Chromatin remodeling protein DDM1

Function

DNA- or chromatin-stimulated ATPase that plays a role in formation, organization, stability and heritability of heterochromatin and thus regulates several physiological traits. Binds to the nucleosome and promotes chromatin remodeling in an ATP-dependent manner; induces nucleosome repositioning on a short DNA fragment, and, possibly, could be guided to target sites (including silent transposable elements) by small interfering RNAs (siRNAs). Can bind both free and nucleosomal DNA. Required for the heritable maintenance of genome integrity and transcriptional gene silencing (TGS), including homology-dependent gene silencing (HDG silencing), via the maintenance of DNA methylation (mostly on cytosine, in both CpG and CpHpG sites, where H is A, T or C) and of histone methylation (e.g. chromatin methylation). May facilitate localization of MBD proteins at specific nuclear domains. Necessary for the maintenance of the genomic imprint at the MEA locus, especially for the silencing of paternally inherited MEA locus. Plays a major role in the inactivation maintenance of retrotransposons (e.g. Tar17, SINE, LINE, ATLN39, CAC1 (CACTAs), Athila elements, and mutator-like elements MULEs and TIR-MULEs) and the silencing of repeated genes and transgenes (e.g. T-DNA insertions). Required for KYP-dependent histone H3 'Lys-9' (H3K9me) methylation, deacetylation of histone H4 'Lys-16' (H4K16) and MET1-dependent DNA methylation. Involved in the chromatin organization of 5S rRNA genes (localized in the pericentromeric heterochromatin of chromosomes 3, 4, and 5) modifications during heterochromatin establishment. Prevents siRNA accumulation (siRNA are probably involved in epigenetic inheritance and in 5S rRNA genes regulation by silencing). Required during plant organogenesis and development, as well as during seed formation.

Classification

Family (Pfam)

PF00271 Helicase_C, PF00176 SNF2-rel_dom

InterPro

Helicase_ATP-bd, Helicase_C-like, HELLS_N, P-loop_NTPase, SNF2-like_sf, SNF2/RAD54-like_C, SNF2_N

Functional cluster

Serine/Threonine Protein Kinases

Experimental structures · PDB · 9

• 7UX9 EM 3.20A
• 8J90 EM 4.71A
• 8KCB EM 3.17A
• 8KCC EM 3.10A
• 8SKZ EM 3.50A
• 8WH5 EM 3.58A
• 8WH8 EM 3.60A
• 8WH9 EM 3.31A
• 8WHA EM 4.05A

A predicted model is available from AlphaFold.

Gene Ontology · 17

• GO:0000785 chromatin
• GO:0000786 nucleosome
• GO:0005634 nucleus
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity
• GO:0140658 ATP-dependent chromatin remodeler activity
• GO:0003682 chromatin binding
• GO:0003677 DNA binding
• GO:0140750 nucleosome array spacer activity
• GO:0006338 chromatin remodeling
• GO:0006346 DNA methylation-dependent constitutive heterochromatin formation
• GO:0009294 DNA-mediated transformation
• GO:0006351 DNA-templated transcription
• GO:0040029 epigenetic regulation of gene expression
• GO:0031507 heterochromatin formation
• GO:0045944 positive regulation of transcription by RNA polymerase II
• GO:0032197 retrotransposition

Neighborhood · nearest proteins

Related proteins · sequence + function similarity

• Lymphocyte-specific helicase 0.91
• Lymphoid-specific helicase 0.90
• Lymphoid-specific helicase 0.89
• ATP-dependent chromatin remodeler CHD6 0.86
• ATP-dependent chromatin remodeler CHD6 0.86
• SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 0.85
• SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 0.84
• DNA excision repair protein ERCC-6-like 0.84
• SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 0.83
• ATP-dependent chromatin remodeler CHD6 0.83
• SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 0.83
• Probable ATP-dependent DNA helicase CHR719 0.83

Co-cited proteins · studied together in the literature

• Helicase protein MOM1 3 shared papers
• DNA (cytosine-5)-methyltransferase 1 3 shared papers
• Anaphase-promoting complex subunit 13 2 shared papers
• Histone-lysine N-methyltransferase MEDEA 2 shared papers
• Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 1 shared papers
• DNA-directed RNA polymerase IV subunit 1 1 shared papers
• Polycomb group protein FERTILIZATION-INDEPENDENT ENDOSPERM 1 shared papers
• Methyl-CpG-binding domain-containing protein 2 1 shared papers
• Methyl-CpG-binding domain-containing protein 5 1 shared papers
• Methyl-CpG-binding domain-containing protein 7 1 shared papers
• Methyl-CpG-binding domain-containing protein 6 1 shared papers
• Histone H3.3 1 shared papers

Literature · 46 cited papers

• Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Plant J. · 2017
• Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa. PLoS ONE · 2013
• Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA transcripts in Arabidopsis. PLoS ONE · 2009
• Invasion of the Arabidopsis genome by the tobacco retrotransposon Tnt1 is controlled by reversible transcriptional gene silencing. Plant Physiol. · 2008
• Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J. · 2007
• Differential epigenetic regulation within an Arabidopsis retroposon family. Genetics · 2007
• Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J. · 2007
• Epigenetic regulation of transcription in intermediate heterochromatin. EMBO Rep. · 2006
• Regulation of seed size by hypomethylation of maternal and paternal genomes. Plant Physiol. · 2006
• Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family in DNA damage response and recombination. Genetics · 2006
• DNA methylation increases throughout Arabidopsis development. Planta · 2005
• DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects their subnuclear localization. Plant Cell · 2005
• … and 34 more in the literature graph