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Mol Cell. 2014 May 8;54(3):418-30. doi: 10.1016/j.molcel.2014.03.019. Epub 2014 Apr 10.

An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis.

Author information

1
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA. Electronic address: zhang731@purdue.edu.
2
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
3
Shanghai Center for Plant Stress Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
4
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
5
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; Shanghai Center for Plant Stress Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. Electronic address: jkzhu@purdue.edu.

Abstract

Rrp6-mediated nuclear RNA surveillance tunes eukaryotic transcriptomes through noncoding RNA degradation and mRNA quality control, including exosomal RNA decay and transcript retention triggered by defective RNA processing. It is unclear whether Rrp6 can positively regulate noncoding RNAs and whether RNA retention occurs in normal cells. Here we report that AtRRP6L1, an Arabidopsis Rrp6-like protein, controls RNA-directed DNA methylation through positive regulation of noncoding RNAs. Discovered in a forward genetic screen, AtRRP6L1 mutations decrease DNA methylation independently of exosomal RNA degradation. Accumulation of Pol V-transcribed scaffold RNAs requires AtRRP6L1 that binds to RNAs in vitro and in vivo. AtRRP6L1 helps retain Pol V-transcribed RNAs in chromatin to enable their scaffold function. In addition, AtRRP6L1 is required for genome-wide Pol IV-dependent siRNA production that may involve retention of Pol IV transcripts. Our results suggest that AtRRP6L1 functions in epigenetic regulation by helping with the retention of noncoding RNAs in normal cells.

PMID:
24726328
PMCID:
PMC4023806
DOI:
10.1016/j.molcel.2014.03.019
[Indexed for MEDLINE]
Free PMC Article
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