Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network Export

@article{citeulike:1463374, abstract = {Author SummaryIt is becoming increasingly appreciated that a new type of gene which does not code for proteins, the regulatory RNAs, constitutes a considerable portion of mammalian genomes, and these genes serve as key players in the regulatory network of living cells. Among these regulatory RNAs are the microRNAs (miRs), small RNAs that mediate posttranscriptional gene silencing through inhibition of protein production or degradation of mRNAs. So far little is known about the extent of regulation by miRs, and their potential cooperation with other regulatory layers in the network. We investigated the potential crosstalk between the miR-mediated posttranscription layer, and the transcriptional regulation layer, whose dominant players, the transcription factors (TFs), regulate the production of protein-coding mRNAs. We found that the extent of miR regulation varies extensively among different genes, some of which, especially those who serve as regulators themselves, are subject to enhanced miR silencing. Further, we identified thousands of genes that are potentially subjected to coordinated regulation by multiple miRs and by specific combinations of TFs and miRs. The regulatory network, comprising transcriptional and posttranscriptional regulation, manifests several recurring architectures, one of which consists of a TF and a miR that together regulate a large set of common genes, and that also appear to regulate one another. Altogether this work provides new insights into the logic and evolution of a new regulatory layer of the mammalian genome, and its effect on other regulatory networks in the cell.}, author = {Shalgi, Reut and Lieber, Daniel and Oren, Moshe and Pilpel, Yitzhak}, citeulike-article-id = {1463374}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.0030131}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17630826}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17630826}, day = {13}, doi = {10.1371/journal.pcbi.0030131}, issn = {1553-7358}, journal = {PLoS Comput Biol}, keywords = {factor, mirna, network, tf, transcription}, month = {July}, number = {7}, pages = {e131+}, posted-at = {2007-07-19 05:06:12}, priority = {1}, publisher = {Public Library of Science}, title = {Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network}, url = {http://dx.doi.org/10.1371/journal.pcbi.0030131}, volume = {3}, year = {2007} }

TY - JOUR ID - citeulike:1463374 L3 - citeulike-article-id:1463374 N2 - Author SummaryIt is becoming increasingly appreciated that a new type of gene which does not code for proteins, the regulatory RNAs, constitutes a considerable portion of mammalian genomes, and these genes serve as key players in the regulatory network of living cells. Among these regulatory RNAs are the microRNAs (miRs), small RNAs that mediate posttranscriptional gene silencing through inhibition of protein production or degradation of mRNAs. So far little is known about the extent of regulation by miRs, and their potential cooperation with other regulatory layers in the network. We investigated the potential crosstalk between the miR-mediated posttranscription layer, and the transcriptional regulation layer, whose dominant players, the transcription factors (TFs), regulate the production of protein-coding mRNAs. We found that the extent of miR regulation varies extensively among different genes, some of which, especially those who serve as regulators themselves, are subject to enhanced miR silencing. Further, we identified thousands of genes that are potentially subjected to coordinated regulation by multiple miRs and by specific combinations of TFs and miRs. The regulatory network, comprising transcriptional and posttranscriptional regulation, manifests several recurring architectures, one of which consists of a TF and a miR that together regulate a large set of common genes, and that also appear to regulate one another. Altogether this work provides new insights into the logic and evolution of a new regulatory layer of the mammalian genome, and its effect on other regulatory networks in the cell. IS - 7 JF - PLoS Comput Biol SN - 1553-7358 TI - Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network PB - Public Library of Science VL - 3 SP - e131 KW - factor KW - mirna KW - network KW - tf KW - transcription AU - Shalgi, Reut AU - Lieber, Daniel AU - Oren, Moshe AU - Pilpel, Yitzhak PY - 2007/07/13/ UR - http://dx.doi.org/10.1371/journal.pcbi.0030131 ER -