Nucleic Acids Research Advance Access originally published online on December 22, 2008
Nucleic Acids Research 2009 37(3):903-915; doi:10.1093/nar/gkn1018
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Nucleic Acids Research, 2009, Vol. 37, No. 3 903-915
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia
1Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, 2CNRS, UMR8541, 46 rue d’Ulm, 75005 Paris, 3Université de Lyon, F-69000, Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
*To whom correspondence should be addressed. Tel: +33 1 44 32 39 48; Fax: +33 1 44 32 39 41; Email: emeyer{at}biologie.ens.fr
Received September 11, 2008. Revised December 4, 2008. Accepted December 7, 2008.
Distinct small RNA pathways are involved in the two types of homology-dependent effects described in Paramecium tetraurelia, as shown by a functional analysis of Dicer and Dicer-like genes and by the sequencing of small RNAs. The siRNAs that mediate post-transcriptional gene silencing when cells are fed with double-stranded RNA (dsRNA) were found to comprise two subclasses. DCR1-dependent cleavage of the inducing dsRNA generates 
23-nt primary siRNAs from both strands, while a different subclass of 24-nt RNAs, characterized by a short untemplated poly-A tail, is strictly antisense to the targeted mRNA, suggestive of secondary siRNAs that depend on an RNA-dependent RNA polymerase. An entirely distinct pathway is responsible for homology-dependent regulation of developmental genome rearrangements after sexual reproduction. During early meiosis, the DCL2 and DCL3 genes are required for the production of a highly complex population of 25-nt scnRNAs from all types of germline sequences, including both strands of exons, introns, intergenic regions, transposons and Internal Eliminated Sequences. A prominent 5'-UNG signature, and a minor fraction showing the complementary signature at positions 21–23, indicate that scnRNAs are cleaved from dsRNA precursors as duplexes with 2-nt 3' overhangs at both ends, followed by preferential stabilization of the 5'-UNG strand.
Present addresses: Gersende Lepère, Laboratoire de Biologie Cellulaire, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), 78026 Versailles Cedex, France
Mariusz Nowacki, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA Vincent Serrano, Institut de Génétique Humaine, Centre National de la Recherche Scientifique, 34396 Montpellier Cedex 5, France
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