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Series GSE38487 Query DataSets for GSE38487
Status Public on Sep 04, 2012
Title Unraveling the KNOTTED1 regulatory network in maize meristems
Organism Zea mays
Experiment type Expression 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 For loss-of-function mutant, kn1-e1 homozygote were compared to heterozygote or wild-type siblings (ears, tassels and shoot apical meristem). For gain-of-function mutant, Kn1-N homozygote were compared to wild-type siblings.Kn1-N heterozygote were compared to wild-type siblings. For each genotype and tissue, 2 biological replicates were sequenced, except for tassels (3 biological replicates). The whole data set thus includes a total of 20 samples/libraries.
 
Contributor(s) Bolduc N, Yilmaz A, Mejia-Guerra MK, Morohashi K, O’Connor D, Grotewold E, Hake S
Citation(s) 22855831
Submission date Jun 05, 2012
Last update date Jun 20, 2017
Contact name Maria Katherine Mejia Guerra
E-mail mejia-guerra.1@osu.edu
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)
GPL15463 Illumina HiSeq 2000 (Zea mays)
Samples (20)
GSM943461 Kn1-N leaf homo #1
GSM943462 Kn1-N leaf homo #2
GSM943463 Kn1-N leaf het #1
Relations
BioProject PRJNA168086
SRA SRP013564

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
GSE38487_Ears_e1_WT.diff.gz 65.2 Kb (ftp)(http) DIFF
GSE38487_KN1_Counted_Reads.xls.gz 1.6 Mb (ftp)(http) XLS
GSE38487_Leaf_Het_WT.diff.gz 1.3 Kb (ftp)(http) DIFF
GSE38487_Leaf_Homo_Het.diff.gz 18.0 Kb (ftp)(http) DIFF
GSE38487_Leaf_Homo_WT.diff.gz 67.9 Kb (ftp)(http) DIFF
GSE38487_SAM_e1_WT.diff.gz 1.3 Kb (ftp)(http) DIFF
GSE38487_Tassels_e1_WT.diff.gz 43.2 Kb (ftp)(http) DIFF
Processed data is available on Series record
Raw data are available in SRA

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