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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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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. |
format | Online Article Text |
id | pubmed-8788457 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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