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

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 domain in nucleotides 31–119 of the inverted SINE B2. This approach will be applicable to determining the structures of other regulatory lncRNAs.

Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids

“…We also showed that IGF1-AS interacts with IGF1 mRNA, creating a 182-bp lncRNA/IGF1 mRNA duplex (Figure S4B), and we do not detect differential expression between small and large dogs for either the lncRNA or IGF1 mRNA (Figure S4C). Knowing that antisense overlapping lncRNAs can regulate mRNA translation rate with no effect on mRNA levels, 29,30 it is possible that IGF1-AS could act as a regulatory mechanism associated with IGF-1 production, perhaps by affecting the affinity of a ribosomal binding motif for the C versus T allele.…”

Structures and target RNA preferences of the RNA-binding protein family of IGF2BPs: An overview

“…We and ll Structure 29, August 5, 2021 11 others have shown the power of combined methods to structurally investigate large RNAs, including entire mRNA UTRs (Kim et al, 2020;Wacker et al, 2020). In particular, SAXS and NMR together provide complementary structural information (Chen et al, 2012;Rambo and Tainer, 2010), recently applied to long non-coding RNAs (lncRNAs) (Ohyama et al, 2020;Zhang et al, 2019). For IMP target RNA arrays, such approaches are promising for both RNA and IMP RNPs.…”

Generation of a Novel Mesothelin-Targeted Oncolytic Herpes Virus and Implemented Strategies for Manufacturing

“…Amatuximab was produced by ourselves by subcloning the variable region of SS1_scFv into Fc-expressing vectors as described previously [ 91 , 92 ]. Antibody was produced by transfection of the expression vectors into the production enhanced cell line HEK293_ES1 [ 93 ] expressing the long non-coding SINEUP [ 94 ] targeting heavy and light chains signal peptide on mRNAs. Monoclonal antibody was purified from cell supernatant by protein A affinity chromatography.…”