title: ATP-dependent chromatin remodeling shapes the long noncoding RNA landscape.
abstract: Long noncoding RNAs (lncRNAs) are pervasively transcribed across eukaryotic genomes, but functions of only a very small subset of them have been demonstrated. This has led to active debate about whether many of them have any biological functions. In addition, very few regulators of lncRNAs have been identified. We developed a novel genetic screen using reconstituted RNAi in Saccharomyces cerevisiae and systematically identified a large number of putative lncRNA repressors. Among them, we found that four highly conserved chromatin remodeling factors are global lncRNA repressors that play major roles in shaping the eukaryotic lncRNA transcriptome. Importantly, we identified >250 antisense lncRNAs (CRRATs [chromatin remodeling-repressed antisense transcripts]) whose repression by these chromatin remodeling factors is required for the maintenance of normal levels of overlapping mRNA transcripts. Our results strongly suggest that regulation of mRNA through repression of antisense lncRNAs is far more broadly used than previously appreciated.
authors.affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Molecular and Cellular Biology Program, Fred Hutchinson Cancer Research Center and University of Washington, Seattle, Washington 98195, USA.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Alcid
authors.affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
authors.forename: Toshio
authors.initials: T
authors.lastname: Tsukiyama
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly / Q000502:physiology*; D015966:Gene Expression Regulation, Fungal; D009154:Mutation; D034622:RNA Interference; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding; D000255:Adenosine Triphosphate
keywords: antisense RNAs; chromatin; chromatin remodeling; lncRNAs