title: R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus.
abstract: Roles for long noncoding RNAs (lncRNAs) in gene expression are emerging, but regulation of the lncRNA itself is poorly understood. We have identified a homeodomain protein, AtNDX, that regulates COOLAIR, a set of antisense transcripts originating from the 3' end of Arabidopsis FLOWERING LOCUS C (FLC). AtNDX associates with single-stranded DNA rather than double-stranded DNA non-sequence-specifically in vitro, and localizes to a heterochromatic region in the COOLAIR promoter in vivo. Single-stranded DNA was detected in vivo as part of an RNA-DNA hybrid, or R-loop, that covers the COOLAIR promoter. R-loop stabilization mediated by AtNDX inhibits COOLAIR transcription, which in turn modifies FLC expression. Differential stabilization of R-loops could be a general mechanism influencing gene expression in many organisms.
authors: Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
authors: Qianwen
authors: Q
authors: Sun
authors: Tibor
authors: T
authors: Csorba
authors: Konstantina
authors: K
authors: Skourti-Stathaki
authors: Nicholas J
authors: NJ
authors: Proudfoot
authors: Caroline
authors: C
authors: Dean
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D002843:Chromatin / Q000378:metabolism; D018744:DNA, Plant / Q000737:chemistry / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D018398:Homeodomain Proteins / Q000737:chemistry / Q000378:metabolism*; D026161:MADS Domain Proteins / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D016372:RNA, Antisense / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D061806:Transcription Termination, Genetic; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D018744:DNA, Plant; D004277:DNA, Single-Stranded; C418902:At5g10140 protein, Arabidopsis; D018398:Homeodomain Proteins; D026161:MADS Domain Proteins; C581154:NDX protein, Arabidopsis; D016372:RNA, Antisense; D062085:RNA, Long Noncoding; D018749:RNA, Plant
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