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| Status |
Public on Mar 01, 2012 |
| Title |
EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by genome tiling array
Genome binding/occupancy profiling by genome tiling array
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| Summary |
EMBRYONIC FLOWER1 (EMF1) is a plant specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment level of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying differentiated cell fates during vegetative development. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism.
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| Overall design |
All experiments were done using two channels per chip, comparing DNA associated with immunoprecipitated EMF1 to control genomic DNA, DNA associated with immunoprecipitated histone H3 methylated at lysine 27 to control genomic DNA, or total RNA (converted to cDNA) to control genomic DNA. Two or three replicates per experiment are included.
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| Contributor(s) |
Zilberman D, Nishimura T |
| Citation(s) |
22457632 |
| |
| Submission date |
Dec 23, 2011 |
| Last update date |
Jan 03, 2013 |
| Contact name |
Toshiro Nishimura |
| E-mail(s) |
tnish@berkeley.edu
|
| Phone |
5106429550
|
| Organization name |
University of California at Berkeley
|
| Department |
Plant and Microbial Biology
|
| Lab |
Daniel Zilberman
|
| Street address |
211 Koshland Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL15056 |
NimbleGen Zilberman Arabidopsis HD2 array [080709_AT8_DZ_ChIP_HX1] |
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| Samples (23)
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| Relations |
| BioProject |
PRJNA150299 |
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