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Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets

Circular RNAs are a special type of RNA that has recently attracted a lot of research interest in studying its formation and function. RNA binding proteins (RBPs) that bind circRNAs are important in these processes, but have been relatively less studied. CLIP-Seq technology has been invented and app...

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Detalles Bibliográficos
Autores principales: Zhang, Minzhe, Wang, Tao, Xiao, Guanghua, Xie, Yang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016857/
https://www.ncbi.nlm.nih.gov/pubmed/31947823
http://dx.doi.org/10.3390/genes11010054
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author Zhang, Minzhe
Wang, Tao
Xiao, Guanghua
Xie, Yang
author_facet Zhang, Minzhe
Wang, Tao
Xiao, Guanghua
Xie, Yang
author_sort Zhang, Minzhe
collection PubMed
description Circular RNAs are a special type of RNA that has recently attracted a lot of research interest in studying its formation and function. RNA binding proteins (RBPs) that bind circRNAs are important in these processes, but have been relatively less studied. CLIP-Seq technology has been invented and applied to profile RBP-RNA interactions on the genome-wide scale. While mRNAs are usually the focus of CLIP-Seq experiments, RBP-circRNA interactions could also be identified through specialized analysis of CLIP-Seq datasets. However, many technical difficulties are involved in this process, such as the usually short read length of CLIP-Seq reads. In this study, we created a pipeline called Clirc specialized for profiling circRNAs in CLIP-Seq data and analyzing the characteristics of RBP-circRNA interactions. In conclusion, to our knowledge, this is one of the first studies to investigate circRNAs and their binding partners through repurposing CLIP-Seq datasets, and we hope our work will become a valuable resource for future studies into the biogenesis and function of circRNAs.
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spelling pubmed-70168572020-02-28 Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets Zhang, Minzhe Wang, Tao Xiao, Guanghua Xie, Yang Genes (Basel) Article Circular RNAs are a special type of RNA that has recently attracted a lot of research interest in studying its formation and function. RNA binding proteins (RBPs) that bind circRNAs are important in these processes, but have been relatively less studied. CLIP-Seq technology has been invented and applied to profile RBP-RNA interactions on the genome-wide scale. While mRNAs are usually the focus of CLIP-Seq experiments, RBP-circRNA interactions could also be identified through specialized analysis of CLIP-Seq datasets. However, many technical difficulties are involved in this process, such as the usually short read length of CLIP-Seq reads. In this study, we created a pipeline called Clirc specialized for profiling circRNAs in CLIP-Seq data and analyzing the characteristics of RBP-circRNA interactions. In conclusion, to our knowledge, this is one of the first studies to investigate circRNAs and their binding partners through repurposing CLIP-Seq datasets, and we hope our work will become a valuable resource for future studies into the biogenesis and function of circRNAs. MDPI 2020-01-03 /pmc/articles/PMC7016857/ /pubmed/31947823 http://dx.doi.org/10.3390/genes11010054 Text en © 2020 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhang, Minzhe
Wang, Tao
Xiao, Guanghua
Xie, Yang
Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets
title Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets
title_full Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets
title_fullStr Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets
title_full_unstemmed Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets
title_short Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets
title_sort large-scale profiling of rbp-circrna interactions from public clip-seq datasets
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016857/
https://www.ncbi.nlm.nih.gov/pubmed/31947823
http://dx.doi.org/10.3390/genes11010054
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