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

Journal article

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: Sun, Q; Csorba, T; Skourti-Stathaki, K; Proudfoot, N; Dean, C

• Publication status: Published
• Journal: Science (New York, N.Y.)
• Volume: 340
• Issue: 6132
• Pages: 619-621
• Publication date: 2013-05-01
• DOI: 10.1126/science.1234848
• EISSN: 1095-9203
• ISSN: 0036-8075
• Language: English
• Keywords: Gene Expression Regulation, Plant; Molecular Sequence Data; Arabidopsis; Arabidopsis Proteins; RNA, Antisense; RNA, Plant; Chromatin; DNA, Single-Stranded; Transcription, Genetic; Nucleic Acid Conformation; RNA, Long Untranslated; Amino Acid Sequence; MADS Domain Proteins; Homeodomain Proteins; Protein Binding; Transcription Termination, Genetic; Promoter Regions, Genetic; DNA, Plant