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Series GSE117391 Query DataSets for GSE117391
Status Public on Aug 31, 2018
Title Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The SWR1 chromatin remodeling complex, which deposits the histone variant H2A.Z into nucleosomes, has been characterized in yeast and animals but had not been purified from plants. We used the conserved SWR1 subunit ACTIN RELATED PROTEIN 6 (ARP6) as bait in tandem affinity purification experiments to isolate associated proteins from Arabidopsis thaliana. We identified all 11 subunits found in yeast SWR1 and the homologous mammalian SRCAP complexes, demonstrating that this complex is conserved in plants. We also identified several additional proteins not previously associated with SWR1, including Methyl-CpG-BINDING DOMAIN 9 (MBD9). Since mbd9 mutant plants were phenotypically similar to arp6 mutants, we further explored a potential role for MBD9 in H2A.Z deposition. We found that MBD9 is required for proper H2A.Z incorporation at thousands of discrete sites, which represent a subset of the regions normally enriched with H2A.Z. Genetic analyses showed that arp6;mbd9 double mutants have far more severe phenotypes than either single mutant. In conjunction with the finding that MBD9 does not appear to be a core subunit of the Arabidopsis SWR1 complex, this suggests that MBD9 also has important roles beyond H2A.Z deposition. Our data establish the SWR1 complex as being conserved across eukaryotes and also provide new insights into the mechanisms that target H2A.Z to chromatin.
 
Overall design ChIP-seq was performed in biological triplicate on 6-day-old WT, arp6-1, and mbd9-1 seedlings using antibodies against histone H2A.Z (Deal et al. [2007] Plant Cell 19) or Acetylated histone H4 (Millipore cat no. 06-866)
Web link https://www.biorxiv.org/content/early/2018/08/30/404152
 
Contributor(s) Deal RB
Citation(s) 31381567
Submission date Jul 19, 2018
Last update date Aug 27, 2019
Contact name Roger B Deal
E-mail(s) roger.deal@emory.edu
Phone 404-727-8087
Organization name Emory University
Department Biology
Street address 1510 Clifton Rd NE
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (21)
GSM3293712 arp_1_H2AZ
GSM3293713 arp_2_H2AZ
GSM3293714 arp_3_H2AZ
Relations
BioProject PRJNA481969
SRA SRP154459

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

Supplementary file Size Download File type/resource
GSE117391_RAW.tar 593.6 Mb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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