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| 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
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| 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.
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| 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.
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| Contributor(s) |
Bolduc N, Yilmaz A, Mejia-Guerra MK, Morohashi K, O’Connor D, Grotewold E, Hake S |
| Citation(s) |
22855831 |
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| Submission date |
Jun 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Erich Grotewold |
| Organization name |
Michigan State University
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| Lab |
Grotewold Laboratory
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| Street address |
603 Wilson Road
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| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48823 |
| Country |
USA |
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| Platforms (1) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA168086 |
| SRA |
SRP013564 |
| 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 |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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