Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
Abstract Although several studies have provided important insights into the general principles of biological networks, the link between network organization and the genome‐scale dynamics of the underlying entities (genes, mRNAs, and proteins) and its role in systems behavior remain unclear. Here we...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2009-08-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/msb.2009.52 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849225763156393984 |
|---|---|
| author | Raja Jothi S Balaji Arthur Wuster Joshua A Grochow Jörg Gsponer Teresa M Przytycka L Aravind M Madan Babu |
| author_facet | Raja Jothi S Balaji Arthur Wuster Joshua A Grochow Jörg Gsponer Teresa M Przytycka L Aravind M Madan Babu |
| author_sort | Raja Jothi |
| collection | DOAJ |
| description | Abstract Although several studies have provided important insights into the general principles of biological networks, the link between network organization and the genome‐scale dynamics of the underlying entities (genes, mRNAs, and proteins) and its role in systems behavior remain unclear. Here we show that transcription factor (TF) dynamics and regulatory network organization are tightly linked. By classifying TFs in the yeast regulatory network into three hierarchical layers (top, core, and bottom) and integrating diverse genome‐scale datasets, we find that the TFs have static and dynamic properties that are similar within a layer and different across layers. At the protein level, the top‐layer TFs are relatively abundant, long‐lived, and noisy compared with the core‐ and bottom‐layer TFs. Although variability in expression of top‐layer TFs might confer a selective advantage, as this permits at least some members in a clonal cell population to initiate a response to changing conditions, tight regulation of the core‐ and bottom‐layer TFs may minimize noise propagation and ensure fidelity in regulation. We propose that the interplay between network organization and TF dynamics could permit differential utilization of the same underlying network by distinct members of a clonal cell population. |
| format | Article |
| id | doaj-art-566319d3c18c406dbdba2b134d6b2a97 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2009-08-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-566319d3c18c406dbdba2b134d6b2a972025-08-24T11:59:31ZengSpringer NatureMolecular Systems Biology1744-42922009-08-015111510.1038/msb.2009.52Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architectureRaja Jothi0S Balaji1Arthur Wuster2Joshua A Grochow3Jörg Gsponer4Teresa M Przytycka5L Aravind6M Madan Babu7Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of HealthBiostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of HealthMRC Laboratory of Molecular BiologyDepartment of Computer Science, University of ChicagoMRC Laboratory of Molecular BiologyNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthMRC Laboratory of Molecular BiologyAbstract Although several studies have provided important insights into the general principles of biological networks, the link between network organization and the genome‐scale dynamics of the underlying entities (genes, mRNAs, and proteins) and its role in systems behavior remain unclear. Here we show that transcription factor (TF) dynamics and regulatory network organization are tightly linked. By classifying TFs in the yeast regulatory network into three hierarchical layers (top, core, and bottom) and integrating diverse genome‐scale datasets, we find that the TFs have static and dynamic properties that are similar within a layer and different across layers. At the protein level, the top‐layer TFs are relatively abundant, long‐lived, and noisy compared with the core‐ and bottom‐layer TFs. Although variability in expression of top‐layer TFs might confer a selective advantage, as this permits at least some members in a clonal cell population to initiate a response to changing conditions, tight regulation of the core‐ and bottom‐layer TFs may minimize noise propagation and ensure fidelity in regulation. We propose that the interplay between network organization and TF dynamics could permit differential utilization of the same underlying network by distinct members of a clonal cell population.https://doi.org/10.1038/msb.2009.52dynamicshierarchynoisesystems biologytranscription network |
| spellingShingle | Raja Jothi S Balaji Arthur Wuster Joshua A Grochow Jörg Gsponer Teresa M Przytycka L Aravind M Madan Babu Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture Molecular Systems Biology dynamics hierarchy noise systems biology transcription network |
| title | Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture |
| title_full | Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture |
| title_fullStr | Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture |
| title_full_unstemmed | Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture |
| title_short | Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture |
| title_sort | genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture |
| topic | dynamics hierarchy noise systems biology transcription network |
| url | https://doi.org/10.1038/msb.2009.52 |
| work_keys_str_mv | AT rajajothi genomicanalysisrevealsatightlinkbetweentranscriptionfactordynamicsandregulatorynetworkarchitecture AT sbalaji genomicanalysisrevealsatightlinkbetweentranscriptionfactordynamicsandregulatorynetworkarchitecture AT arthurwuster genomicanalysisrevealsatightlinkbetweentranscriptionfactordynamicsandregulatorynetworkarchitecture AT joshuaagrochow genomicanalysisrevealsatightlinkbetweentranscriptionfactordynamicsandregulatorynetworkarchitecture AT jorggsponer genomicanalysisrevealsatightlinkbetweentranscriptionfactordynamicsandregulatorynetworkarchitecture AT teresamprzytycka genomicanalysisrevealsatightlinkbetweentranscriptionfactordynamicsandregulatorynetworkarchitecture AT laravind genomicanalysisrevealsatightlinkbetweentranscriptionfactordynamicsandregulatorynetworkarchitecture AT mmadanbabu genomicanalysisrevealsatightlinkbetweentranscriptionfactordynamicsandregulatorynetworkarchitecture |