title: The SRA methyl-cytosine-binding domain links DNA and histone methylation.
abstract: Epigenetic gene silencing suppresses transposon activity and is critical for normal development . Two common epigenetic gene-silencing marks are DNA methylation and histone H3 lysine 9 dimethylation (H3K9me2). In Arabidopsis thaliana, H3K9me2, catalyzed by the methyltransferase KRYPTONITE (KYP/SUVH4), is required for maintenance of DNA methylation outside of the standard CG sequence context. Additionally, loss of DNA methylation in the met1 mutant correlates with a loss of H3K9me2. Here we show that KYP-dependent H3K9me2 is found at non-CG methylation sites in addition to those rich in CG methylation. Furthermore, we show that the SRA domain of KYP binds directly to methylated DNA, and SRA domains with missense mutations found in loss-of-function kyp mutants have reduced binding to methylated DNA in vitro. These data suggest that DNA methylation is required for the recruitment or activity of KYP and suggest a self-reinforcing loop between histone and DNA methylation. Lastly, we found that SRA domains from two Arabidopsis SRA-RING proteins also bind methylated DNA and that the SRA domains from KYP and SRA-RING proteins prefer methylcytosines in different sequence contexts. Hence, unlike the methyl-binding domain (MBD), which binds only methylated-CpG sequences, the SRA domain is a versatile new methyl-DNA-binding motif.
authors.affiliation: Life Science Core Curriculum, University of California, Los Angeles, Los Angeles, California 90095, USA.
authors.forename: Lianna M
authors.initials: LM
authors.lastname: Johnson
authors.forename: Magnolia
authors.initials: M
authors.lastname: Bostick
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhang
authors.forename: Edward
authors.initials: E
authors.lastname: Kraft
authors.forename: Ian
authors.initials: I
authors.lastname: Henderson
authors.forename: Judy
authors.initials: J
authors.lastname: Callis
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D047369:Chromatin Immunoprecipitation; D019175:DNA Methylation; D005455:Fluorescent Antibody Technique; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000378:metabolism*; D008969:Molecular Sequence Data; D020125:Mutation, Missense / Q000235:genetics; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D029681:Arabidopsis Proteins; D006657:Histones; D011495:Histone-Lysine N-Methyltransferase; C471228:SUVH4 protein, Arabidopsis; C506468:SUVH6 protein, Arabidopsis