|
| Status |
Public on Jun 21, 2019 |
| Title |
Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. [ChIPSeq_H2AZ] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Deposition of histone variant H2A.Z by the SWR1 chromatin-remodeling complex is critical for the appropriate expression of many genes in eukaryotes, yet, despite its importance, the composition of the Arabidopsis SWR1 complex has not been thoroughly analyzed. Here we have identified the interacting partners of a conserved Arabidopsis SWR1 subunit, actin-related protein 6 (ARP6). We isolated 9 predicted components, identifying subunits implicated in histone acetylation and interacting partners implicated in chromatin biology. We found that the methyl-CpG-binding domain 9 (MBD9) subunit functioned synergistically with ARP6 to control flowering time. MBD9, in combination with ARP6, was involved in the SWR1-mediated incorporation of the majority of H2A.Z. MBD6 was further required for deposition of H2A.Z at a distinct subset of loci. MBD9 was preferentially bound to nucleosome-depleted regions at the 5’ of genes containing high levels of activating histone marks. Our data suggests a model for MBD9 in recruiting the SWR1 complex to open chromatin of actively transcribing genes.
|
| |
|
| Overall design |
Examination of H2AZ profiles in SWR1 mutants.
|
| |
|
| Contributor(s) |
Potok ME, Jacobsen SE |
| Citation(s) |
31350403 |
| |
| Submission date |
Dec 03, 2018 |
| Last update date |
Aug 06, 2019 |
| Contact name |
magdalena ewelina potok |
| Organization name |
UCLA
|
| Department |
MCDB
|
| Lab |
Jacobsen lab
|
| Street address |
4045 Terasaki Life Sciences Building
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7239 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL21785 |
Illumina HiSeq 4000 (Arabidopsis thaliana) |
|
| Samples (16)
|
|
| This SubSeries is part of SuperSeries: |
| GSE123263 |
Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. |
|
| Relations |
| BioProject |
PRJNA507982 |
| SRA |
SRP172057 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE123259_H2AZ_Col_R1_over_H2AZ_arp6_R1_summits.bed.gz |
333.6 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_Col_R1_over_H2AZ_arp6mbd9_R1_summits.bed.gz |
366.9 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_Col_R1_over_H2AZ_mbd9_R1_summits.bed.gz |
114.2 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_Col_R2_over_H2AZ_arp6_R2_summits.bed.gz |
275.5 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_Col_R2_over_H2AZ_arp6mbd9_R2_summits.bed.gz |
336.9 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_Col_R2_over_H2AZ_mbd9_R2_summits.bed.gz |
81.3 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_arp6_R1_over_H2AZ_arp6mbd9_R1_summits.bed.gz |
16.5 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_arp6_R2_over_H2AZ_arp6mbd9_R2_summits.bed.gz |
29.3 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_over_H3_Col_seed_R1_summits.bed.gz |
403.8 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_over_H3_Col_seed_R2_summits.bed.gz |
354.1 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_over_H3_arp6_seed_R1_summits.bed.gz |
52.1 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_over_H3_arp6_seed_R2_summits.bed.gz |
101.9 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_over_H3_arp6mbd9_seed_R1_summits.bed.gz |
16.9 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_over_H3_arp6mbd9_seed_R2_summits.bed.gz |
17.3 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_over_H3_mbd9_seed_R1_summits.bed.gz |
203.5 Kb |
(ftp)(http) |
BED |
| GSE123259_H2AZ_over_H3_mbd9_seed_R2_summits.bed.gz |
242.1 Kb |
(ftp)(http) |
BED |
| GSE123259_RAW.tar |
400.4 Mb |
(http)(custom) |
TAR (of WIG) |
| GSE123259_bed_information.txt.gz |
236 b |
(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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