Global Mapping of Human RNA-RNA Interactions

Sharma, Eesha; Sterne-Weiler, Tim; O’Hanlon, Dave; Blencowe, Benjamin J.

doi:10.1016/j.molcel.2016.04.030

Cited by 335 publications

(455 citation statements)

References 38 publications

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“…Likewise, a reagent that could distinguish between protections arising from protein binding and those arising from base pairing would yield a quantum advance by providing comprehensive data on base pairing along transcripts and across transcriptomes. Some progress has been made very recently in this direction (3,70,96). Such probes would help determine the extent to which the above-mentioned discrepancies regarding in vivo versus in vitro protections that have arisen in structure-probing studies are the result of protein binding in vivo or of RNA refolding in nonbiological test-tube conditions.…”

Section: Challenges and Future Directionsmentioning

confidence: 99%

Genome-Wide Analysis of RNA Secondary Structure

Bevilacqua¹,

Ritchey²,

et al. 2016

Annu. Rev. Genet.

210

157

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Single-stranded RNA molecules fold into extraordinarily complicated secondary and tertiary structures as a result of intramolecular base pairing. In vivo, these RNA structures are not static. Instead, they are remodeled in response to changes in the prevailing physicochemical environment of the cell and as a result of intermolecular base pairing and interactions with RNAbinding proteins. Remarkable technical advances now allow us to probe RNA secondary structure at single-nucleotide resolution and genome-wide, both in vitro and in vivo. These data sets provide new glimpses into the RNA universe. Analyses of RNA structuromes in HIV, yeast, Arabidopsis, and mammalian cells and tissues have revealed regulatory effects of RNA structure on messenger RNA (mRNA) polyadenylation, splicing, translation, and turnover. Application of new methods for genome-wide identification of mRNA modifications, particularly methylation and pseudouridylation, has shown that the RNA "epitranscriptome" both influences and is influenced by RNA structure. In this review, we describe newly developed genome-wide RNA structure-probing methods and synthesize the information emerging from their application.

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Section: Challenges and Future Directionsmentioning

confidence: 99%

Genome-Wide Analysis of RNA Secondary Structure

Bevilacqua¹,

Ritchey²,

et al. 2016

Annu. Rev. Genet.

210

157

View full text Add to dashboard Cite

show abstract

“…RNA followed by high-throughput sequencing) [45] ( Figure 3C), and MARIO (mapping RNA interactome in vivo) ( Figure 3D) [46]. PARIS employs a psoralenderivative 4′-aminomethyltrioxsalen (AMT) as the nucleic acid cross-linker to cross-link RNA base pairs in living cells [41].…”

Section: Transcriptome-wide Methodsmentioning

confidence: 99%

“…Sequencing-based techniques has characterized more and more novel snoRNA-involved RRIs [34,41,43,45]. In Ref.…”

Section: Snorna Related Interactionsmentioning

confidence: 99%

“…For instance, RNA duplexes usually migrate slower in electrophoresis gel, allowing them to be separated from non-interacting RNA fragments [22,23]. Recently, with the advent of next generation sequencing, new techniques based on deep sequencing have been developed to reveal the full network of RRIs, i.e., the interactome, for all transcripts in a cell [41,43,45,46]. They can also be used to study all interactions concerning a certain RNA, usually combined with RNA pull-down with a set of target-specific antisense probes [38,39].…”

Section: Introductionmentioning

confidence: 99%

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Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale

Gong

Шао

et al. 2018

Quant Biol

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Background: RNA molecules play crucial roles in various biological processes. Their regulation and function are mediated by interacting with other molecules. Among them RNA-RNA interactions (RRIs) are important in many basic cellular activities including transcription, RNA processing, localization, and translation. However, we just start to unveil the complexity of the knowledge and underlying mechanisms of RRIs. Results: In this review, we will summarize approaches for RRI identifications, including both conventional, focused biophysical and biochemical methods and recently developed large scale sequencing-based techniques. We will also discuss discoveries per RRI type revealed by using these technologies, as well as challenges towards a systematic and functional understanding of RRIs. Conclusions: The development of sequencing-based techniques has revolutionized the study of RRIs. Applying these techniques in multiple organisms has identified thousands of RRIs, many of which could potentially regulate multiple aspects of gene expression. However, despite the great breakthrough, the RNA-RNA interactome of any species remains far from complete due to intrinsic complex nature of RRI and limitations in current techniques. More efficient experimental methods and computational framework are needed to obtain the full image of RRI networks, and their possible regulatory roles in biology and medicine.

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“…However, all these methods require prior knowledge of the interacting protein partner for affinity purification and may lead to a high false‐positive detections due to in vitro cross‐linking 110.…”

Section: Next‐generation Sequencing‐based Methods For Global Investigmentioning

confidence: 99%

State of the art technologies to explore long non‐coding RNAs in cancer

Salehi

Taheri

Azarpira

et al. 2017

J Cellular Molecular Medi

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Long non‐coding RNAs (lncRNAs) comprise a vast repertoire of RNAs playing a wide variety of crucial roles in tissue physiology in a cell‐specific manner. Despite being engaged in myriads of regulatory mechanisms, many lncRNAs have still remained to be assigned any functions. A constellation of experimental techniques including single‐molecule RNA in situ hybridization (sm‐RNA FISH), cross‐linking and immunoprecipitation (CLIP), RNA interference (RNAi), Clustered regularly interspaced short palindromic repeats (CRISPR) and so forth has been employed to shed light on lncRNA cellular localization, structure, interaction networks and functions. Here, we review these and other experimental approaches in common use for identification and characterization of lncRNAs, particularly those involved in different types of cancer, with focus on merits and demerits of each technique.

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Global Mapping of Human RNA-RNA Interactions

Cited by 335 publications

References 38 publications

Genome-Wide Analysis of RNA Secondary Structure

Genome-Wide Analysis of RNA Secondary Structure

Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale

State of the art technologies to explore long non‐coding RNAs in cancer

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