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Regulation of expression of the rice SINE, p-SINE1, by siRNA

Research Project

Project/Area Number 18570003
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Genetics/Genome dynamics
Research InstitutionThe University of Tokyo

Principal Investigator

TSUCHIMOTO Suguru  The University of Tokyo, Institute of Molecular and Cellular Biosciences, Assistant Professor (60212057)

Project Period (FY) 2006 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥3,780,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥480,000)
Fiscal Year 2007: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2006: ¥1,700,000 (Direct Cost: ¥1,700,000)
Keywordsrice / SINE / siRNA / retroposon / epigenetic / DNA methylation
Research Abstract

To elucidate the repression mechanism of expression of the rice SINE, p-SINE1, we detected p-SINE1 siRNA by northern analysis using low-molecular-weight RNA purified from transgenic rice cell lines in which expression of each of five rice DCL genes (DCL1 - DCL5) were suppressed. We found that the p-SINE1 siRNA level was reduced in all of the suppression lines, especially in DCL3 and DCL5 suppression lines. This suggests that several DCL proteins, especially DCL3 and DCL5, are involved in production of p-SINE1 siRNA. We then detected p-SINE1 transcripts by northern analysis using total RNA purified from the same cell lines. We found that the p-SINE1 expression level significantly increased in DCL3 and DCL5 suppression lines. These strongly suggest that p-SINE1 siRNA is involved in repression of the p-SINE1 expression. We then examined DNA methylation of p-SINE1 sequences in these cell lines, but could not find correlation between decrease of DNA methylation level of p-SINE1 members and increase of the p-SINE1 expression level. This suggests that the mechanism other than DNA methylation is involved in repression of the p-SINE1 expression.
We also identified three new rice SINEs, OsSN1-OsSN3, which are different from p-SINE1. These had poly (A) sequences at the 3'ends, unlike p-SINE1, and showed no homology to p-SINE1. They, however, preferentially exist in gene-rich regions of chromosomes, like p-SINE1. We found that more than 20% of OsSN3 exist in introns. This suggests that siRNA generated from these SINEs possibly affects expression of genes nearby.

Report

(3 results)
  • 2007 Annual Research Report   Final Research Report Summary
  • 2006 Annual Research Report
  • Research Products

    (10 results)

All 2008 2007 2006

All Journal Article (9 results) (of which Peer Reviewed: 2 results) Presentation (1 results)

  • [Journal Article] New SINE families from rice, OsSN, with poly (A) at the 3' ends.2008

    • Author(s)
      Suguru Tsuchimoto, et al.
    • Journal Title

      Genes & Genetic Systems 83

      Pages: 227-236

    • NAID

      10024396176

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] OsRecQ1, a QDE-3 homologue in rice, is required for RNA silencing induced by particle bombardment for inverted repeat DNA, but notfor double-stranded RNA.2008

    • Author(s)
      Hui Chen, et al.
    • Journal Title

      The Plant Journal 56

      Pages: 274-286

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] New SINE families from rice, OsSN, with poly(A) at the 31 ends.2008

    • Author(s)
      Suguru Tsuchimoto, et al.
    • Journal Title

      Genes & Genetic Systems 83

      Pages: 227-236

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] OsRecQl, a QDE-3 homologue in rice, is required for RNA silencing induced by particle bombardment for inverted repeat DNA, but not for double-stranded RNA.2008

    • Author(s)
      Hui Chen, et al.
    • Journal Title

      The Plant Journal 56

      Pages: 274-286

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] New SINE families from rice, OsSN, with poly(A) at the 3' ends2008

    • Author(s)
      Suguru Tsuchimoto
    • Journal Title

      Genes & Genetic Systems 83

      Pages: 227-236

    • NAID

      10024396176

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] OsRecQ1, a QDE-3 homologue in rice, is required for RNA silencing induced by particle bombardment for inverted repeat DNA, but not for double-stranded RNA2008

    • Author(s)
      Hui Chen
    • Journal Title

      The Plant Journal 56

      Pages: 274-286

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Phylogenetic analysis of Oryza rufipogon strains and their relations to Oryza sativa strains by insertion polymorphism of rice SINEs.2007

    • Author(s)
      Jian-Hong Xu, et al.
    • Journal Title

      Genes & Genetic Systems 82

      Pages: 217-229

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Phylogenetic analysis of Oryza rufipogon strains and their relations to Oryza sativa strains by insertion polymorphism of rice SINEs.2007

    • Author(s)
      Jiang-Hong Xu, et al.
    • Journal Title

      Genes & Genetic Systems 82

      Pages: 217-229

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] イネのレトロポゾンSINE2006

    • Author(s)
      土本 卓
    • Journal Title

      化学と生物 44・2

      Pages: 93-101

    • Related Report
      2006 Annual Research Report
  • [Presentation] イネ科植物に広く分布するSINE, OsSN2007

    • Author(s)
      土本卓
    • Organizer
      日本遺伝学会第79回大会
    • Place of Presentation
      岡山大学理学部
    • Year and Date
      2007-09-19
    • Related Report
      2007 Annual Research Report

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Published: 2006-04-01   Modified: 2016-04-21  

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