Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.
Methylcytosine-binding proteins decipher the epigenetic information encoded by DNA methylation and provide a link between DNA methylation, modification of chromatin structure, and gene silencing. VARIANT IN METHYLATION 1 (VIM1) encodes an SRA (SET- and RING-associated) domain methylcytosine-binding protein in Arabidopsis thaliana, and loss of VIM1 function causes centromere DNA hypomethylation and centromeric heterochromatin decondensation in interphase. In the Arabidopsis genome, there are five VIM genes that share very high sequence similarity and encode proteins containing a PHD domain, two RING domains, and an SRA domain. To gain further insight into the function and potential redundancy among the VIM proteins, we investigated strains combining different vim mutations and transgenic vim knock-down lines that down-regulate multiple VIM family genes. The vim1 vim3 double mutant and the transgenic vim knock-down lines showed decreased DNA methylation primarily at CpG sites in genic regions, as well as repeated sequences in heterochromatic regions. In addition, transcriptional silencing was released in these plants at most heterochromatin regions examined. Interestingly, the vim1 vim3 mutant and vim knock-down lines gained ectopic CpHpH methylation in the 5S rRNA genes against a background of CpG hypomethylation. The vim1 vim2 vim3 triple mutant displayed abnormal morphological phenotypes including late flowering, which is associated with DNA hypomethylation of the 5' region of FWA and release of FWA gene silencing. Our findings demonstrate that VIM1, VIM2, and VIM3 have overlapping functions in maintenance of global CpG methylation and epigenetic transcriptional silencing.
Woo
Hye Ryun
HR
Department of Biology, Washington University in St Louis, St Louis, Missouri, United States of America.
Dittmer
Travis A
TA
Richards
Eric J
EJ
D017360:Arabidopsis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D004275:DNA, Ribosomal / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015226:Dinucleoside Phosphates / Q000235:genetics / Q000378:metabolism*; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D006570:Heterochromatin / Q000235:genetics / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D005810:Multigene Family; D009154:Mutation; D017434:Protein Structure, Tertiary; D012341:RNA, Ribosomal, 5S / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
D029681:Arabidopsis Proteins; D004248:DNA (Cytosine-5-)-Methyltransferases; D018744:DNA, Plant; D004275:DNA, Ribosomal; D004268:DNA-Binding Proteins; D015226:Dinucleoside Phosphates; D006570:Heterochromatin; D018398:Homeodomain Proteins; D012341:RNA, Ribosomal, 5S; D014157:Transcription Factors; C416366:FWA protein, Arabidopsis; C518284:VIM1 protein, Arabidopsis; C531561:VIM2 protein, Arabidopsis; C531562:VIM3 protein, Arabidopsis; C015772:CpG dinucleotide; C499608:MET1 protein, Arabidopsis