|
| Status |
Public on Aug 17, 2018 |
| Title |
Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
DNA methylation functions in gene silencing and the maintenance
of genome integrity. In plants, non-CG DNA methylation is linked
through a self-reinforcing loop with histone 3 lysine 9 dimethylation (H3K9me2). The plant-specific SUPPRESSOR OF VARIEGATION
3–9 HOMOLOG (SUVH) family H3K9 methyltransferases (MTases)
bind to DNA methylation marks and catalyze H3K9 methylation.
Here, we analyzed the structure and function of Arabidopsis thaliana SUVH6 to understand how this class of enzyme maintains
methylation patterns in the genome. We reveal that SUVH6 has
a distinct 5mC base-flipping mechanism involving a thumb loop
element. Autoinhibition of H3 substrate entry is regulated by a
SET domain loop, and a conformational transition in the postSET domain upon cofactor binding may control catalysis. In vitro
DNA binding and in vivo ChIP-seq data reveal that the different
SUVH family H3K9 MTases have distinct DNA binding preferences,
targeting H3K9 methylation to sites with different methylated
DNA sequences, explaining the context biased non-CG DNA methylation in plants.
|
| |
|
| Overall design |
To determine the in vivo relevance of the in vitro binding preferences, we profiled levels of H3K9me2 by chromatin immunoprecipitation coupled to high throughput sequencing (ChIP-seq)
in wild type (WT) and kyp, suvh5, suvh6, and kyp/suvh5/6 mutant
backgrounds.
|
| |
|
| Contributor(s) |
Zhenhui Z, Jake HC |
| Citation(s) |
30150382 |
| |
| Submission date |
May 03, 2018 |
| Last update date |
Mar 03, 2019 |
| Contact name |
Zhenhui Zhong |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, Los Angeles
|
| Department |
Department of Molecular, Cell and Developmental Biology
|
| Lab |
Jacobsen Lab
|
| Street address |
610 Charles E Young Dr East
|
| City |
Los Angeles |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL21785 |
Illumina HiSeq 4000 (Arabidopsis thaliana) |
|
| Samples (10)
|
|
| Relations |
| BioProject |
PRJNA454877 |
| SRA |
SRP144497 |
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