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Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis

Long non-coding RNAs (lncRNAs) have been shown to play a role in the pathogenesis of ulcerative colitis (UC). Although epigenetic processes such as DNA methylation and lncRNA expression are well studied in UC, the importance of the interplay between the two processes has not yet been fully explored....

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Autores principales: Fenton, Christopher G., Ray, Mithlesh Kumar, Meng, Wei, Paulssen, Ruth H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10341861/
https://www.ncbi.nlm.nih.gov/pubmed/37445676
http://dx.doi.org/10.3390/ijms241310500
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author Fenton, Christopher G.
Ray, Mithlesh Kumar
Meng, Wei
Paulssen, Ruth H.
author_facet Fenton, Christopher G.
Ray, Mithlesh Kumar
Meng, Wei
Paulssen, Ruth H.
author_sort Fenton, Christopher G.
collection PubMed
description Long non-coding RNAs (lncRNAs) have been shown to play a role in the pathogenesis of ulcerative colitis (UC). Although epigenetic processes such as DNA methylation and lncRNA expression are well studied in UC, the importance of the interplay between the two processes has not yet been fully explored. It is, therefore, believed that interactions between environmental factors and epigenetics contribute to disease development. Mucosal biopsies from 11 treatment-naïve UC patients and 13 normal controls were used in this study. From each individual sample, both whole-genome bisulfite sequencing data (WGBS) and lncRNA expression data were analyzed. Correlation analysis between lncRNA expression and upstream differentially methylated regions (DMRs) was used to identify lncRNAs that might be regulated by DMRs. Furthermore, proximal protein-coding genes associated with DMR-regulated lncRNAs were identified by correlating their expression. The study identified UC-associated lncRNAs such as MIR4435-2HG, ZFAS1, IL6-AS1, and Pvt1, which may be regulated by DMRs. Several genes that are involved in inflammatory immune responses were found downstream of DMR-regulated lncRNAs, including SERPINB1, CCL18, and SLC15A4. The interplay between lncRNA expression regulated by DNA methylation in UC might improve our understanding of UC pathogenesis.
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spelling pubmed-103418612023-07-14 Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis Fenton, Christopher G. Ray, Mithlesh Kumar Meng, Wei Paulssen, Ruth H. Int J Mol Sci Article Long non-coding RNAs (lncRNAs) have been shown to play a role in the pathogenesis of ulcerative colitis (UC). Although epigenetic processes such as DNA methylation and lncRNA expression are well studied in UC, the importance of the interplay between the two processes has not yet been fully explored. It is, therefore, believed that interactions between environmental factors and epigenetics contribute to disease development. Mucosal biopsies from 11 treatment-naïve UC patients and 13 normal controls were used in this study. From each individual sample, both whole-genome bisulfite sequencing data (WGBS) and lncRNA expression data were analyzed. Correlation analysis between lncRNA expression and upstream differentially methylated regions (DMRs) was used to identify lncRNAs that might be regulated by DMRs. Furthermore, proximal protein-coding genes associated with DMR-regulated lncRNAs were identified by correlating their expression. The study identified UC-associated lncRNAs such as MIR4435-2HG, ZFAS1, IL6-AS1, and Pvt1, which may be regulated by DMRs. Several genes that are involved in inflammatory immune responses were found downstream of DMR-regulated lncRNAs, including SERPINB1, CCL18, and SLC15A4. The interplay between lncRNA expression regulated by DNA methylation in UC might improve our understanding of UC pathogenesis. MDPI 2023-06-22 /pmc/articles/PMC10341861/ /pubmed/37445676 http://dx.doi.org/10.3390/ijms241310500 Text en © 2023 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
Fenton, Christopher G.
Ray, Mithlesh Kumar
Meng, Wei
Paulssen, Ruth H.
Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis
title Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis
title_full Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis
title_fullStr Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis
title_full_unstemmed Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis
title_short Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis
title_sort methylation-regulated long non-coding rna expression in ulcerative colitis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10341861/
https://www.ncbi.nlm.nih.gov/pubmed/37445676
http://dx.doi.org/10.3390/ijms241310500
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