MBD9 methyl-CPG-binding domain 9 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: MBD9
Official Full Name: methyl-CPG-binding domain 9
Primary source: TAIR:AT3G01460
Locus tag: AT3G01460
See related: Araport:AT3G01460
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: ATMBD9; methyl-CPG-binding domain 9; T13O15.10; T13O15_10
Summary: Encodes a protein with a methyl-CpG-binding domain. Has sequence similarity to human MBD proteins. Involved in the modification of the FLC chromatin acetylation state to affect FLC expression. Mutants show an early flowering, and enhanced shoot branching phenotypes.
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Genomic context

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See MBD9 in Genome Data Viewer

Location:: chromosome: 3

Exon count:: 10

Sequence:: Chromosome: 3; NC_003074.8 (173190..182454)

Chromosome 3 - NC_003074.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003074.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Methyl-CpG-BINDING DOMAIN 9 (MBD9), is required for H2A.Z incorporation at thousands of genomic sites that share a distinct histone modification profile. The histone binding properties of MBD9 suggest that it may guide H2A.Z deposition to specific sites by interacting with modified nucleosomes and with the H2A.Z deposition complex.
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.
MBD9 is a SWR1-C interacting protein required for H2A.Z deposition at a subset of actively transcribing genes.
Title: Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition.
AtMBD9 controls flowering time and axillary branching by modulating gene expression through DNA methylation and histone acetylation.
Title: AtMBD9 modulates Arabidopsis development through the dual epigenetic pathways of DNA methylation and histone acetylation.

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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_111012.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables histone acetyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	IPI Inferred from Physical Interaction more info	PubMed
enables methyl-CpG binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Process	Evidence Code	Pubs
involved_in epigenetic regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within photoperiodism, flowering	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within secondary shoot formation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Swr1 complex	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 plasmodesma	HDA more info	PubMed

General protein information

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Preferred Names: methyl-CPG-binding domain 9

NP_186795.1

methyl-CPG-binding domain 9 (MBD9); FUNCTIONS IN: methyl-CpG binding, DNA binding; INVOLVED IN: photoperiodism, flowering, secondary shoot formation, regulation of transcription, DNA-dependent; LOCATED IN: nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, RING-type (InterPro:IPR001841), FY-rich, C-terminal (InterPro:IPR003889), Zinc finger, PHD-type (InterPro:IPR001965), FY-rich, N-terminal (InterPro:IPR003888), DNA-binding, integrase-type (InterPro:IPR016177), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Methyl-CpG DNA binding (InterPro:IPR001739), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: RING/FYVE/PHD-type zinc finger family protein (TAIR:AT1G77250.1); Has 6416 Blast hits to 3988 proteins in 224 species: Archae - 0; Bacteria - 0; Metazoa - 4085; Fungi - 602; Plants - 1260; Viruses - 0; Other Eukaryotes - 469 (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_003074.8 Reference assembly

Range

173190..182454

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_111012.4 → NP_186795.1 methyl-CPG-binding domain 9 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_186795.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9SGH2, Q9SSA6

UniProtKB/TrEMBL

A0A178VJY9, A0A5S9X859, A0A654F351

Conserved Domains (6) summary

cd15519
Location:1289 → 1334

PHD1_Lid2p_like; PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins

pfam01429
Location:258 → 311

MBD; Methyl-CpG binding domain

cl02608
Location:1312 → 1390

BAH; or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...

cl02650
Location:413 → 453

FYRN; F/Y-rich N-terminus

cl02651
Location:671 → 695

FYRC; F/Y rich C-terminus

cl22851
Location:86 → 130

PHD_SF; PHD finger superfamily