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DNA and RNA Epigenetics and Transcriptomics Research, Volume II
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DNA and RNA Epigenetics and Transcriptomics Research, Volume II

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 October 2024 | Viewed by 2152

Special Issue Editors

Prof. Dr. Yan Zhang

E-Mail Website
Guest Editor
School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
Interests: computational biology; epigenomes; tumor bioinformatics; tumor biomarker; database; deep learning; histone modification; chromatin accessibility
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Rujiao Li

E-Mail Website
Guest Editor
National Genomics Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Science (CAS) & China National Center for Bioinformation (CNCB), Beijing 100101, China
Interests: genomics; epigenomes; bioinformatics; big data integration; database development; algorithm development
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jianzhong Su

E-Mail Website
Guest Editor
School of Ophthalmology and Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou 325027, China
Interests: DNA methylation editing; single-cell epigenomes; genetic diagnosis; tumor evolution; organoid regeneration
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Epigenomic regulation refers to heritable alterations in gene expression that do not involve changes in DNA sequences themselves. DNA modifications were proposed as carriers of epigenetic information in early research, with subsequent work revealing that histone modifications, chromatin accessibility, noncoding RNAs, and RNA modifications are also important in this process. The rapidly accelerating, cutting-edge field of epigenomics research has led to remarkable progress in our understanding of molecular mechanisms related to this process, its regulatory functions, and its interaction with other biological process.

This Special Issue, entitled “DNA and RNA Epigenetics and Transcriptomics Research, Volume II”, is the second edition of the Special Issue "DNA and RNA Epigenetics and Transcriptomics Research" (https://www.mdpi.com/journal/genes/special_issues/DNA_and_RNA_Epigenetics_and_Transcriptomics_Research). It will focus on the interplay between regulatory function and epigenomics, including cellular and reprogramming events, epigenetic inheritance across generations, and responses to physiological stimuli and disease. Moreover, this issue will discuss non-coding RNAs; DNA and RNA modifications; and the role of chromatin accessibility in regulating both inheritance and gene expression plasticity.

Prof. Dr. Yan Zhang
Prof. Dr. Rujiao Li
Prof. Dr. Jianzhong Su
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • epigenetic regulation
  • transcriptional regulation
  • DNA modification
  • RNA modification
  • noncoding RNA regulation
  • omics

Published Papers (2 papers)

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Research

20 pages, 15720 KiB  
Article
Integrated Analysis of scRNA-Seq and Bulk RNA-Seq Reveals Metabolic Reprogramming of Liver Cancer and Establishes a Prognostic Risk Model
by Zhuang Xiong, Lizhi Li, Guoliang Wang, Lei Guo, Shangyi Luo, Xiangwen Liao, Jingfeng Liu and Wenhao Teng
Genes 2024, 15(6), 755; https://doi.org/10.3390/genes15060755 (registering DOI) - 8 Jun 2024
Abstract
Liver cancer manifests as a profoundly heterogeneous malignancy, posing significant challenges in terms of both therapeutic intervention and prognostic evaluation. Given that the liver is the largest metabolic organ, a prognostic risk model grounded in single-cell transcriptome analysis and a metabolic perspective can [...] Read more.
Liver cancer manifests as a profoundly heterogeneous malignancy, posing significant challenges in terms of both therapeutic intervention and prognostic evaluation. Given that the liver is the largest metabolic organ, a prognostic risk model grounded in single-cell transcriptome analysis and a metabolic perspective can facilitate precise prevention and treatment strategies for liver cancer. Hence, we identified 11 cell types in a scRNA-seq profile comprising 105,829 cells and found that the metabolic activity of malignant cells increased significantly. Subsequently, a prognostic risk model incorporating tumor heterogeneity, cell interactions, tumor cell metabolism, and differentially expressed genes was established based on eight genes; this model can accurately distinguish the survival outcomes of liver cancer patients and predict the response to immunotherapy. Analyzing the immune status and drug sensitivity of the high- and low-risk groups identified by the model revealed that the high-risk group had more active immune cell status and greater expression of immune checkpoints, indicating potential risks associated with liver cancer-targeted drugs. In summary, this study provides direct evidence for the stratification and precise treatment of liver cancer patients, and is an important step in establishing reliable predictors of treatment efficacy in liver cancer patients. Full article
(This article belongs to the Special Issue DNA and RNA Epigenetics and Transcriptomics Research, Volume II)
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15 pages, 8411 KiB  
Article
Developing CuS for Predicting Aggressiveness and Prognosis in Lung Adenocarcinoma
by Honghao Liu, Haijun Che, Mengyan Zhang, Jinyue Lv, Chengjie Pu, Jiawei Wu, Yan Zhang and Yue Gu
Genes 2023, 14(5), 1055; https://doi.org/10.3390/genes14051055 - 8 May 2023
Cited by 1 | Viewed by 1538
Abstract
Cuproptosis is a newfound cell death form that depends on copper (Cu) ionophores to transport Cu into cancer cells. Studies on the relationship have covered most common cancer types and analyzed the links between cuproptosis-related genes (CRGs) and various aspects of tumor characteristics. [...] Read more.
Cuproptosis is a newfound cell death form that depends on copper (Cu) ionophores to transport Cu into cancer cells. Studies on the relationship have covered most common cancer types and analyzed the links between cuproptosis-related genes (CRGs) and various aspects of tumor characteristics. In this study, we evaluated the role of cuproptosis in lung adenocarcinoma (LUAD) and constructed the cuproptosis-related score (CuS) to predict aggressiveness and prognosis in LUAD, so as to achieve precise treatment for patients. CuS had a better predictive performance than cuproptosis genes, possibly due to the synergy of SLC family genes, and patients with a high CuS had a poor prognosis. Functional enrichment analysis revealed the correlation between CuS and immune and mitochondrial pathways in multiple datasets. Furthermore, we predicted six potential drugs targeting high-CuS patients, including AZD3759, which is a targeted drug for LUAD. In conclusion, cuproptosis is involved in LUAD aggressiveness, and CuS can accurately predict the prognosis of patients. These findings provide a basis for precise treatment of patients with high CuS in LUAD. Full article
(This article belongs to the Special Issue DNA and RNA Epigenetics and Transcriptomics Research, Volume II)
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