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Epigenomes, Volume 10, Issue 1

2026 March - 21 articles

Cover Story: Accumulating evidence has revealed the dysregulation of multiple miRNAs in chronic kidney disease. We provide an integrated overview of miRNA-mediated regulation in kidney interstitial fibrosis, with an emphasis on cell-lineage-specific functions. The figure presents mouse kidneys from sham-operated and unilateral ureteral obstruction models at day 7. F4/80-positive macrophages are shown in green, α-SMA-positive myofibroblasts/smooth muscle cells in red, NG2-positive pericytes in cyan, and Hoechst-stained nuclei in blue. These altered cell–cell interactions are associated with myofibroblast activation, excessive extracellular matrix accumulation, and the progression of kidney fibrosis. Targeting dysregulated miRNAs and other non-coding RNAs may offer a novel therapeutic strategy in this setting. View this paper
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Articles (21)

  • Review
  • Open Access
2 Citations
3,486 Views
30 Pages

MicroRNA Regulation in Kidney Interstitial Fibrosis

  • Hirofumi Sakuma,
  • Satoshi Kawaguchi,
  • Yuya Kobayashi,
  • Akiko Koizumi and
  • Naoki Nakagawa

MicroRNAs (miRNAs) are small non-coding RNAs that play central roles in post-transcriptional gene regulation and cellular homeostasis maintenance. Dysregulation of miRNA expression is increasingly recognized as a key contributor to tissue injury duri...

  • Article
  • Open Access
1 Citations
2,078 Views
25 Pages

Epigenetics of Genes Displaying High and Preferential Expression in Myoblasts

  • Kenneth C. Ehrlich,
  • Michelle Lacey,
  • Sriharsa Pradhan and
  • Melanie Ehrlich

Background/Objectives: Genome-wide studies of differential DNA methylation often focus on its role in turning transcription on or off. Here we report some atypical epigenetic/transcription relationships for 92 genes that are highly and preferentially...

  • Article
  • Open Access
2,359 Views
20 Pages

Mutant KRAS Heterogeneity Shapes Nuclear Architecture During Pancreatic Cancer Initiation

  • Gareth Pollin,
  • Angela J. Mathison,
  • Elise N. Leverence,
  • Thiago Milech De Assuncao and ,
  • Juan Iovanna,
  • Johnny C. Hong,
  • Michael T. Zimmermann,
  • Raul Urrutia and
  • Gwen Lomberk
  • + 4 authors+ 0 author

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) arises predominantly from activating KRAS mutations, yet individual genetic variants differ markedly in signaling output and clinical impact. G12D, the most prevalent variant, strongly dr...

(This article belongs to the Special Issue Epigenetic Signatures in Metabolic Health and Cancer)
  • Article
  • Open Access
1 Citations
1,496 Views
13 Pages

Changes in Blood DNA CpG Methylation Levels in Response to Methadone Maintenance Treatment: Epigenome-Wide Longitudinal Study

  • Orna Levran,
  • Yuli Kim,
  • Justin Li,
  • Anat Sason and ,
  • Miriam Adelson and
  • Einat Peles
  • + 1 author+ 0 author

Background/Objectives: Methadone maintenance treatment (MMT) is one of the major pharmacotherapies for opioid use disorder. The underlying mechanisms of addiction and the treatment response are only partially understood. The study’s main goal w...

  • Brief Report
  • Open Access
979 Views
15 Pages

Background: Protein prenylation is crucial for the function of hundreds of proteins. Aberrant protein prenylation can be caused by the aberrant expression of prenyltransferases (PTases), which has been reported for multiple cancer entities. The reaso...

  • Article
  • Open Access
1,913 Views
17 Pages

Integrative Analysis Reveals Conserved R-Loop Features in Mouse Embryonic Stem Cells

  • Ohbeom Kwon,
  • Hyeonwoo La,
  • Seonho Yoo,
  • Hyeonji Lee and ,
  • Heeji Lee,
  • Hoseong Lim,
  • Chanhyeok Park,
  • Dong Wook Han,
  • Jeong-Tae Do and
  • Kwonho Hong
  • + 7 authors+ 2 authors

R-loops, three-stranded nucleic acid structures formed by an RNA-DNA hybrid, have emerged as important regulators of transcription and genome stability. Although advances in high-throughput sequencing have revealed widespread R-loop landscapes, platf...

  • Review
  • Open Access
2,362 Views
27 Pages

27 February 2026

Cell division is a highly regulated process that actively involves dynamic changes to the genetic material within the nucleus. DNA is faithfully replicated in the S-Phase of the cell cycle, being converted from loose, relaxed chromatin into tight, co...

  • Article
  • Open Access
1 Citations
2,116 Views
23 Pages

Epigenetic Activity of Cancer Therapy Drugs Revealed by HeLa TI Cell-Based Assay

  • Varvara Maksimova,
  • Valeriia Popova,
  • Alyona Kholodova,
  • Julia Makus and ,
  • Olga Usalka,
  • Eugenia Lylova,
  • Aleksandr Kudriashov,
  • Gennady Belitsky,
  • Marianna Yakubovskaya and
  • Kirill Kirsanov
  • + 5 authors+ 0 author

23 February 2026

Background/Objectives: The aberrant epigenetic landscape of cancer cells has attracted wide attention, motivating the search for new epigenetically active drugs both for anticancer therapy and for overcoming the drug resistance promoted by epigenetic...

(This article belongs to the Special Issue Features Papers in Epigenomes 2025)
  • Review
  • Open Access
5 Citations
2,577 Views
28 Pages

The Epigenetic Battleground: Host Chromatin at the Core of Infection

  • Fabrício Castro Machado and
  • Nilmar Silvio Moretti

15 February 2026

Chromatin dynamics are usually modulated by histone epigenetic post-translational modifications, which rapidly and reversibly govern accessibility and transcriptional responsiveness. During microbial infection, this regulatory layer becomes a highly...

(This article belongs to the Special Issue Epigenetics Meets Immunology: Mechanisms, Crosstalk, and Therapeutic Implications)
  • Article
  • Open Access
1,804 Views
16 Pages

Preliminary Evidence of Blood DNA Methylation Changes in Pregnant Women Adhering to a Mediterranean Diet

  • Grace Tavelli,
  • Nikki Schultz,
  • Joanna Brisbane,
  • Nina Kresoje and ,
  • Samantha Lodge,
  • Jeremy K. Nicholson,
  • Nicola J. Armstrong,
  • Desiree Silva,
  • Nina D’Vaz and
  • David Martino
  • + 5 authors+ 0 author

13 February 2026

Background/Objectives: Consumption of a Mediterranean diet (MD) has been associated with reduced incidence of non-communicable diseases and reduced overall mortality, with epigenomic effects representing plausible mediators. The aim of this pilot stu...

(This article belongs to the Special Issue Epigenetic Signatures in Metabolic Health and Cancer)
  • Article
  • Open Access
2 Citations
2,430 Views
34 Pages

Analysis of HERV-K (HML2) Expression in Colorectal Cancer Samples

  • Valentina S. Obrezanenko,
  • Polina M. Shulga,
  • Anastasia G. Volkova,
  • Anastasia A. Primova and ,
  • Yulia A. Remizova,
  • Ivan O. Meshkov,
  • Alexandra D. Kikot,
  • Daria A. Tarasova,
  • Ekaterina S. Bolashova and
  • Anna S. Makarova
  • + 17 authors+ 12 authors

12 February 2026

Background: HML-2 subgroup mobile genetic elements of the HERV-K family were described to participate in carcinogenesis processes, but their expression and epigenetic regulation in molecular subtypes of colorectal cancer (CRC) remain partly character...

(This article belongs to the Special Issue Epigenetic Signatures in Metabolic Health and Cancer)
  • Review
  • Open Access
6 Citations
4,249 Views
33 Pages

Genetic–Epigenetic Interplay in Epilepsy: Pathways, Biomarkers, and Epigenome-Targeted Therapies

  • Andra-Giorgiana Zaruha,
  • Patricia Codreanu,
  • Mădălin-Codruț Coman,
  • Monica Andreea Novac II and ,
  • Simona Gabriela Duță-Ion,
  • Ioana Ruxandra Jugănaru,
  • Iulian Andrei Hotinceanu,
  • Andra Dan,
  • Livia Mălina Burtavel and
  • Viorica-Elena Rădoi
  • + 9 authors+ 4 authors

10 February 2026

Epilepsy is a heterogeneous neurological disorder with a strong genetic basis, yet recent evidence underscores the critical role of epigenetic mechanisms in its pathogenesis. This review synthesizes current knowledge on how chromatin remodeling, hist...

  • Article
  • Open Access
2,521 Views
11 Pages

Epigenetic Liquid Biopsy Marks Atrial Fibrillation: Evidence from the AF Big Picture Study

  • Riccardo Proietti,
  • Nicola Tidbury,
  • Joshua Preston,
  • Maanya Vittal and ,
  • Philippa McCabe,
  • Garry McDowell,
  • Gregory Y. H. Lip and
  • Manlio Vinciguerra
  • + 3 authors+ 0 author

Background/Objectives: Atrial fibrillation (AF) is currently the most common arrhythmia worldwide, and it is linked to increased mortality and morbidity, hence the need for a better clinical stratification of AF patients. Histone complexes or nucleos...

(This article belongs to the Special Issue Epigenetic Signatures in Metabolic Health and Cancer)
  • Article
  • Open Access
2 Citations
2,763 Views
13 Pages

Differences in MicroRNA Expression in Firefighters Responding to a Train Derailment and Fire in East Palestine, Ohio

  • Jaclyn M. Goodrich,
  • Yaodong Xin,
  • Shawn C. Beitel,
  • John Gulotta and ,
  • Lu Wang,
  • Bhavya Thotakura,
  • Judith M. Graber,
  • Derek Urwin,
  • Alexander C. Mayer and
  • Jefferey L. Burgess
  • + 9 authors+ 4 authors

Background/Objectives: High-risk, low-frequency incidents such as building collapses and large chemical fires can result in acute, high-dose exposures to toxic agents for first responders and the surrounding community. While these exposures may last...

  • Article
  • Open Access
1,709 Views
12 Pages

An Hsp70 Chaperone Is Involved in Meiotic Silencing by Unpaired DNA

  • Victor T. Sy,
  • Sterling S. Trawick,
  • Hagen M. Tatarsky and
  • Patrick K. T. Shiu

In the filamentous fungus Neurospora crassa, a gene not having a pairing partner during meiosis is seen as a potential intruder and is targeted by a mechanism called meiotic silencing by unpaired DNA (MSUD). MSUD employs core RNA interference (RNAi)...

(This article belongs to the Collection Feature Papers in Epigenomes)
  • Article
  • Open Access
1 Citations
1,295 Views
11 Pages

ARS2, a Cofactor of CBC, Promotes Meiotic Silencing by Unpaired DNA

  • Michael M. Vierling,
  • Victor T. Sy,
  • Logan M. Decker,
  • Hua Xiao and ,
  • Justine N. Hemaya and
  • Patrick K. T. Shiu
  • + 1 author+ 0 author

The presence of an extra DNA segment in a genome could indicate a transposon or another repetitive element on the move. In Neurospora crassa, a surveillance mechanism called meiotic silencing by unpaired DNA (MSUD) is maintained to monitor these self...

(This article belongs to the Collection Feature Papers in Epigenomes)
  • Review
  • Open Access
2,247 Views
18 Pages

Something Old, Something New, Something Borrowed… About the Placenta

  • Nadezhda Milova,
  • Maria Nikolova,
  • Angel Yordanov,
  • Antoan Milov and
  • Stoilka Mandadzhieva

The connection between the mother and the child has been considered one of the strongest bonds in nature. Though there are numerous factors that can influence the establishment of pregnancy, in its essence, three are considered major: a good quality...

(This article belongs to the Collection Feature Papers in Epigenomes)
  • Review
  • Open Access
5 Citations
2,168 Views
12 Pages

Epigenetic Alterations in Colitis-Associated Colorectal Cancer

  • Nisha Ganesh,
  • William M. Grady and
  • Andrew M. Kaz

Colitis-associated colorectal cancer (CAC) represents a distinct subtype of colorectal malignancy that arises in the setting of chronic inflammatory bowel disease (IBD). Unlike sporadic colorectal cancer, CAC develops through inflammation-driven mole...

(This article belongs to the Special Issue Epigenetic Signatures in Metabolic Health and Cancer)
  • Article
  • Open Access
2,090 Views
17 Pages

Fisetin Suppresses the Proliferative and Migratory Behavior of HeLa Cells by Modulating Aberrant Epigenetic Marks (Writers and Erasers)

  • Nazia Afroze,
  • Reham I. Alagal,
  • Lujain A. Almousa,
  • Ritu Raina and ,
  • Prathap Bava,
  • Lizna Mohamed Ali,
  • Tarique Noorul Hasan and
  • Arif Hussain
  • + 3 authors+ 0 author

Purpose: The reversible deviant in epigenomic modulations is the highlight of developing new anti-cancer drugs, necessitating the use of fisetin as an epigenetic modifier in the study. Methods: In silico and molecular studies were performed to analyz...

  • Article
  • Open Access
2,006 Views
16 Pages

Epigenetic Regulation and Gene Expression Profiles in Cervical Swabs: Toward Non-Invasive Biomarkers of Cervical Lesion Progression

  • Ivana Kašubová,
  • Andrea Hornáková,
  • Lucia Kotúľová,
  • Tomáš Rokos and ,
  • Zuzana Kolková,
  • Andrea Kapinová,
  • Terézia Pribulová,
  • Erik Kozubík,
  • Michal Kalman and
  • Veronika Holubeková
  • + 7 authors+ 2 authors

Background/Objectives: Cervical cancer is a common malignancy in women worldwide, closely associated with persistent human papillomavirus (HPV) infection. Epigenetic mechanisms, particularly promoter methylation, may contribute to tumour progression....

(This article belongs to the Special Issue Epigenetic Signatures in Metabolic Health and Cancer)
  • Article
  • Open Access
1,344 Views
19 Pages

Upregulation of a MicroRNA Signature Involving miR-17-5p, miR-26b-5p, miR-106a-5p, and miR-146a-5p During Cervical Epithelial Transformation

  • Andrea Hornakova,
  • Zuzana Kolkova,
  • Lucia Kotulova,
  • Tomas Rokos and ,
  • Ivana Kasubova,
  • Terezia Pribulova,
  • Erik Kozubik,
  • Kamil Biringer,
  • Erik Kudela and
  • Veronika Holubekova
  • + 5 authors+ 0 author

Background: Cervical cancer remains the fourth most common malignancy among women worldwide. Despite vaccination and regular screening, new molecular biomarkers are needed for improved early detection and risk assessment. MicroRNAs (miRNAs) play cruc...

(This article belongs to the Special Issue Epigenetic Signatures in Metabolic Health and Cancer)
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Epigenomes - ISSN 2075-4655