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Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing

J. Armando Casas-Mollano, Jennifer Rohr, Eun-Jeong Kim, Eniko Balassa, Karin van Dijk and Heriberto Cerutti
Genetics May 1, 2008 vol. 179 no. 1 69-81; https://doi.org/10.1534/genetics.107.086546
J. Armando Casas-Mollano
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Jennifer Rohr
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Eun-Jeong Kim
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Eniko Balassa
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Karin van Dijk
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Heriberto Cerutti
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Abstract

Small RNA-guided gene silencing is an evolutionarily conserved process that operates by a variety of molecular mechanisms. In multicellular eukaryotes, the core components of RNA-mediated silencing have significantly expanded and diversified, resulting in partly distinct pathways for the epigenetic control of gene expression and genomic parasites. In contrast, many unicellular organisms with small nuclear genomes seem to have lost entirely the RNA-silencing machinery or have retained only a basic set of components. We report here that Chlamydomonas reinhardtii, a unicellular eukaryote with a relatively large nuclear genome, has undergone extensive duplication of Dicer and Argonaute polypeptides after the divergence of the green algae and land plant lineages. Chlamydomonas encodes three Dicers and three Argonautes with DICER-LIKE1 (DCL1) and ARGONAUTE1 being more divergent than the other paralogs. Interestingly, DCL1 is uniquely involved in the post-transcriptional silencing of retrotransposons such as TOC1. Moreover, on the basis of the subcellular distribution of TOC1 small RNAs and target transcripts, this pathway most likely operates in the nucleus. However, Chlamydomonas also relies on a DCL1-independent, transcriptional silencing mechanism(s) for the maintenance of transposon repression. Our results suggest that multiple, partly redundant epigenetic processes are involved in preventing transposon mobilization in this green alga.

Footnotes

  • Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession no. EU368690.

  • ↵1 These authors contributed equally to this work.

  • ↵2 Present address: Department of Biology, Creighton University, Omaha, NE 68178.

  • Communicating editor: S. Dutcher

  • Received December 28, 2007.
  • Accepted March 5, 2008.
  • Copyright © 2008 by the Genetics Society of America
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PUBLICATION INFORMATION

Volume 179 Issue 1, May 2008

Genetics: 179 (1)

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Special Section: Chlamydomonas
Chlamydomonas Investigations
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Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing

J. Armando Casas-Mollano, Jennifer Rohr, Eun-Jeong Kim, Eniko Balassa, Karin van Dijk and Heriberto Cerutti
Genetics May 1, 2008 vol. 179 no. 1 69-81; https://doi.org/10.1534/genetics.107.086546
J. Armando Casas-Mollano
  • Find this author on Google Scholar
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Jennifer Rohr
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Eun-Jeong Kim
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Eniko Balassa
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Karin van Dijk
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Heriberto Cerutti
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Citation

Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing

J. Armando Casas-Mollano, Jennifer Rohr, Eun-Jeong Kim, Eniko Balassa, Karin van Dijk and Heriberto Cerutti
Genetics May 1, 2008 vol. 179 no. 1 69-81; https://doi.org/10.1534/genetics.107.086546
J. Armando Casas-Mollano
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jennifer Rohr
  • Find this author on Google Scholar
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Eun-Jeong Kim
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  • Search for this author on this site
Eniko Balassa
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  • Search for this author on this site
Karin van Dijk
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Heriberto Cerutti
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  • Reconstructing the Mitochondrial Protein Import Machinery of Chlamydomonas reinhardtii
  • Gene Expression Profiling of Flagellar Disassembly in Chlamydomonas reinhardtii
  • Metabolomics- and Proteomics-Assisted Genome Annotation and Analysis of the Draft Metabolic Network of Chlamydomonas reinhardtii
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