Cargando…
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...
Autores principales: | , , , |
---|---|
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 |
_version_ | 1783497072036544512 |
---|---|
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. |
format | Online Article Text |
id | pubmed-7016857 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT zhangminzhe largescaleprofilingofrbpcircrnainteractionsfrompublicclipseqdatasets AT wangtao largescaleprofilingofrbpcircrnainteractionsfrompublicclipseqdatasets AT xiaoguanghua largescaleprofilingofrbpcircrnainteractionsfrompublicclipseqdatasets AT xieyang largescaleprofilingofrbpcircrnainteractionsfrompublicclipseqdatasets |