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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.

Original publication

DOI

10.1126/science.1234848

Type

Journal article

Journal

Science

Publication Date

03/05/2013

Volume

340

Pages

619 - 621

Keywords

Amino Acid Sequence, Arabidopsis, Arabidopsis Proteins, Chromatin, DNA, Plant, DNA, Single-Stranded, Gene Expression Regulation, Plant, Homeodomain Proteins, MADS Domain Proteins, Molecular Sequence Data, Nucleic Acid Conformation, Promoter Regions, Genetic, Protein Binding, RNA, Antisense, RNA, Long Noncoding, RNA, Plant, Transcription Termination, Genetic, Transcription, Genetic