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DDM1 (decrease in DNA methylation) genes in rice (Oryza sativa).

Hiromi Higo1, Muhammad Tahir, Kazuya Takashima

  • 1CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan.

Molecular Genetics and Genomics : MGG
|August 24, 2012
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Summary

Researchers identified two rice genes, OsDDM1a and OsDDM1b, similar to Arabidopsis DDM1, crucial for maintaining plant DNA methylation. Knockdown of OsDDM1a in rice caused genomic hypomethylation, affecting repetitive sequences and increasing transposon activity.

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Area of Science:

  • Plant Molecular Biology
  • Epigenetics
  • Genomics

Background:

  • Cytosine methylation is crucial for plant epigenetic regulation and development.
  • Arabidopsis thaliana's Decrease in DNA Methylation 1 (DDM1) is a key regulator, but its homologs in other plants are understudied.
  • Understanding DDM1 homologs is vital for agricultural applications.

Purpose of the Study:

  • To identify and characterize DDM1 homologs in rice (Oryza sativa).
  • To investigate the function of rice DDM1 homologs in regulating genomic DNA methylation.
  • To explore the potential of these homologs in functional genomics and transposon research.

Main Methods:

  • Bioinformatic analysis to identify rice genes similar to Arabidopsis DDM1.
  • Cloning and expression of rice DDM1 homologs (OsDDM1a and OsDDM1b) in transgenic rice.
  • Analysis of genomic DNA methylation levels in transgenic rice lines using antisense expression of OsDDM1a.
  • Quantification of transcript levels for transposon-related loci.

Main Results:

  • Two rice genes, OsDDM1a and OsDDM1b, were identified with high amino acid sequence identity (93%).
  • Both OsDDM1a and OsDDM1b are transcribed during rice development.
  • Antisense expression of OsDDM1a in transgenic rice led to significant genomic DNA hypomethylation.
  • Repetitive DNA sequences were more affected by hypomethylation than single-copy sequences.
  • Transcripts from endogenous transposon-related loci were upregulated in OsDDM1a knockdown lines.

Conclusions:

  • OsDDM1a and OsDDM1b are functional homologs of Arabidopsis DDM1 in rice.
  • OsDDM1a plays a critical role in maintaining DNA methylation in rice, particularly in repetitive regions.
  • The study opens avenues for utilizing active transposons in rice functional genomics through manipulation of OsDDM1 homologs.