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PMID: 23641115 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Science (New York, N.Y.) ·Vol. 340 ·No. 6132 ·2013-05-03 ·Pages 619-21

Sun Q, Csorba T, Skourti-Stathaki K, Proudfoot NJ, Dean C

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.

MeSH Terms
Amino Acid Sequence Arabidopsis/genetics,metabolism Arabidopsis Proteins/chemistry,genetics,metabolism Chromatin/metabolism DNA, Plant/chemistry,metabolism DNA, Single-Stranded/chemistry,metabolism Gene Expression Regulation, Plant Homeodomain Proteins/chemistry,metabolism MADS Domain Proteins/genetics,metabolism Molecular Sequence Data Nucleic Acid Conformation Promoter Regions, Genetic Protein Binding RNA, Antisense/chemistry,genetics,metabolism RNA, Long Noncoding/chemistry,genetics,metabolism RNA, Plant/chemistry,genetics,metabolism Transcription Termination, Genetic Transcription, Genetic
Chemicals
Arabidopsis Proteins Chromatin DNA, Plant DNA, Single-Stranded FLF protein, Arabidopsis Homeodomain Proteins MADS Domain Proteins NDX protein, Arabidopsis RNA, Antisense RNA, Long Noncoding RNA, Plant
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Sun Qianwen
Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
Csorba Tibor
Skourti-Stathaki Konstantina
Proudfoot Nicholas J
Dean Caroline
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Article Info
Journal
Science (New York, N.Y.)
Abbr.
Science
ISSN
1095-9203
DOI
10.1126/science.1234848
Published
2013-05-03
Pages
619-21
Language
English
Region
United States
NLM ID
0404511
PMCID
PMC5144995
Subset
IM
Grants
Wellcome Trust · 091805 · United Kingdom
Biotechnology and Biological Sciences Research Council · BBS/E/J/000CA369 · United Kingdom
Corrections
CommentIn
PMID: 23746348
External Links
PubMed source DOI: 10.1126/science.1234848 PMC Full Text View journal details
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