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Series GSE39161 Query DataSets for GSE39161
Status Public on Sep 04, 2012
Title Unraveling the KNOTTED1 regulatory network in maize meristems (ChIP-seq)
Organism Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary KNOTTED1(KN1)-like homeobox (KNOX) transcription factors function in plant meristems, self-renewing structures consisting of stem cells and their immediate daughters. Despite their importance for plant development, the genomic network targeted by KNOX proteins is poorly understood. Using ChIP-seq, we defined the KN1 cistrome in maize inflorescences and found that KN1 binds to several thousand loci. To understand how these binding occupancies correlate with changes in transcriptional regulation, we performed RNA-seq on immature ears and tassels, and compared expression profiles between normal and loss-of-function kn1 plants, in addition to immature leaves from normal and gain-of-function Kn1 plants. We found that 643 of the KN1 targets were modulated in one or multiple tissues, with a strong enrichment for transcription factors (including other homeobox genes) and genes participating in several hormonal pathways, most significantly auxin, implicating KN1 at the crossroads of plant hormone signaling. The loss-of-function kn1 phenotype is reminiscent of auxin mutants and kn1 mis-expression in leaves correlates with increased auxin signaling. Our results demonstrate that KN1 plays a key role in orchestrating the upper levels of a hierarchical gene regulatory network that impacts plant meristem identity and function.
Overall design ChIP-seq was performed using ear primordia and tassel primordia. Input DNA from each sample was used as a normalization control
Contributor(s) Bolduc N, Yilmaz A, Mejia-Guerra MK, Morohashi K, O’Connor D, Grotewold E, Hake S
Citation(s) 22855831
Submission date Jul 06, 2012
Last update date May 23, 2013
Contact name Maria Katherine Mejia Guerra
Organization name The Ohio State University
Lab Grotewold Laboratory
Street address 1060 Carmack Road, Rightmire Hall
City Columbus
State/province OH
ZIP/Postal code 43210
Country USA
Platforms (1)
GPL9361 Illumina Genome Analyzer II (Zea mays)
Samples (6)
GSM957186 tassel1-ChIP
GSM957187 tassel1-Total input
GSM957188 tassel2 and 3-ChIP
BioProject PRJNA170127
SRA SRP014143

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
GSE39161_RAW.tar 890.0 Kb (http)(custom) TAR (of BED)
Raw data are available in SRA
Processed data provided as supplementary file

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