Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

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.

Multitrait genome‐wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits

“…Another gene associated with leaf morphology, Potri.001G173900, encodes a Tudor-like RNA-binding protein with conserved ENT and Agenet domains. There is emerging evidence that the latter domain may be involved in transcriptional regulation in Arabidopsis (Zhang C. et al, 2018). This gene was co-expressed with 49 other genes with putative roles in protein degradation or RNA regulation, as well as nine genes with annotations related to carbohydrate metabolism (Tables S6, S7).…”

The Long-Sought-After Plant Heterochromatin Protein 1

“…Using a 3D-carbene SPRi platform to screen Arabidopsis ''Royal Family'' proteins that contain the Chromo, Tudor, PWWP, MBT, or Agenet domains, Shuai Zhao and colleagues from Tsinghua University, China, identified an Agenet domain-containing protein (ADCP1) showing strong binding activity preferentially with H3K9me2 peptide (Zhao et al, 2019). Meanwhile, Cuijun Zhang and colleagues from Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences identified AGDP1, identical to ADCP1, by incubating nuclear extracts of Arabidopsis flowers with synthesized biotinylated H3K9me peptides followed by mass spectrometry analysis (Zhang et al, 2018). ADCP1/AGDP1 contains six conserved Agenet domains arranged as three tandem cassettes.…”

“…ADCP1/AGDP1 contains six conserved Agenet domains arranged as three tandem cassettes. Both Zhang et al (2018) and Zhao et al (2019) solved the structures of tandem Agenet domains in complex with an H3K9me2 peptide. Structure analyses revealed that the H3K9me2 peptide adopts a unique a helix and is well accommodated by an aromatic cage formed by two agent domains.…”

“…Structure analyses revealed that the H3K9me2 peptide adopts a unique a helix and is well accommodated by an aromatic cage formed by two agent domains. Because the aromatic cages formed by ADCP1/AGDP1 are relatively narrow and covered by the negatively charged residues, leading to preferential binding with the free proton-containing dimethyllysine (Zhang et al, 2018). ADCP1/AGDP1 co-localizes in vivo with H3K9me2 and is significantly enriched in heterochromatin regions, most of which contain transposable elements (TEs), especially long TEs.…”

“…Consistently, biochemical and molecular analyses using adcp1/agdp1 mutants indicated that ADCP1/ AGDP1 is required for maintaining global H3K9me2 and CHG/ CHH (H refers to A, T, or C) methylation levels, and plays an important role in transcriptional silencing of TEs. More specifically, SUVH4/5/6-dependent CHG and CHH methylation are affected in agdp1 (Zhang et al, 2018). It is known that the methyltransferases SUVH4/5/6 mediate H3K9 dimethylation in Arabidopsis.…”