Study of an RNA helicase implicates small RNA–noncoding RNA interactions in programmed DNA elimination in Tetrahymena

Lucia Aronica; Janna Bednenko; Tomoko Noto; Leroi V. DeSouza; K.W. Michael Siu; Josef Loidl; Ronald E. Pearlman; Martin A. Gorovsky; Kazufumi Mochizuki

doi:10.1101/gad.481908

Study of an RNA helicase implicates small RNA–noncoding RNA interactions in programmed DNA elimination in Tetrahymena

¹ Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), A-1030 Vienna, Austria;
² Department of Biology, University of Rochester, Rochester, New York 14627, USA;
³ Department of Chemistry and Center for Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada;
⁴ Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria;
⁵ Department of Biology and Center for Research in Mass Spectronomy, York University, Toronto, Ontario M3J 1P3, Canada

↵6 These authors contributed equally to this work.

Abstract

Tetrahymena eliminates micronuclear-limited sequences from the developing macronucleus during sexual reproduction. Homology between the sequences to be eliminated and ∼28-nucleotide small RNAs (scnRNAs) associated with an Argonaute family protein Twi1p likely underlies this elimination process. However, the mechanism by which Twi1p–scnRNA complexes identify micronuclear-limited sequences is not well understood. We show that a Twi1p-associated putative RNA helicase Ema1p is required for the interaction between Twi1p and chromatin. This requirement explains the phenotypes of EMA1 KO strains, including loss of selective down-regulation of scnRNAs homologous to macronuclear-destined sequences, loss of H3K9 and K27 methylation in the developing new macronucleus, and failure to eliminate DNA. We further demonstrate that Twi1p interacts with noncoding transcripts derived from parental and developing macronuclei and this interaction is greatly reduced in the absence of Ema1p. We propose that Ema1p functions in DNA elimination by stimulating base-pairing interactions between scnRNAs and noncoding transcripts in both parental and developing new macronuclei.

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Footnotes

↵7 Corresponding author.

↵7 E-MAIL kazufumi.mochizuki{at}imba.oeaw.ac.at; FAX 43-1-79044-110.
Supplemental material is available at http://www.genesdev.org.
Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.481908.
- Received April 7, 2008.
- Accepted June 25, 2008.