DRD1 SNF2 domain-containing protein / helicase domain-containing protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: DRD1
Official Full Name: SNF2 domain-containing protein / helicase domain-containing protein
Primary source: TAIR:AT2G16390
Locus tag: AT2G16390
See related: Araport:AT2G16390
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: CHR35; DEFECTIVE IN MERISTEM SILENCING 1; DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1; DMS1; F16F14.11; F16F14_11
Summary: Putative chromatin remodeling protein, member of a plant-specific subfamily of SWI2/SNF2-like proteins. Mutations nearly eliminate non-CpG methylation at a target promoter but do not affect rDNA or centromere methylation. Cooperates with PolIVb to facilitate RNA-directed de novo methylation and silencing of homologous DNA. Endogenous targets include intergenic regions near retrotransposon LTRs or short RNA encoding sequences that might epigenetically regulate adjacent genes. May be used to establish a basal yet reversible level of silencing in euchromatin.
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Genomic context

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See DRD1 in Genome Data Viewer

Location:: chromosome: 2

Exon count:: 6

Sequence:: Chromosome: 2; NC_003071.7 (7097280..7101351)

Chromosome 2 - NC_003071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003071.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data show that all DDR complex components DNA-Directed RNA Polymerases (DRD1), defective in meristem silencing 3 (DMS3) and RNA-DIRECTED DNA METHYLATION 1 (RDM1) co-localize with RNA polymerase V (Pol V).
Title: CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation.
SWI2/SNF2 chromatin remodeling proteins such as DRD1 and DDM1 may influence leaf senescence possibly via epigenetic regulation
Title: A Mutation in Plant-Specific SWI2/SNF2-Like Chromatin-Remodeling Proteins, DRD1 and DDM1, Delays Leaf Senescence in Arabidopsis thaliana.
Genome-wide chromatin association of NRPE1 is dependent on all members of a putative chromatin-remodeling complex termed DDR, which includes the proteins DRD1, DMS3 and RDM1.
Title: DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons.
DRD1-Pol V-dependent de novo methylation may play a role in restraining the inappropriate silencing of active protein-coding genes in plants.
Title: DRD1-Pol V-dependent self-silencing of an exogenous silencer restricts the non-cell autonomous silencing of an endogenous target gene.
Pol IVb/Pol V function provides a solution to a paradox of epigenetic control: the need for transcription in order to transcriptionally silence the same region
Title: Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes.
DRD1, together with RNAi and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis.
Title: RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis.
DRD1 and Pol IVb establish a basal level of silencing that can potentially be reversed in euchromatin, and further reinforced in heterochromatin by other proteins that induce more stable modifications.[DRD1]
Title: Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis.
DRD1 is essential for RNA-directed de novo methylation and acts on different target promoters. [DRD1]
Title: A SNF2-like protein facilitates dynamic control of DNA methylation.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

NM_127193.2

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables ATP-dependent chromatin remodeler activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent constitutive heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to exogenous dsRNA	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within defense response to fungus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epigenetic regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gene silencing by siRNA-directed DNA methylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA methylation-dependent heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of chromatin binding	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within siRNA processing	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
part_of RNA polymerase IV transcription regulator complex	IMP Inferred from Mutant Phenotype more info	PubMed
part_of RNA polymerase V complex	IMP Inferred from Mutant Phenotype more info	PubMed
NOT located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info
located_in pericentric heterochromatin	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: SNF2 domain-containing protein / helicase domain-containing protein

NP_179232.1

DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1); FUNCTIONS IN: helicase activity, DNA binding, ATP binding, nucleic acid binding; INVOLVED IN: DNA methylation, production of siRNA involved in RNA interference; LOCATED IN: cellular_component unknown; EXPRESSED IN: 9 plant structures; EXPRESSED DURING: 6 growth stages; CONTAINS InterPro DOMAIN/s: DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), SNF2-related (InterPro:IPR000330); BEST Arabidopsis thaliana protein match is: chromatin remodeling 34 (TAIR:AT2G21450.1); Has 13448 Blast hits to 11886 proteins in 1506 species: Archae - 91; Bacteria - 3564; Metazoa - 3285; Fungi - 3284; Plants - 1229; Viruses - 105; Other Eukaryotes - 1890 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_003071.7 Reference assembly

Range

7097280..7101351

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001335476.1 → NP_001324537.1 SNF2 domain-containing protein / helicase domain-containing protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A178VR01, A0A1P8B0G3, A0A384KTB7, A0A7G2E6P8

Conserved Domains (2) summary

cd18793
Location:689 → 826

SF2_C_SNF; C-terminal helicase domain of the SNF family helicases

cd18007
Location:353 → 569

DEXHc_ATRX-like; DEXH-box helicase domain of ATRX-like proteins
NM_127193.2 → NP_179232.1 SNF2 domain-containing protein / helicase domain-containing protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_179232.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9SIW2

UniProtKB/TrEMBL

A0A7G2E6P8

Conserved Domains (3) summary

smart00487
Location:349 → 555

DEXDc; DEAD-like helicases superfamily

pfam00271
Location:695 → 812

Helicase_C; Helicase conserved C-terminal domain

cl21455
Location:349 → 495

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases