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

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 in...

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Autores principales: Wu, Wei-Sheng, Brown, Jordan S., Chen, Pin-Hao, Shiue, Sheng-Cian, Lee, Dong-En, Lee, Heng-Chi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8788457/
https://www.ncbi.nlm.nih.gov/pubmed/35076587
http://dx.doi.org/10.3390/ncrna8010006
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author Wu, Wei-Sheng
Brown, Jordan S.
Chen, Pin-Hao
Shiue, Sheng-Cian
Lee, Dong-En
Lee, Heng-Chi
author_facet Wu, Wei-Sheng
Brown, Jordan S.
Chen, Pin-Hao
Shiue, Sheng-Cian
Lee, Dong-En
Lee, Heng-Chi
author_sort Wu, Wei-Sheng
collection PubMed
description 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.
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spelling pubmed-87884572022-01-26 CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data Wu, Wei-Sheng Brown, Jordan S. Chen, Pin-Hao Shiue, Sheng-Cian Lee, Dong-En Lee, Heng-Chi Noncoding RNA Article 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. MDPI 2022-01-12 /pmc/articles/PMC8788457/ /pubmed/35076587 http://dx.doi.org/10.3390/ncrna8010006 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Wu, Wei-Sheng
Brown, Jordan S.
Chen, Pin-Hao
Shiue, Sheng-Cian
Lee, Dong-En
Lee, Heng-Chi
CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data
title CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data
title_full CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data
title_fullStr CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data
title_full_unstemmed CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data
title_short CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data
title_sort clash analyst: a web server to identify in vivo rna–rna interactions from clash data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8788457/
https://www.ncbi.nlm.nih.gov/pubmed/35076587
http://dx.doi.org/10.3390/ncrna8010006
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