Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 112, Issue 34, Pages E4802-E4810Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1513609112
Keywords
genome-wide; circadian clock; clock-controlled outputs; transcriptional regulation
Categories
Funding
- Ruth L. Kirschstein National Research Service Award [F32GM090375]
- National Science Foundation [0906055]
- National Institutes of General Medicine of the NIH Awards [R01GM056006, R01GM067837, RC2GM092412]
- National Science Foundation Award [MCB-1024999]
- Howard Hughes Medical Institute (HHMI)
- Gordon and Betty Moore Foundation (GBMF) Award [GBMF3034]
- Div Of Biological Infrastructure
- Direct For Biological Sciences [0906055] Funding Source: National Science Foundation
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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.
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