The Epigenetic Roles of lncRNAs

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Epigenomics".

Deadline for manuscript submissions: closed (20 February 2025) | Viewed by 1727

Special Issue Editors


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Guest Editor
The LncRNA, Epigenetics, and Genome Organization Laboratory, Department of Cell Biology and Physiology, School of Medicine, University of New Mexico, Albuquerque, NM, USA
Interests: lncRNA; epigenetics; chromatin biology; cancer biology

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Guest Editor
Department of Cell Biology and Physiology, School of Medicine, University of New Mexico, Albuquerque, NM, USA
Interests: epigenetics; functional genomics; eye diseases; cancer; omics

Special Issue Information

Dear Colleagues,

Attention has recently increased toward long non-coding RNAs (lncRNAs) because of their capacity to impact gene expression through diverse epigenetic pathways, in both cis and trans functions. This is significant because it emphasizes the influence of lncRNAs on a wide range of biological processes, such as growth, specialization, the advancement of diseases, and reactions to environmental stimuli. Their tissue- and cell-specific expression patterns make them potential candidates for targeted interventions. The late 2010s saw developments in chromatin immunoprecipitation, genome-wide gene expression analysis, and next-generation sequencing technologies that enabled the identification of chromatin-associated functions of lncRNAs. Lately, emerging high-resolution single-molecule imaging and ultra-long-read sequencing technologies have opened up several avenues of research on lncRNAs’ role in epigenetic regulations.

Epigenetics is a dynamic and heritable modification that happens without respect for the DNA sequence and provides a variable level of control over gene expression. Numerous epigenetic mechanisms are regulated by DNA methylation and histone modifications orchestrated by lncRNAs. LncRNAs play a broad role in cellular function, from chromosome organization to extracellular and circulating signaling molecules. They engage in nuclear organization, such as maintaining chromatin architecture and heterochromatin, organizing topologically associated domains, chromatin loops, R-loops, chaperoning, and so on. Their critical roles in epigenetic regulation include genetic imprinting and serving as enhancer RNAs interacting with specific histone modification and transcription factors to modulate gene expression; therefore, understanding the interplay between lncRNA expression patterns, localization, and associated epigenetic signatures as well as function can provide us with the information required for developing a possible combination of biomarkers and therapeutic targets.    

In this Special Issue, “The Epigenetic Roles of lncRNAs”, for Genes, I am delighted to invite a compilation of articles exploring the epigenetic functions of lncRNAs. This Special Issue aims to investigate the many and developing functions of lncRNAs in influencing epigenetic processes, providing insight into their potential as essential controllers of gene expression and cellular function. The articles in this Special Issue will encompass various subjects, such as identifying and characterizing lncRNAs, their interactions with chromatin and chromatin-modifying complexes, and their role in epigenetic modifications like DNA methylation, histone modifications, imprinting, and chromatin remodeling. 

This Special Issue will provide an excellent resource for scholars and scientists to comprehend the complex connection between lncRNAs and epigenetic control. The compilation of publications in this Special Issue will thoroughly examine the present understanding of this swiftly developing and captivating domain. We anticipate that it will stimulate further research and cooperation in deciphering the epigenetic functions of lncRNAs.

Dr. Arun Kumar Ganesan
Dr. Gurdeep Singh
Guest Editors

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Keywords

  • epigenetic regulation
  • long non-coding RNAs
  • chromatin organization
  • histone modification
  • biomarkers

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Published Papers (1 paper)

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17 pages, 7699 KiB  
Systematic Review
Long Non-Coding RNAs as Diagnostic Biomarkers for Ischemic Stroke: A Systematic Review and Meta-Analysis
by Jianwei Pan, Weijian Fan, Chenjie Gu, Yongmei Xi, Yu Wang and Peter Wang
Genes 2024, 15(12), 1620; https://doi.org/10.3390/genes15121620 - 18 Dec 2024
Viewed by 1255
Abstract
Ischemic stroke is a serious cerebrovascular disease, highlighting the urgent need for reliable biomarkers for early diagnosis. Recent reports suggest that long non-coding RNAs (lncRNAs) can be potential biomarkers for ischemic stroke. Therefore, our study seeks to investigate the potential diagnostic value of [...] Read more.
Ischemic stroke is a serious cerebrovascular disease, highlighting the urgent need for reliable biomarkers for early diagnosis. Recent reports suggest that long non-coding RNAs (lncRNAs) can be potential biomarkers for ischemic stroke. Therefore, our study seeks to investigate the potential diagnostic value of lncRNAs for ischemic stroke by analyzing existing research. A comprehensive literature search was conducted across the PubMed, ScienceDirect, Wiley Online Library, and Web of Science databases for articles published up to July 10, 2024. Statistical analyses were performed using Stata 17.0 software to calculate pooled sensitivity, specificity, positive likelihood ratio (PLR), diagnostic odds ratio (DOR), negative likelihood ratio (NLR), and area under the curve (AUC). Heterogeneity was explored with the Cochran-Q test and the I2 statistical test, and publication bias was assessed with Deeks’ funnel plot. A total of 44 articles were included, involving 4302 ischemic stroke patients and 3725 healthy controls. Results demonstrated that lncRNAs H19, GAS5, PVT1, TUG1, and MALAT1 exhibited consistent trends across multiple studies. The pooled sensitivity of lncRNAs in the diagnosis of ischemic stroke was 79% (95% CI: 73–84%), specificity was 88% (95% CI: 77–94%), PLR was 6.63 (95% CI: 3.11–14.15), NLR was 0.23 (95% CI: 0.16–0.33), DOR was 28.5 (95% CI: 9.88–82.21), and AUC was 0.88 (95% CI: 0.85–0.90). Furthermore, the results of subgroup analysis indicated that lncRNA H19 had superior diagnostic performance. LncRNAs demonstrated strong diagnostic accuracy in distinguishing ischemic stroke patients from healthy controls, underscoring their potential as reliable biomarkers. Because most of the articles included in this study originate from China, large-scale, high-quality, multi-country prospective studies are required to further validate the reliability of lncRNAs as biomarkers for ischemic stroke. Full article
(This article belongs to the Special Issue The Epigenetic Roles of lncRNAs)
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