@article{f4f86f17267c47869d8d57de0617c634,
title = "A SWI/SNF Chromatin-Remodeling Complex Acts in Noncoding RNA-Mediated Transcriptional Silencing",
abstract = "RNA-mediated transcriptional silencing prevents deleterious effects of transposon activity and controls the expression of protein-coding genes. It involves long noncoding RNAs (lncRNAs). In Arabidopsis thaliana, some of those lncRNAs are produced by a specialized RNA Polymerase V (Pol V). The mechanism by which lncRNAs affect chromatin structure and mRNA production remains mostly unknown. Here we identify the SWI/SNF ATP-dependent nucleosome-remodeling complex as a component of the RNA-mediated transcriptional silencing pathway. We found that SWI3B, an essential subunit of the SWI/SNF complex, physically interacts with a lncRNA-binding protein, IDN2. SWI/SNF subunits contribute to lncRNA-mediated transcriptional silencing. Moreover, Pol V mediates stabilization of nucleosomes on silenced regions. We propose that Pol V-produced lncRNAs mediate transcriptional silencing by guiding the SWI/SNF complex and establishing positioned nucleosomes on specific genomic loci. We further propose that guiding ATP-dependent chromatin-remodeling complexes may be a more general function of lncRNAs.",
author = "Yongyou Zhu and Rowley, {M. Jordan} and Gudrun B{\"o}hmdorfer and Wierzbicki, {Andrzej T.}",
note = "Funding Information: We thank Ken Cadigan and David Engelke for critical reading of the manuscript, Eva Czarnecka-Verner, Steve Jacobsen, and Tomasz Sarnowski for reagents, and David Akey for helpful suggestions. We also thank Robert Lyons and Brendan Tarrier from the University of Michigan DNA Sequencing Core for performing next generation sequencing. This work was supported by National Science Foundation grant MCB 1120271 to A.T.W. and Austrian Science Fund (FWF) fellowship J3199-B09 to G.B. M.J.R. was supported by the NIH National Research Service Award number 5-T32-GM07544. Y.Z. initiated the yeast two-hybrid screen, performed all protein-protein interaction experiments, obtained and analyzed IDN2 M8 mutant and transgenic plants, performed RT-PCRs shown in Figures 3 A–3E and 4 A–4C, performed all DNA methylation assays, and generated anti-IDN2 and anti-SWI3B antibodies. M.J.R performed all ChIP and ChIP-seq experiments as well as all bioinformatic analyses. G.B. performed RNA IP shown in Figures 1 A and 1B, RT-PCR shown in Figures 4 D–4H, and prepared samples for RNA-seq and MNase-seq. A.T.W. wrote the manuscript. ",
year = "2013",
month = jan,
day = "24",
doi = "10.1016/j.molcel.2012.11.011",
language = "English (US)",
volume = "49",
pages = "298--309",
journal = "Molecular Cell",
issn = "1097-2765",
publisher = "Cell Press",
number = "2",
}