Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus.
We use the multigenic pattern of gene expression across suprachiasmatic nuclei (SCN) regions and time to understand the dynamics within the SCN in response to a circadian phase-resetting light pulse. Global gene expression studies of the SCN indicate that circadian functions like phase resetting are...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3360606?pdf=render |
| _version_ | 1828892044826771456 |
|---|---|
| author | Haisun Zhu Rajanikanth Vadigepalli Rachel Rafferty Gregory E Gonye David R Weaver James S Schwaber |
| author_facet | Haisun Zhu Rajanikanth Vadigepalli Rachel Rafferty Gregory E Gonye David R Weaver James S Schwaber |
| author_sort | Haisun Zhu |
| collection | DOAJ |
| description | We use the multigenic pattern of gene expression across suprachiasmatic nuclei (SCN) regions and time to understand the dynamics within the SCN in response to a circadian phase-resetting light pulse. Global gene expression studies of the SCN indicate that circadian functions like phase resetting are complex multigenic processes. While the molecular dynamics of phase resetting are not well understood, it is clear they involve a "functional gene expression program", e.g., the coordinated behavior of functionally related genes in space and time. In the present study we selected a set of 89 of these functionally related genes in order to further understand this multigenic program. By use of high-throughput qPCR we studied 52 small samples taken by anatomically precise laser capture from within the core and shell SCN regions, and taken at time points with and without phase resetting light exposure. The results show striking regional differences in light response to be present in the mouse SCN. By using network-based analyses, we are able to establish a highly specific multigenic correlation between genes expressed in response to light at night and genes normally activated during the day. The light pulse triggers a complex and highly coordinated network of gene regulation. The largest differences marking neuroanatomical location are in transmitter receptors, and the largest time-dependent differences occur in clock-related genes. Nighttime phase resetting appears to recruit transcriptional regulatory processes normally active in the day. This program, or mechanism, causes the pattern of core region gene expression to transiently shift to become more like that of the shell region. |
| first_indexed | 2024-12-13T13:27:55Z |
| format | Article |
| id | doaj.art-bf923f2e34df4722a3a4f9817ea72b80 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T13:27:55Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-bf923f2e34df4722a3a4f9817ea72b802022-12-21T23:44:15ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0175e3783310.1371/journal.pone.0037833Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus.Haisun ZhuRajanikanth VadigepalliRachel RaffertyGregory E GonyeDavid R WeaverJames S SchwaberWe use the multigenic pattern of gene expression across suprachiasmatic nuclei (SCN) regions and time to understand the dynamics within the SCN in response to a circadian phase-resetting light pulse. Global gene expression studies of the SCN indicate that circadian functions like phase resetting are complex multigenic processes. While the molecular dynamics of phase resetting are not well understood, it is clear they involve a "functional gene expression program", e.g., the coordinated behavior of functionally related genes in space and time. In the present study we selected a set of 89 of these functionally related genes in order to further understand this multigenic program. By use of high-throughput qPCR we studied 52 small samples taken by anatomically precise laser capture from within the core and shell SCN regions, and taken at time points with and without phase resetting light exposure. The results show striking regional differences in light response to be present in the mouse SCN. By using network-based analyses, we are able to establish a highly specific multigenic correlation between genes expressed in response to light at night and genes normally activated during the day. The light pulse triggers a complex and highly coordinated network of gene regulation. The largest differences marking neuroanatomical location are in transmitter receptors, and the largest time-dependent differences occur in clock-related genes. Nighttime phase resetting appears to recruit transcriptional regulatory processes normally active in the day. This program, or mechanism, causes the pattern of core region gene expression to transiently shift to become more like that of the shell region.http://europepmc.org/articles/PMC3360606?pdf=render |
| spellingShingle | Haisun Zhu Rajanikanth Vadigepalli Rachel Rafferty Gregory E Gonye David R Weaver James S Schwaber Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus. PLoS ONE |
| title | Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus. |
| title_full | Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus. |
| title_fullStr | Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus. |
| title_full_unstemmed | Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus. |
| title_short | Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus. |
| title_sort | integrative gene regulatory network analysis reveals light induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus |
| url | http://europepmc.org/articles/PMC3360606?pdf=render |
| work_keys_str_mv | AT haisunzhu integrativegeneregulatorynetworkanalysisrevealslightinducedregionalgeneexpressionphaseshiftprogramsinthemousesuprachiasmaticnucleus AT rajanikanthvadigepalli integrativegeneregulatorynetworkanalysisrevealslightinducedregionalgeneexpressionphaseshiftprogramsinthemousesuprachiasmaticnucleus AT rachelrafferty integrativegeneregulatorynetworkanalysisrevealslightinducedregionalgeneexpressionphaseshiftprogramsinthemousesuprachiasmaticnucleus AT gregoryegonye integrativegeneregulatorynetworkanalysisrevealslightinducedregionalgeneexpressionphaseshiftprogramsinthemousesuprachiasmaticnucleus AT davidrweaver integrativegeneregulatorynetworkanalysisrevealslightinducedregionalgeneexpressionphaseshiftprogramsinthemousesuprachiasmaticnucleus AT jamessschwaber integrativegeneregulatorynetworkanalysisrevealslightinducedregionalgeneexpressionphaseshiftprogramsinthemousesuprachiasmaticnucleus |