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Series GSE67655 Query DataSets for GSE67655
Status Public on Jun 30, 2016
Title Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids
Organism Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary we determine genome-wide binding profiles of a maize CCA1 homolog, ZmCCA1b, in maize inbreds and F1 hybrids at different times of the day. ZmCCA1b is characterized as a central clock regulator gene with evolutionarily conserved molecular and circadian functions and nonadditively expressed in F1 hybrid seedlings. ZmCCA1b binds to over 4,300 target genes in the maize genomes, of which annotation confirms energy metabolic pathways as the main output. We report that an altered temporal binding activity of ZmCCA1b in the hybrid seedlings, which increases expression of carbon fixation genes, increases carbon fixation rates and biomass, demonstrating a novel example of how circadian-regulatory networks directly contribute to growth vigor in maize hybrids. These results collectively offer new insights into clock-mediated regulation of growth vigor in hybrid plants and crops.
 
Overall design Profiling genome-wide binding events of ZmCCA1b in the maize inbreds and F1 hybrids at ZT3, ZT9 and ZT15 using chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). 2 biological replicates for each sample were used. Input DNA sample corresponding to each ChIP sample was also sequenced in parallel.
We have developed a native antibody for the protein (GRMZM2G014902; epitope: residues 11-77) for the ChIP-seq study.
 
Contributor(s) Ko DK, Song Q, Chen ZJ
Citation(s) 27467757
Submission date Apr 08, 2015
Last update date May 15, 2019
Contact name Dae Kwan Ko
E-mail(s) dkko@msu.edu
Phone 512-300-7521
Organization name Michigan State University
Department Plant Research Laboratories
Lab The Brandizzi Lab
Street address 612 Wilson Rd. Plant Biology RM 122
City East Lansing
State/province MI
ZIP/Postal code 48824
Country USA
 
Platforms (1)
GPL17628 Illumina HiSeq 2500 (Zea mays)
Samples (48)
GSM1652858 B_ChIP_ZT3_rep1
GSM1652859 BM_ChIP_ZT3_rep1
GSM1652860 MB_ChIP_ZT3_rep1
Relations
BioProject PRJNA280575
SRA SRP056961

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
GSE67655_B73_peaks.txt.gz 108.0 Kb (ftp)(http) TXT
GSE67655_BM_peaks.txt.gz 90.1 Kb (ftp)(http) TXT
GSE67655_MB_peaks.txt.gz 61.0 Kb (ftp)(http) TXT
GSE67655_Mo17_peaks.txt.gz 67.3 Kb (ftp)(http) TXT
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Processed data are available on Series record
Raw data are available in SRA

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