The Elaborate Architecture of Rna

Dolgin, Elie

doi:10.1038/523398a

Cited by 4 publications

(2 citation statements)

References 7 publications

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“…These simulations may remind us of the proximity-guided search model proposed by Quinodoz and Guttman [22], in which lncRNAs localize to target sites on genomes with a probability in proportion to its concentration with spatial gradient locally generated in the nucleus. In our model, however, there might be additional factors to be considered, one of which is the three-dimensional complex structures of the lncRNAs [56], which would determine distance between the two motifs, referred to here as linkers, and more conceivably, accessibilities around their target sites on genomes.…”

Section: Resultsmentioning

confidence: 99%

Convergence in LINE-1 nucleotide variations can benefit redundantly forming triplexes with lncRNA in mammalian X-chromosome inactivation

2019

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Background Associations between X-inactive transcript (Xist)–long noncoding RNA (lncRNA) and chromatin are critical intermolecular interactions in the X-chromosome inactivation (XCI) process. Despite high-resolution analyses of the Xist RNA-binding sites, specific interaction sequences are yet to be identified. Based on elusive features of the association between Xist RNA and chromatin and the possible existence of multiple low-affinity binding sites in Xist RNA, we defined short motifs (≥5 nucleotides), termed as redundant UC/TC (r-UC/TC) or AG (r-AG) motifs, which may help in the mediation of triplex formation between the lncRNAs and duplex DNA. Results The study showed that r-UC motifs are densely dispersed throughout mouse and human Xist/XIST RNAs, whereas r-AG motifs are even more densely dispersed along opossum RNA-on-the-silent X (Rsx) RNA, and also along both full-length and truncated long interspersed nuclear elements (LINE-1s, L1s) of the three species. Predicted secondary structures of the lncRNAs showed that the length range of these sequence motifs available for forming triplexes was even shorter, mainly 5- to 9-nucleotides long. Quartz crystal microbalance (QCM) measurements and Monte Carlo (MC) simulations indicated that minimum-length motifs can reinforce the binding state by increasing the copy number of the motifs in the same RNA or DNA molecule. Further, r-AG motifs in L1s had a similar length-distribution pattern, regardless of the similarities in the length or sequence of L1s across the three species; this also applies to high-frequency mutations in r-AG motifs, which suggests convergence in L1 sequence variations. Conclusions Multiple short motifs in both RNA and duplex DNA molecules could be brought together to form triplexes with either Hoogsteen or reverse Hoogsteen hydrogen bonding, by which their associations are cooperatively enhanced. This novel triplex interaction could be involved in associations between lncRNA and chromatin in XCI, particularly at the sites of L1s. Potential binding of Xist/XIST/Rsx RNAs specifically at L1s is most likely preserved through the r-AG motifs conserved in mammalian L1s through convergence in L1 nucleotide variations and by maintaining a particular r-UC/r-AG motif ratio in each of these lncRNAs, irrespective of their poorly conserved sequences. Electronic supplementary material The online version of this article (10.1186/s13100-019-0173-4) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Convergence in LINE-1 nucleotide variations can benefit redundantly forming triplexes with lncRNA in mammalian X-chromosome inactivation

2019

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“…1 DNA generally forms a predictable double helix, while RNA consists of a single strand that folds into elaborate bulges, loops, hairpins, pseudo-knots, hammerheads, and other threedimensional conformations. 2,3 RNA folding is an indispensable process underlying RNA function, and it delineates the process by which an RNA molecule transitions from an unfolded/disordered state to the native/functional conformation. 4,5 The desire to know the diverse functions of RNA has driven extensive research to uncover details of its folding.…”

Section: Introductionmentioning

confidence: 99%

Regulatory effects of cotranscriptional RNA structure formation and transitions

Liu

Zhang

2016

WIREs RNA

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RNAs, which play significant roles in many fundamental biological processes of life, fold into sophisticated and precise structures. RNA folding is a dynamic and intricate process, which conformation transition of coding and noncoding RNAs form the primary elements of genetic regulation. The cellular environment contains various intrinsic and extrinsic factors that potentially affect RNA folding in vivo, and experimental and theoretical evidence increasingly indicates that the highly flexible features of the RNA structure are affected by these factors, which include the flanking sequence context, physiochemical conditions, cis RNA-RNA interactions, and RNA interactions with other molecules. Furthermore, distinct RNA structures have been identified that govern almost all steps of biological processes in cells, including transcriptional activation and termination, transcriptional mutagenesis, 5'-capping, splicing, 3'-polyadenylation, mRNA export and localization, and translation. Here, we briefly summarize the dynamic and complex features of RNA folding along with a wide variety of intrinsic and extrinsic factors that affect RNA folding. We then provide several examples to elaborate RNA structure-mediated regulation at the transcriptional and posttranscriptional levels. Finally, we illustrate the regulatory roles of RNA structure and discuss advances pertaining to RNA structure in plants. WIREs RNA 2016, 7:562-574. doi: 10.1002/wrna.1350 For further resources related to this article, please visit the WIREs website.

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RNA sequencing as a tool for understanding biological complexity of abiotic stress in plants

Malik¹

2015

J. Plant Biochem. Biotechnol.

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The Elaborate Architecture of Rna

Cited by 4 publications

References 7 publications

Convergence in LINE-1 nucleotide variations can benefit redundantly forming triplexes with lncRNA in mammalian X-chromosome inactivation

Convergence in LINE-1 nucleotide variations can benefit redundantly forming triplexes with lncRNA in mammalian X-chromosome inactivation

Regulatory effects of cotranscriptional RNA structure formation and transitions

RNA sequencing as a tool for understanding biological complexity of abiotic stress in plants

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