Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis.
The circadian clock in Arabidopsis exerts a critical role in timing multiple biological processes and stress responses through the regulation of up to 80% of the transcriptome. As a key component of the clock, the Myb-like transcription factor CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is able to initiate and set the phase of clock-controlled rhythms and has been shown to regulate gene expression by binding directly to the evening element (EE) motif found in target gene promoters. However, the precise molecular mechanisms underlying clock regulation of the rhythmic transcriptome, specifically how clock components connect to clock output pathways, is poorly understood. In this study, using ChIP followed by deep sequencing of CCA1 in constant light (LL) and diel (LD) conditions, more than 1,000 genomic regions occupied by CCA1 were identified. CCA1 targets are enriched for a myriad of biological processes and stress responses, providing direct links to clock-controlled pathways and suggesting that CCA1 plays an important role in regulating a large subset of the rhythmic transcriptome. Although many of these target genes are evening expressed and contain the EE motif, a significant subset is morning phased and enriched for previously unrecognized motifs associated with CCA1 function. Furthermore, this work revealed several CCA1 targets that do not cycle in either LL or LD conditions. Together, our results emphasize an expanded role for the clock in regulating a diverse category of genes and key pathways in Arabidopsis and provide a comprehensive resource for future functional studies.
Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089;
Dawn H
DH
Nagel
Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089; San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093;
Colleen J
CJ
Doherty
Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093;
Jose L
JL
Pruneda-Paz
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
Robert J
RJ
Schmitz
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037.
Joseph R
JR
Ecker
Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089; stevekay@dornsife.usc.edu.
Steve A
SA
Kay
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D018745:Genome, Plant; D014157:Transcription Factors / Q000235:genetics*; D059467:Transcriptome
D029681:Arabidopsis Proteins; C114425:CCA1 protein, Arabidopsis; D014157:Transcription Factors
circadian clock; clock-controlled outputs; genome-wide; transcriptional regulation