Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Making Sense Of Junk RNA

Robert A. Martienssen¹ , Zach Lippman¹ , Bruce May¹ , Mikel Zaratiegui¹ , Danielle Irvine¹ , Derek Goto¹ , Zac Cande² , Yota Murakami³ , Vincent Colot⁴ , Rebecca W. Doerge⁵

¹  Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA

²  Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA

³  Department of Viral Oncology, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan

⁴  Unité de Recherche en Génomique Végétale (URGV), INRA/CNRS/UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France

⁵  Department of Statistics, Purdue University, West Lafayette, IN 47907, USA

Heterochromatin is composed of transposable elements (TE) and related repeats. Like transposable elements, heterochromatin silences genes located nearby, and plays a major role in
epigenetic regulation of the genome. Small interfering RNA corresponding to heterochromatic sequences can be detected in plants, animals and fission yeast, indicating that these sequences are transcribed. We have used tiling microarrays to examine these transcripts and their regulation in plants and fission yeast. In plants, small interfering RNAs(iRNA) corresponding to different classes of TE depends on DNA methyltransferase MET1, the SWI/SNF ATPase, DDM1, or both, but not on the histone deacetylase SIL1. All three genes are required for silencing transposons in the absence of RNAi. In fission yeast and in Arabidopsis, centromeric repeats are continually transcribed on one strand, but the transcripts are rapidly turned over by RNA interference, through the combined action of RNA polymerase II, and the Argonaute (RITS) and RNA dependent RNA polymerase (RdRP) complexes, each of which is associated with heterochromatin. Histone H3K9me2 depends in part on RNAi, mediated by the Rik1-Clr4 complex. Rik1 has similarity to both DNA and RNA binding proteins, and may play a role in RNA processing. In pombe, mating type silencing in the absence of RNAi depends on histone deacetylation, resembling Tf2 LTR retrotransposons in this respect. In Arabidopsis, LTR retroelements inserted into pericentromeric repeats can also silence them, in the absence of RNAi. Thus both RNAi-dependent and RNAi-independent mechanisms are required to silence different TEs, involving different histone modifications in each case.