Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules

 

Autores
Michael, Todd P.; Mockler, Todd C.; Breton, Ghislain; McEntee, Connor; Byer, Amanda; Trout, Jonathan D.; Hazen, Samuel P.; Shen, Rongkun; Priest, Henry D.; Sullivan, Christopher M.; Givan, Scott A.; Yanovsky, Marcelo Javier; Hong, Fangxin; Kay, Steve A.; Chory, Joanne
Tipo de recurso
artículo
Estado
Versión publicada
Año de publicación
2008
País
Argentina
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
Repositorio
CONICET Digital (CONICET)
Descripción
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.
Idioma
inglés
OAI Identifier
oai:ri.conicet.gov.ar:11336/22700
Enlace del recurso
http://hdl.handle.net/11336/22700
Nivel de acceso
Acceso abierto
Materia
Bioquímica y Biología Molecular
Ciencias Biológicas
CIENCIAS NATURALES Y EXACTAS