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Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin
- Source :
- Nature Communications, Vol 9, Iss 1, Pp 1-14 (2018), Nature Communications
- Publication Year :
- 2018
- Publisher :
- Nature Publishing Group, 2018.
-
Abstract
- Heterochromatin is a tightly packed form of chromatin that is associated with DNA methylation and histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2-binding protein, Agenet domain (AGD)-containing p1 (AGDP1), in Arabidopsis thaliana. Here we find that AGDP1 can specifically recognize the H3K9me2 mark by its three pairs of tandem AGDs. We determine the crystal structure of the Agenet domain 1 and 2 cassette (AGD12) of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 specifically recognizes the H3K4me0 and H3K9me2 marks by hydrogen bonding and hydrophobic interactions. In addition, we find that AGDP1 is required for transcriptional silencing, non-CG DNA methylation, and H3K9 dimethylation at some loci. ChIP-seq data show that AGDP1 preferentially occupies long transposons and is associated with heterochromatin marks. Our findings suggest that, as a heterochromatin-binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions.<br />DNA methylation and H3K9 dimethylation are two linked epigenetic marks of silenced chromatin in plants that depend on the activity of CMT3/2 and SUVH4/5/6. Here the authors identify AGDP1 as an H3K9me2-binding protein required for heterochromatic non-CG DNA methylation, H3K9 dimethylation, and transcriptional silencing.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Heterochromatin
Science
Arabidopsis
General Physics and Astronomy
01 natural sciences
DNA-binding protein
General Biochemistry, Genetics and Molecular Biology
Article
Protein Structure, Secondary
03 medical and health sciences
Epigenetics
Amino Acid Sequence
Gene Silencing
lcsh:Science
Regulation of gene expression
Multidisciplinary
biology
Chemistry
Arabidopsis Proteins
Lysine
General Chemistry
Methylation
DNA Methylation
Chromatin
Cell biology
030104 developmental biology
Histone
Genetic Loci
DNA methylation
biology.protein
DNA Transposable Elements
lcsh:Q
Peptides
010606 plant biology & botany
Protein Binding
Subjects
Details
- Language :
- English
- ISSN :
- 20411723
- Volume :
- 9
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Nature Communications
- Accession number :
- edsair.doi.dedup.....29f508a9b2435baf7710ef7794644f2c