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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.

SUBMITTER: Sun Q

PROVIDER: S-EPMC5144995 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus.

Sun Qianwen Q Csorba Tibor T Skourti-Stathaki Konstantina K Proudfoot Nicholas J NJ Dean Caroline C

Science (New York, N.Y.) 20130501 6132

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-stran ...[more]

PMID: 23641115

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