A comparative genomics approach to identifying the plasticity transcriptome
<p>Abstract</p> <p>Background</p> <p>Neuronal activity regulates gene expression to control learning and memory, homeostasis of neuronal function, and pathological disease states such as epilepsy. A great deal of experimental evidence supports the involvement of two par...
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| Format: | Article |
| Language: | English |
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BMC
2007-03-01
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| Series: | BMC Neuroscience |
| Online Access: | http://www.biomedcentral.com/1471-2202/8/20 |
| _version_ | 1818806269379608576 |
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| author | Schwartz Russell Pfenning Andreas R Barth Alison L |
| author_facet | Schwartz Russell Pfenning Andreas R Barth Alison L |
| author_sort | Schwartz Russell |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Neuronal activity regulates gene expression to control learning and memory, homeostasis of neuronal function, and pathological disease states such as epilepsy. A great deal of experimental evidence supports the involvement of two particular transcription factors in shaping the genomic response to neuronal activity and mediating plasticity: CREB and zif268 (egr-1, krox24, NGFI-A). The gene targets of these two transcription factors are of considerable interest, since they may help develop hypotheses about how neural activity is coupled to changes in neural function.</p> <p>Results</p> <p>We have developed a computational approach for identifying binding sites for these transcription factors within the promoter regions of annotated genes in the mouse, rat, and human genomes. By combining a robust search algorithm to identify discrete binding sites, a comparison of targets across species, and an analysis of binding site locations within promoter regions, we have defined a group of candidate genes that are strong CREB- or zif268 targets and are thus regulated by neural activity. Our analysis revealed that CREB and zif268 share a disproportionate number of targets in common and that these common targets are dominated by transcription factors.</p> <p>Conclusion</p> <p>These observations may enable a more detailed understanding of the regulatory networks that are induced by neural activity and contribute to the plasticity transcriptome. The target genes identified in this study will be a valuable resource for investigators who hope to define the functions of specific genes that underlie activity-dependent changes in neuronal properties.</p> |
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| format | Article |
| id | doaj.art-7bf07f11ffb94c36a99fd5bfb06bb22f |
| institution | Directory Open Access Journal |
| issn | 1471-2202 |
| language | English |
| last_indexed | 2024-12-18T19:07:05Z |
| publishDate | 2007-03-01 |
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| series | BMC Neuroscience |
| spelling | doaj.art-7bf07f11ffb94c36a99fd5bfb06bb22f2022-12-21T20:56:23ZengBMCBMC Neuroscience1471-22022007-03-01812010.1186/1471-2202-8-20A comparative genomics approach to identifying the plasticity transcriptomeSchwartz RussellPfenning Andreas RBarth Alison L<p>Abstract</p> <p>Background</p> <p>Neuronal activity regulates gene expression to control learning and memory, homeostasis of neuronal function, and pathological disease states such as epilepsy. A great deal of experimental evidence supports the involvement of two particular transcription factors in shaping the genomic response to neuronal activity and mediating plasticity: CREB and zif268 (egr-1, krox24, NGFI-A). The gene targets of these two transcription factors are of considerable interest, since they may help develop hypotheses about how neural activity is coupled to changes in neural function.</p> <p>Results</p> <p>We have developed a computational approach for identifying binding sites for these transcription factors within the promoter regions of annotated genes in the mouse, rat, and human genomes. By combining a robust search algorithm to identify discrete binding sites, a comparison of targets across species, and an analysis of binding site locations within promoter regions, we have defined a group of candidate genes that are strong CREB- or zif268 targets and are thus regulated by neural activity. Our analysis revealed that CREB and zif268 share a disproportionate number of targets in common and that these common targets are dominated by transcription factors.</p> <p>Conclusion</p> <p>These observations may enable a more detailed understanding of the regulatory networks that are induced by neural activity and contribute to the plasticity transcriptome. The target genes identified in this study will be a valuable resource for investigators who hope to define the functions of specific genes that underlie activity-dependent changes in neuronal properties.</p>http://www.biomedcentral.com/1471-2202/8/20 |
| spellingShingle | Schwartz Russell Pfenning Andreas R Barth Alison L A comparative genomics approach to identifying the plasticity transcriptome BMC Neuroscience |
| title | A comparative genomics approach to identifying the plasticity transcriptome |
| title_full | A comparative genomics approach to identifying the plasticity transcriptome |
| title_fullStr | A comparative genomics approach to identifying the plasticity transcriptome |
| title_full_unstemmed | A comparative genomics approach to identifying the plasticity transcriptome |
| title_short | A comparative genomics approach to identifying the plasticity transcriptome |
| title_sort | comparative genomics approach to identifying the plasticity transcriptome |
| url | http://www.biomedcentral.com/1471-2202/8/20 |
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