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Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome

G-quadruplexes are the non-canonical nucleic acid structures that are preferentially formed in G-rich regions. This structure has been shown to be associated with many biological functions. Regardless of the broad efforts on DNA G-quadruplexes, we still have limited knowledge on RNA G-quadruplexes,...

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Autores principales: Zhang, Rongxin, Liu, Yajun, Zhang, Xingxing, Xiao, Ke, Hou, Yue, Liu, Hongde, Sun, Xiao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8347560/
https://www.ncbi.nlm.nih.gov/pubmed/34360778
http://dx.doi.org/10.3390/ijms22158012
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author Zhang, Rongxin
Liu, Yajun
Zhang, Xingxing
Xiao, Ke
Hou, Yue
Liu, Hongde
Sun, Xiao
author_facet Zhang, Rongxin
Liu, Yajun
Zhang, Xingxing
Xiao, Ke
Hou, Yue
Liu, Hongde
Sun, Xiao
author_sort Zhang, Rongxin
collection PubMed
description G-quadruplexes are the non-canonical nucleic acid structures that are preferentially formed in G-rich regions. This structure has been shown to be associated with many biological functions. Regardless of the broad efforts on DNA G-quadruplexes, we still have limited knowledge on RNA G-quadruplexes, especially in a transcriptome-wide manner. Herein, by integrating the DMS-seq and the bioinformatics pipeline, we profiled and depicted the RNA G-quadruplexes in the human transcriptome. The genes that contain RNA G-quadruplexes in their specific regions are significantly related to immune pathways and the COVID-19-related gene sets. Bioinformatics analysis reveals the potential regulatory functions of G-quadruplexes on miRNA targeting at the scale of the whole transcriptome. In addition, the G-quadruplexes are depleted in the putative, not the real, PAS-strong poly(A) sites, which may weaken the possibility of such sites being the real cleaved sites. In brief, our study provides insight into the potential function of RNA G-quadruplexes in post-transcription.
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spelling pubmed-83475602021-08-08 Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome Zhang, Rongxin Liu, Yajun Zhang, Xingxing Xiao, Ke Hou, Yue Liu, Hongde Sun, Xiao Int J Mol Sci Article G-quadruplexes are the non-canonical nucleic acid structures that are preferentially formed in G-rich regions. This structure has been shown to be associated with many biological functions. Regardless of the broad efforts on DNA G-quadruplexes, we still have limited knowledge on RNA G-quadruplexes, especially in a transcriptome-wide manner. Herein, by integrating the DMS-seq and the bioinformatics pipeline, we profiled and depicted the RNA G-quadruplexes in the human transcriptome. The genes that contain RNA G-quadruplexes in their specific regions are significantly related to immune pathways and the COVID-19-related gene sets. Bioinformatics analysis reveals the potential regulatory functions of G-quadruplexes on miRNA targeting at the scale of the whole transcriptome. In addition, the G-quadruplexes are depleted in the putative, not the real, PAS-strong poly(A) sites, which may weaken the possibility of such sites being the real cleaved sites. In brief, our study provides insight into the potential function of RNA G-quadruplexes in post-transcription. MDPI 2021-07-27 /pmc/articles/PMC8347560/ /pubmed/34360778 http://dx.doi.org/10.3390/ijms22158012 Text en © 2021 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
Zhang, Rongxin
Liu, Yajun
Zhang, Xingxing
Xiao, Ke
Hou, Yue
Liu, Hongde
Sun, Xiao
Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome
title Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome
title_full Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome
title_fullStr Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome
title_full_unstemmed Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome
title_short Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome
title_sort detecting and profiling endogenous rna g-quadruplexes in the human transcriptome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8347560/
https://www.ncbi.nlm.nih.gov/pubmed/34360778
http://dx.doi.org/10.3390/ijms22158012
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