Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.
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.
Michael
Todd P
TP
Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America.
Mockler
Todd C
TC
Breton
Ghislain
G
McEntee
Connor
C
Byer
Amanda
A
Trout
Jonathan D
JD
Hazen
Samuel P
SP
Shen
Rongkun
R
Priest
Henry D
HD
Sullivan
Christopher M
CM
Givan
Scott A
SA
Yanovsky
Marcelo
M
Hong
Fangxin
F
Kay
Steve A
SA
Chory
Joanne
J
D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000096:biosynthesis / Q000235:genetics; D002940:Circadian Rhythm / Q000235:genetics* / Q000502:physiology; D004268:DNA-Binding Proteins / Q000235:genetics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D017930:Genes, Reporter; D018745:Genome, Plant; D008156:Luciferases / Q000235:genetics; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics / Q000502:physiology; D017440:Photoperiod; D030821:Plants, Genetically Modified; D032107:Populus / Q000235:genetics / Q000502:physiology; D013045:Species Specificity; D013696:Temperature; D014157:Transcription Factors / Q000235:genetics
D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; C113192:LHY protein, Arabidopsis; C411822:TOC1 protein, Arabidopsis; D014157:Transcription Factors; D008156:Luciferases