An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors.
Traditionally the gene expression pathway has been regarded as being comprised of independent steps, from RNA transcription to protein translation. To date there is increasing evidence of coupling between the different processes of the pathway, specifically between transcription and splicing. To stu...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC3405991?pdf=render |
| _version_ | 1818144613320359936 |
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| author | Idit Kosti Predrag Radivojac Yael Mandel-Gutfreund |
| author_facet | Idit Kosti Predrag Radivojac Yael Mandel-Gutfreund |
| author_sort | Idit Kosti |
| collection | DOAJ |
| description | Traditionally the gene expression pathway has been regarded as being comprised of independent steps, from RNA transcription to protein translation. To date there is increasing evidence of coupling between the different processes of the pathway, specifically between transcription and splicing. To study the interplay between these processes we derived a transcription-splicing integrated network. The nodes of the network included experimentally verified human proteins belonging to three groups of regulators: transcription factors, splicing factors and kinases. The nodes were wired by instances of predicted transcriptional and alternative splicing regulation. Analysis of the network indicated a pervasive cross-regulation among the nodes; specifically, splicing factors are significantly more connected by alternative splicing regulatory edges relative to the two other subgroups, while transcription factors are more extensively controlled by transcriptional regulation. Furthermore, we found that splicing factors are the most regulated of the three regulatory groups and are subject to extensive combinatorial control by alternative splicing and transcriptional regulation. Consistent with the network results, our bioinformatics analyses showed that the subgroup of kinases have the highest density of predicted phosphorylation sites. Overall, our systematic study reveals that an organizing principle in the logic of integrated networks favor the regulation of regulatory proteins by the specific regulation they conduct. Based on these results, we propose a new regulatory paradigm postulating that gene expression regulation of the master regulators in the cell is predominantly achieved by cross-regulation. |
| first_indexed | 2024-12-11T11:50:21Z |
| format | Article |
| id | doaj.art-e4fcba45920e480d8c9e385777ccd965 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-11T11:50:21Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-e4fcba45920e480d8c9e385777ccd9652022-12-22T01:08:22ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582012-01-0187e100260310.1371/journal.pcbi.1002603An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors.Idit KostiPredrag RadivojacYael Mandel-GutfreundTraditionally the gene expression pathway has been regarded as being comprised of independent steps, from RNA transcription to protein translation. To date there is increasing evidence of coupling between the different processes of the pathway, specifically between transcription and splicing. To study the interplay between these processes we derived a transcription-splicing integrated network. The nodes of the network included experimentally verified human proteins belonging to three groups of regulators: transcription factors, splicing factors and kinases. The nodes were wired by instances of predicted transcriptional and alternative splicing regulation. Analysis of the network indicated a pervasive cross-regulation among the nodes; specifically, splicing factors are significantly more connected by alternative splicing regulatory edges relative to the two other subgroups, while transcription factors are more extensively controlled by transcriptional regulation. Furthermore, we found that splicing factors are the most regulated of the three regulatory groups and are subject to extensive combinatorial control by alternative splicing and transcriptional regulation. Consistent with the network results, our bioinformatics analyses showed that the subgroup of kinases have the highest density of predicted phosphorylation sites. Overall, our systematic study reveals that an organizing principle in the logic of integrated networks favor the regulation of regulatory proteins by the specific regulation they conduct. Based on these results, we propose a new regulatory paradigm postulating that gene expression regulation of the master regulators in the cell is predominantly achieved by cross-regulation.http://europepmc.org/articles/PMC3405991?pdf=render |
| spellingShingle | Idit Kosti Predrag Radivojac Yael Mandel-Gutfreund An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. PLoS Computational Biology |
| title | An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. |
| title_full | An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. |
| title_fullStr | An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. |
| title_full_unstemmed | An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. |
| title_short | An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. |
| title_sort | integrated regulatory network reveals pervasive cross regulation among transcription and splicing factors |
| url | http://europepmc.org/articles/PMC3405991?pdf=render |
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