvia
authors: Ofer
authors: O
authors: Biham
authors: Hanah
authors: H
authors: Margalit
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D020029:Base Pairing; D003198:Computer Simulation; D004269:DNA, Bacterial / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D006207:Half-Life; D007700:Kinetics; D008957:Models, Genetic; D011485:Protein Binding; D011499:Protein Processing, Post-Translational; D012323:RNA Processing, Post-Transcriptional; D012329:RNA, Bacterial / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D022661:RNA, Untranslated / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated; D014157:Transcription Factors