An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs

Nucleic Acids Research
Takako OhyamaPiero Carninci

Abstract

Long non-coding RNAs (lncRNAs) are attracting widespread attention for their emerging regulatory, transcriptional, epigenetic, structural and various other functions. Comprehensive transcriptome analysis has revealed that retrotransposon elements (REs) are transcribed and enriched in lncRNA sequences. However, the functions of lncRNAs and the molecular roles of the embedded REs are largely unknown. The secondary and tertiary structures of lncRNAs and their embedded REs are likely to have essential functional roles, but experimental determination and reliable computational prediction of large RNA structures have been extremely challenging. We report here the nuclear magnetic resonance (NMR)-based secondary structure determination of the 167-nt inverted short interspersed nuclear element (SINE) B2, which is embedded in antisense Uchl1 lncRNA and upregulates the translation of sense Uchl1 mRNAs. By using NMR 'fingerprints' as a sensitive probe in the domain survey, we successfully divided the full-length inverted SINE B2 into minimal units made of two discrete structured domains and one dynamic domain without altering their original structures after careful boundary adjustments. This approach allowed us to identify a structured do...Continue Reading

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Citations

Jan 10, 2021·International Journal of Molecular Sciences·Guendalina FroechlichNicola Zambrano
Oct 9, 2021·Essays in Biochemistry·Stefano EspinozaStefano Gustincich

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Datasets Mentioned

BETA
GSE146407

Methods Mentioned

BETA
nuclear magnetic resonance
NMR
electrophoresis
in
PCR
icSHAPE
footprinting

Software Mentioned

Mfold
icSHAPE
ImageJ
IGV Genome Viewer
RNAstructure
Vsfold5
Sparky
RNAfold
forna
TopSpin

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