Network Discovery Pipeline Elucidates Conserved Time-of-Day-Specific cis-Regulatory Modules. Export

@article{citeulike:2544661, abstract = {Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89\% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.}, author = {Michael, Todd P P. and Mockler, Todd C C. and Breton, Ghislain and McEntee, Connor and Byer, Amanda and Trout, Jonathan D D. and Hazen, Samuel P P. and Shen, Rongkun and Priest, Henry D D. and Sullivan, Christopher M M. and Givan, Scott A A. and Yanovsky, Marcelo and Hong, Fangxin and Kay, Steve A A. and Chory, Joanne}, citeulike-article-id = {2544661}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pgen.0040014}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18248097}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18248097}, day = {1}, doi = {10.1371/journal.pgen.0040014}, issn = {1553-7404}, journal = {PLoS Genet}, keywords = {arabidopsis, clock, eucariotic\_transcription\_regulation}, month = {February}, number = {2}, posted-at = {2008-10-28 17:15:31}, priority = {4}, title = {Network Discovery Pipeline Elucidates Conserved Time-of-Day-Specific cis-Regulatory Modules.}, url = {http://dx.doi.org/10.1371/journal.pgen.0040014}, volume = {4}, year = {2008} }

TY - JOUR ID - citeulike:2544661 L3 - citeulike-article-id:2544661 N2 - Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation. IS - 2 JF - PLoS Genet SN - 1553-7404 TI - Network Discovery Pipeline Elucidates Conserved Time-of-Day-Specific cis-Regulatory Modules. VL - 4 KW - arabidopsis KW - clock KW - eucariotic_transcription_regulation AU - Michael, Todd P AU - Mockler, Todd C AU - Breton, Ghislain AU - McEntee, Connor AU - Byer, Amanda AU - Trout, Jonathan D AU - Hazen, Samuel P AU - Shen, Rongkun AU - Priest, Henry D AU - Sullivan, Christopher M AU - Givan, Scott A AU - Yanovsky, Marcelo AU - Hong, Fangxin AU - Kay, Steve A AU - Chory, Joanne PY - 2008/02/01/ UR - http://dx.doi.org/10.1371/journal.pgen.0040014 ER -