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Series GSE123259 Query DataSets for GSE123259
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)
GSM3498728 ChIPSeq_H3_WT_R1
GSM3498729 ChIPSeq_H3_mbd9-3_R1
GSM3498730 ChIPSeq_H3_arp6-1_R1
This SubSeries is part of SuperSeries:
GSE123263 Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition.
BioProject PRJNA507982
SRA SRP172057

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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Raw data are available in SRA
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