Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factora1

Gomafu (also referred to as RNCR2/MIAT) was originally identified as a noncoding RNA expressed in a particular set of neurons. Unlike protein-coding mRNAs, the Gomafu RNA escapes nuclear export and stably accumulates in the nucleus, making a unique nuclear compartment. Although recent studies have r...

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Bibliographic Details
Published in:Genes to cells : devoted to molecular & cellular mechanisms 2011-05, Vol.16 (5), p.479-490
Main Authors: Tsuiji, Hitomi, Yoshimoto, Rei, Hasegawa, Yuko, Furuno, Masaaki, Yoshida, Minoru, Nakagawa, Shinichi
Format: Article
Language:English
Subjects:
Conserved sequence
Evolution
Exons
genomics
Introns
Kinetics
Molecular modelling
mRNA
Neurons
Nuclear transport
Nucleotide sequence
RNA
RNA transport
Saccharomyces cerevisiae
splicing factors
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Summary:Gomafu (also referred to as RNCR2/MIAT) was originally identified as a noncoding RNA expressed in a particular set of neurons. Unlike protein-coding mRNAs, the Gomafu RNA escapes nuclear export and stably accumulates in the nucleus, making a unique nuclear compartment. Although recent studies have revealed the functional relevance of Gomafu in a series of physiological processes, the underlying molecular mechanism remains largely uncharacterized. In this report, we identified a chicken homologue of Gomafu using a comparative genomic approach to search for functionally important and conserved sequence motifs among evolutionarily distant species. Unexpectedly, we found that all Gomafu RNA examined shared a distinctive feature: tandem repeats of UACUAAC, a sequence that has been identified as a conserved intron branch point in the yeast Saccharomyces cerevisiae. The tandem UACUAAC Gomafu RNA repeats bind to the SF1 splicing factor with a higher affinity than the divergent branch point sequence in mammals, which affects the kinetics of the splicing reaction in vitro. We propose that the Gomafu RNA regulates splicing efficiency by changing the local concentration of splicing factors within the nucleus.
ISSN:1356-9597
1365-2443
DOI:10.1111/j.1365-2443.2011.01502.x