Molecular basis of plant-based SUVH6 enzyme catalytic site-specific H3K9 methylation

The international academic journal PNAS published a research paper
entitled "Molecular Basis of Locus-specific H3K9 Methylation Catalyzed by SUVH6 in Plants" in collaboration between Duan Chengguo Research Group of the Center for Excellence in Molecular Plant Science of the Chinese Academy of Sciences and Du Jiamu Research Group of Southern University of Science and Technology.
The study revealed a novel mechanism
of conserved SUVH6 histone methyltransferase family catalytic site-specific H3K9 methylation in plants.
In this mechanism, an unresolved peptide structure at the N-terminus of the SUVH6 family can be specifically recognized
by the BAH domain of the chromatin regulator ASI1.
The SUVH6-ASI1 module controls the deposition of H3K9me2 on most SUVH6 targets and produces different regulatory patterns for gene expression depending on the location of the target site, including transcriptional silencing or post-transcriptional regulation
.
What's more, this mechanism and its key amino acid sites persist in plants, suggesting a co-evolution
between SUVH6 and ASI1.

As a marker of eukaryotic heterochromatin, histone H3K9 methylation also plays a regulatory role
in the autochromatin region.
H3K9me2 in the model plant Arabidopsis thaliana is mainly catalyzed by SUVH4 (KYP), SUVH5 and SUVH6, and there is a positive feedback regulation with DNA methylation to enhance heterochromatinization
in this region.
Among them, SUHV4 is the most important catalytic enzyme, and SUVH5 and SUVH6 have certain functional redundancy
as auxiliary enzymes.
However, in addition to DNA methylation-mediated mechanisms of SUVH recruitment, it is unclear whether there are other mechanisms in plants that more finely determine the specificity of the site catalyzed by
SUVH.

The team identified ASI1
, an interaction protein of SUVH6 by immunoprecipitation mass spectrometry in Arabidopsis thaliana and rice, respectively.
ASI1 is a key component of the AAE (Asi1-Aipp1-Edm2) complex discovered by Duan's group to identify H3K9me2 and control RNA processing (Duan et al.
, 2017; You et al.
, 2021; Zhang et al.
, 2021）
。 After protein truncation interaction experiments, the interaction was localized to a n-terminal segment of the SUVH6 family protein that had never been reported, and biochemical evidence showed that this peptide was necessary
for the interaction between SUVH6 and ASI1 。 Through cooperation with Professor Du Jiamu's research group, the high-resolution crystal structure of ASI1-BAH domain and SUVH-N-terminal polypeptide was analyzed, and it was found that ASI1-BAH has a classical aromatic cage that can specifically identify arginine residues at the N-terminus of SUVH6 through cation-π interaction, and this single arginine residue plays a decisive role
in ASI1-SUVH6 interaction 。 Chromatin immunoprecipitation sequencing (ChIP-seq) analysis showed that most of the chromatin sites bound by SUVH6 were covered by ASI1, and the localization of ASI1 and SUVH6 on the common target depended on this interaction, and the mutation of key arginine could directly affect the chromatin localization
of SUVH6 。 H3K9me2 ChIP-seq analysis showed that the ASI1-SUVH6 interaction module promotes the deposition of H3K9me2 at the target site and affects gene expression in a position-dependent manner: promoting transcriptional silencing or full-length transcript processing
of post-transcriptional mRNA.
Interestingly, the N-terminal polypeptides of ASI and SUVH6 are only present in plants and are expressed simultaneously in most plants, suggesting evolutionary consistency
.
In conclusion, the study identified a conservative H3K9me2 self-reinforcing positive feedback loop in plants that interacts with DNA methylation-mediated SUVH histone methyltransferase recruitment mechanism to enhance the deposition
of H3K9me2 at specific chromatin sites.

Jian Zhang, a doctoral student at the Center for Excellence in Molecular Plant Science, Jianlong Yuan, a graduate doctoral student, and Juncheng Lin, an associate professor at Fujian Agriculture and Forestry University, are co-first authors
of the paper.
Professor Duan Chengguo of the Center of Excellence in Molecular Plants of the Chinese Academy of Sciences and Professor Du Jiamu of Southern University of Science and Technology are co-corresponding authors
of the paper.
The research was supported
by the pilot project of the Chinese Academy of Sciences, the Shenzhen Science and Technology Program Project, and the Guangdong Provincial Key Laboratory of Molecular Design of Plant Cell Factory in Ordinary Universities.

Link to paper: style="box-sizing: border-box; margin-top: 0px; margin-bottom: 20px; line-height: 1.
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Figure 1.
A.
Schematic diagram of the structure of the N-terminal conserved peptide of the SUVH6 family and the BAH of the ASI1 family; B-C.
Schematic diagram of the interaction structure and key amino acids between ASI1-BAH and SUVH-N peptides; D-F.
Colocalization and interdependence of ASI1 and SUVH6 on chromatin; G.
APA sites controlled by ASI1-SUVH6 modules in rice; H.
Schematic diagram of the co-evolution of the SUVH family of plant populations

Figure 2.
A working model of the SUVH6-ASI1 module regulating H3K9me2 deposition and gene expression