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An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change

Recently, accumulating evidence has supported that circular RNA (circRNA) plays important roles in tumorigenesis by regulating gene expression at transcriptional and post-transcriptional levels. Expression of circRNAs can be epigenetically silenced by DNA methylation; however, the underlying regulat...

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Autores principales: Xu, Tianyi, Wang, LiPing, Jia, Peilin, Song, Xiaofeng, Zhao, Zhongming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8227141/
https://www.ncbi.nlm.nih.gov/pubmed/34201256
http://dx.doi.org/10.3390/biomedicines9060657
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author Xu, Tianyi
Wang, LiPing
Jia, Peilin
Song, Xiaofeng
Zhao, Zhongming
author_facet Xu, Tianyi
Wang, LiPing
Jia, Peilin
Song, Xiaofeng
Zhao, Zhongming
author_sort Xu, Tianyi
collection PubMed
description Recently, accumulating evidence has supported that circular RNA (circRNA) plays important roles in tumorigenesis by regulating gene expression at transcriptional and post-transcriptional levels. Expression of circRNAs can be epigenetically silenced by DNA methylation; however, the underlying regulatory mechanisms of circRNAs by DNA methylation remains largely unknown. We explored this regulation in hepatocellular carcinoma (HCC) using genome-wide DNA methylation and RNA sequencing data of the primary tumor and matched adjacent normal tissues from 20 HCC patients. Our pipeline identified 1012 upregulated and 747 downregulated circRNAs (collectively referred to as differentially expressed circRNAs, or DE circRNAs) from HCC RNA-seq data. Among them, 329 DE circRNAs covered differentially methylated sites (adjusted p-value < 0.05, |ΔM| > 0.5) in circRNAs’ interior and/or flanking regions. Interestingly, the corresponding parental genes of 46 upregulated and 31 downregulated circRNAs did not show significant expression change in the HCC tumor versus normal samples. Importantly, 34 of the 77 DE circRNAs (44.2%) had significant correlation with DNA methylation change in HCC (Spearman’s rank-order correlation, p-value < 0.05), suggesting that aberrant DNA methylation might regulate circular RNA expression in HCC. Our study revealed genome-wide differential circRNA expression in HCC. The significant correlation with DNA methylation change suggested that epigenetic regulation might act on both mRNA and circRNA expression. The specific regulation in HCC and general view in other cancer or disease requires further investigation.
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spelling pubmed-82271412021-06-26 An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change Xu, Tianyi Wang, LiPing Jia, Peilin Song, Xiaofeng Zhao, Zhongming Biomedicines Article Recently, accumulating evidence has supported that circular RNA (circRNA) plays important roles in tumorigenesis by regulating gene expression at transcriptional and post-transcriptional levels. Expression of circRNAs can be epigenetically silenced by DNA methylation; however, the underlying regulatory mechanisms of circRNAs by DNA methylation remains largely unknown. We explored this regulation in hepatocellular carcinoma (HCC) using genome-wide DNA methylation and RNA sequencing data of the primary tumor and matched adjacent normal tissues from 20 HCC patients. Our pipeline identified 1012 upregulated and 747 downregulated circRNAs (collectively referred to as differentially expressed circRNAs, or DE circRNAs) from HCC RNA-seq data. Among them, 329 DE circRNAs covered differentially methylated sites (adjusted p-value < 0.05, |ΔM| > 0.5) in circRNAs’ interior and/or flanking regions. Interestingly, the corresponding parental genes of 46 upregulated and 31 downregulated circRNAs did not show significant expression change in the HCC tumor versus normal samples. Importantly, 34 of the 77 DE circRNAs (44.2%) had significant correlation with DNA methylation change in HCC (Spearman’s rank-order correlation, p-value < 0.05), suggesting that aberrant DNA methylation might regulate circular RNA expression in HCC. Our study revealed genome-wide differential circRNA expression in HCC. The significant correlation with DNA methylation change suggested that epigenetic regulation might act on both mRNA and circRNA expression. The specific regulation in HCC and general view in other cancer or disease requires further investigation. MDPI 2021-06-08 /pmc/articles/PMC8227141/ /pubmed/34201256 http://dx.doi.org/10.3390/biomedicines9060657 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
Xu, Tianyi
Wang, LiPing
Jia, Peilin
Song, Xiaofeng
Zhao, Zhongming
An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change
title An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change
title_full An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change
title_fullStr An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change
title_full_unstemmed An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change
title_short An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change
title_sort integrative transcriptomic and methylation approach for identifying differentially expressed circular rnas associated with dna methylation change
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8227141/
https://www.ncbi.nlm.nih.gov/pubmed/34201256
http://dx.doi.org/10.3390/biomedicines9060657
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