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Series GSE70533 Query DataSets for GSE70533
Status Public on Jul 26, 2015
Title Genome-wide Identification of CCA1 Targets Uncovers an Expanded Clock Network in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The plant circadian clock exerts a critical role in the regulation of multiple biological processes including responses to biotic and abiotic stresses. It is estimated that the clock regulates up to 80% of the transcriptome in Arabidopsis, thus understanding the molecular mechanisms that control this rhythmic transcriptome requires identification of the targets of each clock component. The Arabidopsis core clock is partially comprised of a transcriptional regulatory loop between the MYB domain containing transcription factors CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and TIMING OF CAB EXPRESSION1 (TOC1). As a key component of the clock, CCA1 is able to initiate and set the phase of clock-controlled rhythms. CCA1 regulates the transcription of several genes by directly binding to the evening element (EE) motif primarily found in the promoters of evening expressed genes. Using a genome-wide approach we have identified direct targets of CCA1 in plants grown in constant (LL) and driven conditions (LD). These CCA1 targets are enriched for a myriad of biological processes and stress responses. While many of these target genes are evening phased and contain the EE in their promoter regions, a significant subset is morning phased and lack an EE. Furthermore, several CCA1 targets do not cycle in either LL or LD or both. Expression analysis in CCA1 overexpressing plants confirms CCA1 regulation of analyzed targets. Our results emphasize an expanded role for the circadian clock in regulation of key pathways in Arabidopsis, and provide a comprehensive and solid resource for future functional studies.
 
Overall design ChIP-Seq of CCA1-GFP plants under control of the CCA1 promoter in continuous light and diel conditions
 
Contributor(s) Doherty CJ
Citation(s) 26261339
Submission date Jul 06, 2015
Last update date May 15, 2019
Contact name Colleen J Doherty
E-mail(s) colleen_doherty@ncsu.edu
Organization name North Carolina State University
Department Biochemistry
Lab Colleen Doherty
Street address 128 Polk Hall CB7622
City Raleigh
State/province NC
ZIP/Postal code 27695-7622
Country USA
 
Platforms (2)
GPL9302 Illumina Genome Analyzer II (Arabidopsis thaliana)
GPL11221 Illumina Genome Analyzer IIx (Arabidopsis thaliana)
Samples (7)
GSM1808449 CCA1_ChIPSeq_LL1
GSM1808450 CCA1_ChIPSeq_LL2
GSM1808451 CCA1_ChIPSeq_LL3
Relations
BioProject PRJNA288957
SRA SRP060360

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE70533_LD.peaks.txt.gz 46.4 Kb (ftp)(http) TXT
GSE70533_LDAnnotatedPeaks.txt.gz 114.7 Kb (ftp)(http) TXT
GSE70533_LL.peaks.txt.gz 40.5 Kb (ftp)(http) TXT
GSE70533_LLAnnotatedPeaks.txt.gz 101.7 Kb (ftp)(http) TXT
GSE70533_RAW.tar 101.6 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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