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Series GSE231563 Query DataSets for GSE231563
Status Public on Aug 28, 2023
Title Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation [ChIP-seq]
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Epigenetic inheritance refers to the faithful replication of DNA and histone modification independent of DNA sequence. Nucleosomes block access to DNA methyltransferase during S phase, unless they are remodeled by Decrease in DNA methylation 1 (DDM1[Lsh/HELLS]), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 activity results in replacement of the transcriptional histone variant H3.3 for the replicative variant H3.1. Inddm1mutants, DNA methylation can be restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals direct engagement at SHL2 with histone H3.3 at or near variant residues required for assembly, as well as with the deacetylated H4 tail. An N-terminal autoinhibitory domain binds H2A variants to allow remodeling, while a di-sulphide bond in the helicase domain is essential for activity in vivo and in vitro. Differential remodeling of H3 and H2A variants in vitro reflects preferential deposition in vivo. DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1[Dnmt1]. DDM1 localization to the chromosome is blocked by H4K16 acetylation, which accumulates at DDM1 targets in ddm1 mutants, as does the sperm cell specific H3.3 variant MGH3 in pollen, which acts as a placeholder nucleosome and contributes to epigenetic inheritance.
Overall design Chromatin Immunoprecipitation sequencing was performed on wild-type and ddm1 mutants for DDM1 (vs Input), H3.3 (vs H3), H3K27me1 (vs H3), H4K16ac (vs H4) and MGH3 (vs Input)
Please note that processed data generated from both ChIP and Input/control sample is linked to the corresponding ChIP sample records.
Contributor(s) Lee SC, Cahn J, Martienssen RA
Citation(s) 37643610
Submission date May 03, 2023
Last update date Nov 27, 2023
Contact name Jonathan Cahn
Organization name CSHL
Street address 1 Bungtown Rd
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
Platforms (3)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL30821 NextSeq 2000 (Arabidopsis thaliana)
Samples (36)
GSM7290814 DDM1 ChIP-seq in WT biol Rep1
GSM7290815 Input for DDM1 ChIP-seq in WT biol Rep1
GSM7290816 DDM1 ChIP-seq in WT biol Rep2
This SubSeries is part of SuperSeries:
GSE231565 Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation.
BioProject PRJNA967122

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Supplementary file Size Download File type/resource
GSE231563_RAW.tar 7.8 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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