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| Status |
Public on Jun 07, 2017 |
| Title |
ATX3, ATX4, and ATX5 encode putative H3K4 methyltransferases and are critical for plant development |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Methylation of lysine residues in the tail of the H3 histone is a key regulator of chromatin state and gene expression, conferred by a large family of enzymes containing an evolutionarily-conserved SET domain. One of the main types of SET domain proteins are those controlling H3K4 di- and trimethylation. The genome of Arabidopsis encodes 12 such proteins, including five ARABIDOPSIS TRITHORAX (ATX) proteins and seven ATX-Related (ATXR) proteins. Here we examined three until-now-unexplored ATX proteins, ATX3, ATX4, and ATX5. We found that they exhibit similar domain structures and expression patterns, and are redundantly required for vegetative and reproductive development. Concurrent disruption of the ATX3, ATX4, and ATX5 genes caused marked reduction in H3K4me2 and H3K4me3 levels genome-wide, and resulted in thousands of genes expressed ectopically. Furthermore, atx3/atx4/atx5 triple mutants resulted in exaggerated phenotypes when combined with the atx2 mutant but not with atx1. Together, we conclude that ATX3, ATX4, and ATX5 are redundantly required for H3K4 di- and trimethylation at thousands of sites located across the genome, and genomic features associated with targeted regions are different from the ATXR3/SDG2-controlled sites in Arabidopsis.
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| Overall design |
ChIP-seq and RNA-seq technologies were undertaken to investigate genomic regions or genes targeted by three uncharacterized H3K4me2/3 genes in Arabidopsis.
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| Contributor(s) |
He Y |
| Citation(s) |
28550207 |
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| Submission date |
Oct 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yan He |
| E-mail(s) |
yh352@cau.edu.cn
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| Organization name |
China Agricultural University
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| Department |
Plant Genetics and Breeding
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| Lab |
He Lab
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| Street address |
2 Yuanmingyuan West Road
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA298628 |
| SRA |
SRP064752 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE73972_RAW.tar |
219.7 Mb |
(http)(custom) |
TAR (of BED, WIG) |
| GSE73972_atxvsWT_gene_exp_diff.txt.gz |
995.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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