DML1 demeter-like 1 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: DML1
Official Full Name: demeter-like 1
Primary source: TAIR:AT2G36490
Locus tag: AT2G36490
See related: Araport:AT2G36490
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: AtROS1; demeter-like 1; F1O11.12; F1O11_12; REPRESSOR OF SILENCING1; ROS1
Summary: A repressor of transcriptional gene silencing. Functions by demethylating the target promoter DNA. Interacts physically with RPA2/ROR1. In the ros1 mutants, an increase in methylation is observed in a number of gene promoters. Among the loci affected by ros1, a few (RD29A and At1g76930) are affected in cytosine methylation in all sequence contexts (CpG, CpNpG or CpNpN), although many others are affected primarily in non-CpG contexts.
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Genomic context

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See DML1 in Genome Data Viewer

Location:: chromosome: 2

Exon count:: 21

Sequence:: Chromosome: 2; NC_003071.7 (15307907..15314807, complement)

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?

The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions.
Title: The Arabidopsis active demethylase ROS1 cis-regulates defence genes by erasing DNA methylation at promoter-regulatory regions.
Regulation of DNA (de)Methylation Positively Impacts Seed Germination during Seed Development under Heat Stress.
Title: Regulation of DNA (de)Methylation Positively Impacts Seed Germination during Seed Development under Heat Stress.
SIZ1-Mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis.
Title: SIZ1-Mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis.
ound that DOGL4 negatively affects seed dormancy and response to the phytohormone abscisic acid and that ROS1 controls these processes by regulating DOGL4
Title: DNA demethylase ROS1 negatively regulates the imprinting of DOGL4 and seed dormancy in Arabidopsis thaliana.
DDB2 forms a complex with ROS1 and AGO4 and that they act at the ROS1 locus to modulate levels of DNA methylation and therefore ROS1 expression. DDB2 acts as a critical regulator of ROS1-mediated active DNA demethylation.
Title: Dual control of ROS1-mediated active DNA demethylation by DNA damage-binding protein 2 (DDB2).
Results provide evidence that ROS1 expression is regulated by MET18 which is required for its activity. ROS1 binds to the iron-sulfur cluster of MET18.
Title: The cytosolic Fe-S cluster assembly component MET18 is required for the full enzymatic activity of ROS1 in active DNA demethylation.
ROS1 preferentially targets transposable elements (TEs) and intergenic regions. Compared with most TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting that ROS1 may prevent DNA methylation spreading from TEs to nearby genes.
Title: The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications.
Transgenic tobacco overexpressing AtROS1 showed tolerance to salt stress that could have been due to the higher expression levels of the genes encoding enzymes of the flavonoid biosynthetic and antioxidant pathways.
Title: AtROS1 overexpression provides evidence for epigenetic regulation of genes encoding enzymes of flavonoid biosynthesis and antioxidant pathways during salt stress in transgenic tobacco.
Our results suggest that ROS1-mediated active DNA demethylation requires MET18-dependent transfer of the iron-sulfur cluster, highlighting an important role of the CIA pathway in epigenetic regulation.
Title: MET18 Connects the Cytosolic Iron-Sulfur Cluster Assembly Pathway to Active DNA Demethylation in Arabidopsis.
We propose that the ROS1 locus functions as an epigenetic rheostat, tuning the level of demethylase activity in response to methylation alterations, thus ensuring epigenomic stability.
Title: Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_129207.5

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA N-glycosylase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA N-glycosylase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables DNA N-glycosylase activity	TAS Traceable Author Statement more info	PubMed
enables DNA demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA demethylase activity	IEA Inferred from Electronic Annotation more info
enables DNA demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-(apurinic or apyrimidinic site) endonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-(apurinic or apyrimidinic site) endonuclease activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables class I DNA-(apurinic or apyrimidinic site) endonuclease activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in base-excision repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within defense response to fungus	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: demeter-like 1

NP_181190.3

demeter-like 1 (DML1); FUNCTIONS IN: protein binding, DNA N-glycosylase activity, DNA-(apurinic or apyrimidinic site) lyase activity; INVOLVED IN: DNA repair, chromatin silencing, negative regulation of chromatin silencing, DNA methylation, DNA demethylation; LOCATED IN: nucleus; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: DNA glycosylase (InterPro:IPR011257), Endonuclease III-like, iron-sulphur cluster loop motif (InterPro:IPR003651), HhH-GPD domain (InterPro:IPR003265); BEST Arabidopsis thaliana protein match is: HhH-GPD base excision DNA repair family protein (TAIR:AT5G04560.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (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

15307907..15314807 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_129207.5 → NP_181190.3 demeter-like 1 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_181190.3

Status: REVIEWED

UniProtKB/Swiss-Prot

Q7Y1X6, Q9SJQ6

UniProtKB/TrEMBL

A0A654F0U0

Conserved Domains (3) summary

smart00478
Location:886 → 1035

ENDO3c; endonuclease III

pfam15628
Location:1280 → 1381

RRM_DME; RRM in Demeter

pfam15629
Location:1250 → 1277

Perm-CXXC; Permuted single zf-CXXC unit