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PMID: 18430920 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids.

Genetics ·Vol. 178 ·No. 4 ·2008-04-00 ·Pages 1845-58

Chen M, Ha M, Lackey E, Wang J, Chen ZJ

Abstract

Changes in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecica is a natural allotetraploid derived from the extant A. thaliana and A. arenosa genomes that are homeologous in the allotetraploid. Here we report that RNAi of met1 reduced DNA methylation and altered the expression of approximately 200 genes, many of which encode transposons, predicted proteins, and centromeric and heterochromatic RNAs. Reduced DNA methylation occurred frequently in promoter regions of the upregulated genes, and an En/Spm-like transposon was reactivated in met1-RNAi A. suecica lines. Derepression of transposons, heterochromatic repeats, and centromeric small RNAs was primarily derived from the A. thaliana genome, and A. arenosa homeologous loci were less affected by methylation defects. A high level of A. thaliana centromeric small RNA accumulation was correlated with hypermethylation of A. thaliana centromeres. The greater effects of reduced DNA methylation on transposons and centromeric repeats in A. thaliana than in A. arenosa are consistent with the repression of many genes that are expressed at higher levels in A. thaliana than in A. arenosa in the resynthesized allotetraploids. Moreover, non-CG (CC) methylation in the promoter region of A. thaliana At2g23810 remained in the resynthesized allotetraploids, and the methylation spread within the promoter region in natural A. suecica, leading to silencing of At2g23810. At2g23810 was demethylated and reactivated in met1-RNAi A. suecica lines. We suggest that many A. thaliana genes are transcriptionally repressed in resynthesized allotetraploids, and a subset of A. thaliana loci including transposons and centromeric repeats are heavily methylated and subjected to homeologous genome-specific RNA-mediated DNA methylation in natural allopolyploids.

MeSH Terms
Arabidopsis/genetics Arabidopsis Proteins/genetics Centromere/metabolism Chromosomes, Plant/genetics DNA (Cytosine-5-)-Methyltransferases/genetics DNA Methylation DNA Transposable Elements/genetics Gene Expression Regulation, Plant Genes, Plant Genome, Plant/genetics Heterochromatin/genetics Polyploidy Promoter Regions, Genetic/genetics RNA Interference RNA, Plant/genetics,metabolism RNA, Small Interfering/genetics,metabolism Up-Regulation/genetics
Chemicals
Arabidopsis Proteins DNA Transposable Elements Heterochromatin RNA, Plant RNA, Small Interfering MET1 protein, Arabidopsis DNA (Cytosine-5-)-Methyltransferases
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Chen Meng
Intercollegiate Genetics Program, Texas A&M University, College Station, Texas 77843, USA.
Ha Misook
Lackey Erika
Wang Jianlin
Chen Z Jeffrey
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Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
0016-6731
DOI
10.1534/genetics.107.086272
Published
2008-04-00
Pages
1845-58
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC2323781
Subset
IM
Grants
NIGMS NIH HHS · R01 GM067015 · United States
NIGMS NIH HHS · GM067015 · United States
External Links
PubMed source DOI: 10.1534/genetics.107.086272 PMC Full Text View journal details
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