scholarly journals CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data

2022 ◽  
Vol 8 (1) ◽  
pp. 6
Author(s):  
Wei-Sheng Wu ◽  
Jordan S. Brown ◽  
Pin-Hao Chen ◽  
Sheng-Cian Shiue ◽  
Dong-En Lee ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Web Server ◽  
Published Data ◽  
Base Pairing ◽  
Target Molecules ◽  
Non Coding Rnas ◽  
Regulatory Rnas ◽  
Pairing Interactions

Non-coding RNAs, such as miRNAs and piRNAs, play critical roles in gene regulation through base-pairing interactions with their target molecules. The recent development of the crosslinking, ligation, and sequencing of hybrids (CLASH) method has allowed scientists to map transcriptome-wide RNA–RNA interactions by identifying chimeric reads consisting of fragments from regulatory RNAs and their targets. However, analyzing CLASH data requires scientists to use advanced bioinformatics, and currently available tools are limited for users with little bioinformatic experience. In addition, many published CLASH studies do not show the full scope of RNA–RNA interactions that were captured, highlighting the importance of reanalyzing published data. Here, we present CLASH Analyst, a web server that can analyze raw CLASH data within a fully customizable and easy-to-use interface. CLASH Analyst accepts raw CLASH data as input and identifies the RNA chimeras containing the regulatory and target RNAs according to the user’s interest. Detailed annotation of the captured RNA–RNA interactions is then presented for the user to visualize within the server or download for further analysis. We demonstrate that CLASH Analyst can identify miRNA- and piRNA-targeting sites reported from published CLASH data and should be applicable to analyze other RNA–RNA interactions. CLASH Analyst is freely available for academic use.

scholarly journals Clues of in vivo nuclear gene regulation by mitochondrial short non-coding RNAs

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marco Passamonti ◽  
Marco Calderone ◽  
Manuel Delpero ◽  
Federico Plazzi
Keyword(s):  
Gene Regulation ◽  
Nuclear Gene ◽  
Non Coding Rnas ◽  
Nuclear Gene Regulation

scholarly journals Processing of Intron-Encoded Box C/D Small Nucleolar RNAs Lacking a 5′,3′-Terminal Stem Structure

2000 ◽  
Vol 20 (13) ◽  
pp. 4522-4531 ◽  
Author(s):  
Xavier Darzacq ◽  
Tamás Kiss
Keyword(s):  
Metabolic Stability ◽  
Small Nucleolar Rnas ◽  
Base Pairing ◽  
Flanking Sequences ◽  
Pairing Interactions ◽  
Precursor Rna ◽  
Nucleolar Rnas ◽  
Stem Structure

ABSTRACT The C and D box-containing (box C/D) small nucleolar RNAs (snoRNAs) function in the nucleolytic processing and 2′-O-methylation of precursor rRNA. In vertebrates, most box C/D snoRNAs are processed from debranched pre-mRNA introns by exonucleolytic activities. Elements directing accurate snoRNA excision are located within the snoRNA itself; they comprise the conserved C and D boxes and an adjoining 5′,3′-terminal stem. Although the terminal stem has been demonstrated to be essential for snoRNA accumulation, many snoRNAs lack a terminal helix. To identify thecis-acting elements supporting the accumulation of intron-encoded box C/D snoRNAs devoid of a terminal stem, we have investigated the in vivo processing of the human U46 snoRNA and an artificial snoRNA from the human β-globin pre-mRNA. We demonstrate that internal and/or external stem structures located within the snoRNA or in the intronic flanking sequences support the accumulation of mammalian box C/D snoRNAs lacking a canonical terminal stem. In the intronic precursor RNA, transiently formed external and/or stable internal base-pairing interactions fold the C and D boxes together and therefore facilitate the binding of snoRNP proteins. Since the external intronic stems are degraded during snoRNA processing, we propose that the C and D boxes alone can provide metabolic stability for the mature snoRNA.

scholarly journals RNA base pairing complexity in living cells visualized by correlated chemical probing

2019 ◽  
Author(s):  
Anthony M. Mustoe ◽  
Nicole Lama ◽  
Patrick S. Irving ◽  
Samuel W. Olson ◽  
Kevin M. Weeks
Keyword(s):  
Single Molecule ◽  
Rna Structure ◽  
Dimethyl Sulfate ◽  
Detection Methods ◽  
Base Pairing ◽  
Base Pairs ◽  
Chemical Probing ◽  
Pairing Interactions ◽  
In Cells

ABSTRACTRNA structure and dynamics are critical to biological function. However, strategies for determining RNA structure in vivo are limited, with established chemical probing and newer duplex detection methods each having notable deficiencies. Here we convert the common reagent dimethyl sulfate (DMS) into a useful probe of all four RNA nucleotides. Building on this advance, we introduce PAIR-MaP, which uses single-molecule correlated chemical probing to directly detect base pairing interactions in cells. PAIR-MaP has superior resolution and accuracy compared to alternative experiments, can resolve alternative pairing interactions of structurally dynamic RNAs, and enables highly accurate structure modeling, including of RNAs containing multiple pseudoknots and extensively bound by proteins. Application of PAIR-MaP to human RNase MRP and two bacterial mRNA 5'-UTRs reveals new functionally important and complex structures undetectable by conventional analyses. PAIR-MaP is a powerful, experimentally concise, and broadly applicable strategy for directly visualizing RNA base pairs and dynamics in cells.

scholarly journals RNA base-pairing complexity in living cells visualized by correlated chemical probing

2019 ◽  
Vol 116 (49) ◽  
pp. 24574-24582 ◽  
Author(s):  
Anthony M. Mustoe ◽  
Nicole N. Lama ◽  
Patrick S. Irving ◽  
Samuel W. Olson ◽  
Kevin M. Weeks
Keyword(s):  
Single Molecule ◽  
Rna Structure ◽  
Messenger Rna ◽  
Dimethyl Sulfate ◽  
Detection Methods ◽  
Base Pairing ◽  
Chemical Probing ◽  
Pairing Interactions ◽  
In Cells

RNA structure and dynamics are critical to biological function. However, strategies for determining RNA structure in vivo are limited, with established chemical probing and newer duplex detection methods each having deficiencies. Here we convert the common reagent dimethyl sulfate into a useful probe of all 4 RNA nucleotides. Building on this advance, we introduce PAIR-MaP, which uses single-molecule correlated chemical probing to directly detect base-pairing interactions in cells. PAIR-MaP has superior resolution compared to alternative experiments, can resolve multiple sets of pairing interactions for structurally dynamic RNAs, and enables highly accurate structure modeling, including of RNAs containing multiple pseudoknots and extensively bound by proteins. Application of PAIR-MaP to human RNase MRP and 2 bacterial messenger RNA 5′ untranslated regions reveals functionally important and complex structures undetected by prior analyses. PAIR-MaP is a powerful, experimentally concise, and broadly applicable strategy for directly visualizing RNA base pairs and dynamics in cells.

scholarly journals Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jules Deforges ◽  
Rodrigo S. Reis ◽  
Philippe Jacquet ◽  
Dominique Jacques Vuarambon ◽  
Yves Poirier
Keyword(s):  
Base Pairing ◽  
In Trans ◽  
Non Coding Rnas ◽  
Pairing Interactions

scholarly journals Contribution of base-pairing interactions between group II intron fragments during trans-splicing in vivo

RNA ◽  
2011 ◽  
Vol 17 (12) ◽  
pp. 2212-2221 ◽  
Author(s):  
C. Quiroga ◽  
L. Kronstad ◽  
C. Ritlop ◽  
A. Filion ◽  
B. Cousineau
Keyword(s):  
Group Ii Intron ◽  
Base Pairing ◽  
Trans Splicing ◽  
Pairing Interactions ◽  
Group Ii

scholarly journals Direct Interactions with Nascent Transcripts Is Potentially a Common Targeting Mechanism of Long Non-Coding RNAs

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1483
Author(s):  
Ivan Antonov ◽  
Yulia Medvedeva
Keyword(s):  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Pilot Project ◽  
Base Pairing ◽  
Nascent Transcript ◽  
Active Transcription ◽  
Wet Lab ◽  
In Trans ◽  
Non Coding Rnas ◽  
Nascent Transcripts

Although thousands of mammalian long non-coding RNAs (lncRNAs) have been reported in the last decade, their functional annotation remains limited. A wet-lab approach to detect functions of a novel lncRNA usually includes its knockdown followed by RNA sequencing and identification of the deferentially expressed genes. However, identification of the molecular mechanism(s) used by the lncRNA to regulate its targets frequently becomes a challenge. Previously, we developed the ASSA algorithm that detects statistically significant inter-molecular RNA-RNA interactions. Here we designed a workflow that uses ASSA predictions to estimate the ability of an lncRNA to function via direct base pairing with the target transcripts (co- or post-transcriptionally). The workflow was applied to 300+ lncRNA knockdown experiments from the FANTOM6 pilot project producing statistically significant predictions for 71 unique lncRNAs (104 knockdowns). Surprisingly, the majority of these lncRNAs were likely to function co-transcriptionally, i.e., hybridize with the nascent transcripts of the target genes. Moreover, a number of the obtained predictions were supported by independent iMARGI experimental data on co-localization of lncRNA and chromatin. We detected an evolutionarily conserved lncRNA CHASERR (AC013394.2 or LINC01578) that could regulate target genes co-transcriptionally via interaction with a nascent transcript by directing CHD2 helicase. The obtained results suggested that this nuclear lncRNA may be able to activate expression of the target genes in trans by base-pairing with the nascent transcripts and directing the CHD2 helicase to the regulated promoters leading to open the chromatin and active transcription. Our study highlights the possible importance of base-pairing between nuclear lncRNAs and nascent transcripts for the regulation of gene expression.

A GATA3 Targeting Nucleic Acid Nanocapsule for In Vivo Gene Regulation in Asthma

ACS Nano ◽  
2021 ◽  
Author(s):  
Tyler D. Gavitt ◽  
Alyssa K. Hartmann ◽  
Shraddha S. Sawant ◽  
Arlind B. Mara ◽  
Steven M. Szczepanek ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Nucleic Acid

scholarly journals Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

2021 ◽  
Vol 49 (7) ◽  
pp. 3856-3875
Author(s):  
Marina Kulik ◽  
Melissa Bothe ◽  
Gözde Kibar ◽  
Alisa Fuchs ◽  
Stefanie Schöne ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Dna Binding ◽  
Receptor Binding ◽  
Binding Sites ◽  
Specific Gene ◽  
Functional Diversification ◽  
Enhancer Activity ◽  
Sequence Composition

Abstract The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied them in an equivalent cellular context. Analysis of chromatin and sequence suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR to interact with relatively inaccessible chromatin. Divergent genomic binding patterns can also be the result of subtle differences in DNA binding preference between AR and GR. Furthermore, the sequence composition of large regions (>10 kb) surrounding selectively occupied binding sites differs significantly, indicating a role for the sequence environment in guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, shared binding sites display receptor-specific enhancer activity, cofactor recruitment and changes in histone modifications. Genomic deletion of shared binding sites demonstrates their contribution to directing receptor-specific gene regulation. Together, these data suggest that differences in genomic occupancy as well as divergence in the events that occur downstream of receptor binding direct functional diversification among transcription factor paralogs.

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