Tatsuo Kanno ¹, M. Florian Mette ², David P. Kreil ³, Werner Aufsatz ¹, Marjori Matzke ¹ *, and Antonius J.M. Matzke ¹

¹ Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, UZAII, Althanstrasse 14, A-1090 Vienna, Austria
² Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, D-06466 Gatersleben, Germany
³ Department of Genetics/Inference Group, University of Cambridge, Cambridge, CB2 3EH, United Kingdom

^*Correspondence: Marjori Matzke: +43-662-63961-26 (phone): +43-662-63961-53 (fax)
E-mail:  marjori.matzke@gmi.oeaw.ac.at

In plants, the mechanism by which RNA can induce de novo cytosine methylation of homologous DNA is
poorly understood. Cytosines in all sequence contexts become modified in response to RNA signals [1, 2].
Recent work has implicated the de novo DNA methyltransferases (DMTases), DRM1 and DRM2, in
establishing RNA-directed methylation of the constitutive nopaline synthase promoter [3], as well as the
DMTase MET1 [4] and the putative histone deacetylase HDA6 [5] in maintaining or enhancing CpG
methylation induced by RNA. Despite the identification of enzymes that catalyze epigenetic modifications in
response to RNA signals, it is unclear how RNA targets DNA for methylation. A screen for mutants defective
in RNA-directed DNA methylation identified a novel putative chromatin-remodeling protein, DRD1. This
protein belongs to a previously undefined, plant-specific subfamily of SWI2/SNF2-like proteins most similar to
the RAD54/ATRX subfamily. In drd1 mutants, RNA-induced non-CpG methylation is almost eliminated at a
target promoter, resulting in reactivation, whereas methylation of centromeric and rDNA repeats is unaffected.
Thus, unlike the SNF2-like proteins DDM1/Lsh1 [6, 7] and ATRX [8, 9], which regulate methylation of
repetitive sequences, DRD1 is not a global regulator of cytosine methylation. DRD1 is the first SNF2-like
protein implicated in an RNA-guided, epigenetic modification of the genome.

1. Sleutels F, Zwart R, and Barlow DP, "The non-coding Air RNA is required for silencing autosomal imprinted genes".

2. Sleutels F, Tjon G, Ludwig T, and Barlow DP, "Imprinted silencing of Slc22a2 and Slc22a3 does not need transcriptional overlap between Igf2r and Air".

3. Seitz H, Youngson N, Lin S-P, Dalbert S, Paulsen M, Bachellerie J-P, Ferguson-Smith AC, and Cavaille J, "Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene".

4. Dallosso AR, Hancock AL, Brown KW, Williams AC, Jackson S, and Malik K, "Genomic imprinting at the WT1 gene involves a novel coding transcript (AWT1) that shows deregulation in Wilms' tumours".

5. Nikaido I, Saito C, Wakamoto A, Tomaru Y, Arakawa T, Hayashizaki Y, and Okazaki Y, "EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes".

6. Han M-H, Goud S, Song L, and Fedoroff N, "The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation".

7. Lai EC, Wiel C, and Rubin GM, "Complementary miRNA pairs suggest a regulatory role for miRNA:miRNA duplexes".

8. Sen G, Wehrman TS, Myers JW, and Blau HM, "Restriction enzyme-generated siRNA (REGS) vectors and libraries".

Further Topics in:  Euchromatin,  active DNA, and  RNA  ribo-regulators:

Links to Euchromatin Activator RNA Reviews:
Links to Euchromatin Activator RNA Research:
Links to Ultrastructural Probes of DNase I-Sensitive Sites:
Links to RNA as a Therapeutic Agent:
Links to Hodgkin Lymphoma Immuno-Pathology:
Links to Activated T-Lymphocyte Immunotherapy:
Links to Medical Systems Biology:

"Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".

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