Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer

Hallmarks of Cancer: The Next Generation

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Regulation of Hepatic Long Noncoding RNAs by Pregnane X Receptor and Constitutive Androstane Receptor Agonists in Mouse Liver

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Epigenetic plasticity potentiates a rapid cyclical shift to and from an aggressive cancer phenotype

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Overexpression of anillin is related to poor prognosis in patients with hepatocellular carcinoma

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DNA methylation signatures associated with prognosis of gastric cancer

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Integrative Analysis of Epigenome and Transcriptome Data Reveals Aberrantly Methylated Promoters and Enhancers in Hepatocellular Carcinoma

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DNA methylation in adult diffuse gliomas

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Novel Assay for Quantitative Analysis of DNA Methylation at Single-Base Resolution

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Maternal hypercholesterolemia exacerbates atherosclerosis lesions in female offspring through potentiating macrophage polarization toward an inflammatory M1 phenotype

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Perturbed DNA methylation by Gadd45b induces chromatin disorganization, DNA strand breaks and dopaminergic neuron death

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CBFB-MYH11 Fusion Sequesters RUNX1 in Cytoplasm to Prevent DNMT3A Recruitment to Target Genes in AML

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Integrative Genome-Wide DNA Methylome and Transcriptome Analysis of Ovaries from Hu Sheep with High and Low Prolific

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Identification of the ultrahigh-risk subgroup in neuroblastoma cases through DNA methylation analysis and its treatment exploiting cancer metabolism

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Genome-wide DNA methylation of Munro’s microabscess reveals the epigenetic regulation in the pathogenesis of psoriasis

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Effect of epigenetics on vitamin D levels: a systematic review until December 2020

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Epigenetic hallmarks in pulmonary fibrosis: New advances and perspectives

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Comparative computational analysis to distinguish mesenchymal stem cells from fibroblasts

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Whole-Genome DNA Methylation Profiling of Intrahepatic Cholangiocarcinoma Reveals Prognostic Subtypes with Distinct Biological Drivers

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Identification of a class of human cancer germline genes with transcriptional silencing refractory to the hypomethylating drug 5-aza-2ˈ-deoxycytidine

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Genome-wide DNA methylation differences according to oestrogen receptor beta status in colorectal cancer

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Mechanism of methylation and acetylation of high GDNF transcription in glioma cells: A review

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Gene–methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk

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Multi-Omics Characterization of Inflammatory Bowel Disease-Induced Hyperplasia/Dysplasia in the Rag2−/−/Il10−/− Mouse Model

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The methyl donor S-adenosyl methionine reverses the DNA methylation signature of chronic neuropathic pain in mouse frontal cortex

Topham, L., Grégoire, S., Kang, H., Salmon‐Divon, M., Lax, E., Millecamps, M., Moshe Szyf, A., & Stone, L. S. (2021) · PAIN Reports · doi:10.1097/pr9.0000000000000944 · Cited by 18

CASK Silence Overcomes Sorafenib Resistance of Hepatocellular Carcinoma Through Activating Apoptosis and Autophagic Cell Death

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Integrated Analysis of DNA methylation and transcriptome profile to identify key features of age-related macular degeneration

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Transcriptional implications of intragenic DNA methylation in the oestrogen receptor alpha gene in breast cancer cells and tissues

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Intra-Gene DNA Methylation Variability Is a Clinically Independent Prognostic Marker in Women’s Cancers

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The Role of Epigenetic Regulation in Transcriptional Memory in the Immune System

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Putative biomarkers of malignant transformation of sinonasal inverted papilloma into squamous cell carcinoma

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Death-ision: the link between cellular resilience and cancer resistance to treatments

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Isoform switching and exon skipping induced by the DNA methylation inhibitor 5-Aza-2′-deoxycytidine

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Changes in the rearing environment cause reorganization of molecular networks associated with DNA methylation

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DNA methylation-activated full-length EMX1 facilitates metastasis through EMX1-EGFR-ERK axis in hepatocellular carcinoma

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The Effect of Maternal Diet and Physical Activity on the Epigenome of the Offspring

Panagiotidou, A., Chatzakis, C., Ververi, A., Eleftheriades, M. I., & Sotiriadis, A. (2024) · Genes · doi:10.3390/genes15010076 · Cited by 20

Analyzing the relationship of RNA and DNA methylation with gene expression

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Identifying Reproducible Molecular Biomarkers for Gastric Cancer Metastasis with the Aid of Recurrence Information

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Highly sensitive detection of M.SssI DNA methyltransferase activity using a personal glucose meter

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The Role of Aberrant DNA Methylation in Misregulation of Gene Expression in Gonadotroph Nonfunctioning Pituitary Tumors

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Hepatocyte gene expression and DNA methylation as ancestry-dependent mechanisms in African Americans

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NNK-mediated upregulation of DEPDC1 stimulates the progression of oral squamous cell carcinoma by inhibiting CYP27B1 expression.

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Regulation of Canonical Oncogenic Signaling Pathways in Cancer via DNA Methylation

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Radiation-induced cardiovascular disease: an overlooked role for DNA methylation?

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PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification

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Epigenetic landscape change analysis during human EMT sheds light on a key EMT mediator TRIM29

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Transgenerational transmission of maternal stimulatory experience in domesticated birds

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Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics

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Whole-Methylome Analysis of Circulating Monocytes in Acute Diabetic Charcot Foot Reveals Differentially Methylated Genes Involved in the Formation of Osteoclasts

Pasquier, J., Spurgeon, M., Bradić, M., Thomas, B., Robay, A., Chidiac, O. M., Dib, M., Turjoman, R., Liberska, A., Staudt, M. R., et al. (2018) · Epigenomics · doi:10.2217/epi-2018-0144 · Cited by 16

DNA methylation dynamic of bone marrow hematopoietic stem cells after allogeneic transplantation

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Epigenetics of Aberrant Cardiac Wound Healing

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Omics approaches: Role in acute myeloid leukemia biomarker discovery and therapy

Shafiei, F. S., Abroun, S., Vahdat, S., & Rafiee, M. (2025) · Cancer Genetics · doi:10.1016/j.cancergen.2024.12.006 · Cited by 15

ZBP1 pathway promotes tumor immunogenicity in the combination of anti-HER2 therapy and epigenetic therapy

Wang, Q., Wu, Z., Yang, Y., Yang, C., Deng, H., Zhou, X., Xu, S., Wu, L., Hong, X., Yu, X., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116314 · Cited by 16

Contributions of DNA methylation aberrancies in shaping the cancer epigenome

Weisenberger, D. J., & Liang, G. (2015) · Translational Cancer Research · doi:10.21037/4482 · Cited by 15

Rethinking the Epigenetic Framework to Unravel the Molecular Pathology of Schizophrenia

Cariaga-Martínez, A. E., & Alelú‐Paz, R. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18040790 · Cited by 15

Transcriptomic and epigenomics atlas of myotubes reveals insight into the circadian control of metabolism and development

Altıntaş, A., Laker, R. C., Garde, C., Barrès, R., & Zierath, J. R. (2020) · Epigenomics · doi:10.2217/epi-2019-0391 · Cited by 15

Comparative Analysis of Skeletal Muscle DNA Methylation and Transcriptome of the Chicken Embryo at Different Developmental Stages

Ran, J., Li, J., Yin, L., Zhang, D., Yu, C., Du, H., Jiang, X., Yang, C., & Liu, Y. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.697121 · Cited by 16

Unified Description of Ultrafast Excited State Decay Processes in Epigenetic Deoxycytidine Derivatives

Kabaciński, P., Romanelli, M., Ponkkonen, E., Jaiswal, V. K., Carell, T., Garavelli, M., Cerullo, G., & Conti, I. (2021) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.1c02909 · Cited by 15

Differential usage of DNA modifications in neurons, astrocytes, and microglia

Tooley, K. B., Chucair‐Elliott, A. J., Ocañas, S. R., Machalinski, A. H., Pham, K. D., Hoolehan, W., Kulpa, A. M., Stanford, D. R., & Freeman, W. M. (2023) · Epigenetics & Chromatin · doi:10.1186/s13072-023-00522-6 · Cited by 13

Tet-mediated DNA methylation dynamics affect chromosome organization

Tian, H., Luan, P., Liu, Y., & Li, G. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae054 · Cited by 15

Race-specific coregulatory and transcriptomic profiles associated with DNA methylation and androgen receptor in prostate cancer

Ramakrishnan, S., Cortes-Gomez, E., Athans, S. R., Attwood, K. M., Rosario, S. R., Kim, S. J., Mager, D. E., Isenhart, E., Hu, Q., Wang, J., et al. (2024) · Genome Medicine · doi:10.1186/s13073-024-01323-6 · Cited by 15

Targeting DNA Methylation Machinery in Pediatric Solid Tumors

Cristalli, C., & Scotlandi, K. (2024) · Cells · doi:10.3390/cells13141209 · Cited by 14

Epigenetic modifications in KDM lysine demethylases associate with survival of early-stage NSCLC

Wei, Y., Liang, J., Zhang, R., Guo, Y., Shen, S., Li, S., Lin, X., Morán, S., Helland, Å., Bjaanæs, M. M., et al. (2018) · Clinical Epigenetics · doi:10.1186/s13148-018-0474-3 · Cited by 15

Epigenetic Heterogeneity in Human Colorectal Tumors Reveals Preferential Conservation And Evidence of Immune Surveillance

Ryser, M. D., Yu, M., Grady, W. M., Siegmund, K. D., & Shibata, D. K. (2018) · Scientific Reports · doi:10.1038/s41598-018-35621-y · Cited by 17

Aberrant Transcriptional Regulation of Super-enhancers by RET Finger Protein-histone Deacetylase 1 Complex in Glioblastoma: Chemoresistance to Temozolomide

Natsume, A., Hirano, M., Ranjit, M., Aoki, K., & Wakabayashi, T. (2019) · Neurologia medico-chirurgica · doi:10.2176/nmc.ra.2019-0049 · Cited by 15

Hypermethylation of CSF3R is a novel cisplatin resistance marker and predictor of response to postoperative chemotherapy in hepatoblastoma

Fujiyoshi, S., Honda, S., Minato, M., Ara, M., Suzuki, H., Hiyama, E., & Taketomi, A. (2020) · Hepatology Research · doi:10.1111/hepr.13479 · Cited by 15

Differentially Methylated Regions in Desmoid-Type Fibromatosis: A Comparison Between CTNNB1 S45F and T41A Tumors

Timbergen, M. J. M., Boers, R., Vriends, A. L. M., Boers, J., van IJcken, W. F. J., Lavrijsen, M., Grünhagen, D. J., Verhoef, C. K., Sleijfer, S., Smits, R., et al. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.565031 · Cited by 15

miR-29b restrains cholangiocarcinoma progression by relieving DNMT3B-mediated repression of CDKN2B expression

Cao, K., Li, B., Zhang, Y., Song, H., Chen, Y.-G., Gong, Y., Li, H., & Zuo, S. (2021) · Aging · doi:10.18632/aging.202549 · Cited by 15

Genome-Wide Differentially Methylated Region Analysis to Reveal Epigenetic Differences of Articular Cartilage in Kashin–Beck Disease and Osteoarthritis

Fan, Y., Gao, D., Zhang, Y., Zhu, J., Zhang, F., Wang, L., Wen, Y. F., Guo, X., & Sun, S. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.636291 · Cited by 16

High Expression of PDLIM2 Predicts a Poor Prognosis in Prostate Cancer and Is Correlated with Epithelial-Mesenchymal Transition and Immune Cell Infiltration

Piao, S., Zheng, L., Zheng, H.-H., Zhou, M., Feng, Q., Zhou, S., Ke, M., Yang, H., & Wang, X. (2022) · Journal of Immunology Research · doi:10.1155/2022/2922832 · Cited by 15

Identified in blood diet-related methylation changes stratify liver biopsies of NAFLD patients according to fibrosis grade

Sokolowska, K. E., Maciejewska, D., Bińkowski, J., Palma, J., Taryma‐Leśniak, O., Kozłowska‐Petriczko, K., Borowski, K., Baśkiewicz-Hałasa, M., Hawryłkowicz, V., Załęcka, P., et al. (2022) · Clinical Epigenetics · doi:10.1186/s13148-022-01377-6 · Cited by 15

Comparative DNA methylation analysis to decipher common and cell type-specific patterns among multiple cell types

Yang, X., Shao, X., Gao, L., & Zhang, S. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw013 · Cited by 15

Histone deacetylase 9 promoter hypomethylation associated with adipocyte dysfunction is a statin-related metabolic effect

Khamis, A., Boutry, R., Canouil, M., Mathew, S., Lobbens, S., Crouch, H. K., Andrew, T., Abderrahmani, A., Tamanini, F., & Froguel, P. (2020) · Clinical Epigenetics · doi:10.1186/s13148-020-00858-w · Cited by 16

CTLA-4 methylation regulates the pathogenesis of myasthenia gravis and the expression of related cytokines

Fang, T.-K., Yan, C., & Du, J. (2018) · Medicine · doi:10.1097/md.0000000000010620 · Cited by 15

Versatile fluorescence biosensors based on CRISPR/Cas12a for determination of site-specific DNA methylation from blood and tissues

Ding, L., Cao, S., Bai, L., He, S., He, L., Wang, Y., Wu, Y., & Yu, S. (2024) · Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy · doi:10.1016/j.saa.2024.125520 · Cited by 14

Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer

Ren, C., Tang, X., & Lan, H. (2021) · PeerJ · doi:10.7717/peerj.11377 · Cited by 14

GENECI: A novel evolutionary machine learning consensus-based approach for the inference of gene regulatory networks

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Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato

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Alterations of DNA methylation profile in peripheral blood of children with simple obesity

Ren, Y., Huang, P. F., Huang, X., Zhang, L., Liu, L., Xiang, W., Liu, L., & He, X. (2024) · Health Information Science and Systems · doi:10.1007/s13755-024-00275-w · Cited by 14

Subtle Alterations in DNA Methylation Patterns in Normal Cells in Response to Dietary Stilbenoids

Beetch, M., Lubecka, K., Kristofzski, H., Suderman, M. J., & Stefañska, B. (2018) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201800193 · Cited by 14

Childhood Adversity Is Associated With Increased KITLG Methylation in Healthy Individuals but Not in Bipolar Disorder Patients

He, Y., Vinkers, C. H., Houtepen, L. C., de Witte, L. D., & Boks, M. P. (2019) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2018.00743 · Cited by 14

The Cord Blood Insulin and Mitochondrial DNA Content Related Methylome

Reimann, B., Janssen, B. G., Alfano, R., Ghantous, A., Espín-Pérez, A., de Kok, T. M. C. M., Saenen, N. D., Cox, B., Robinson, O., Chadeau‐Hyam, M., et al. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00325 · Cited by 15

LMX1B mRNA expression and its gene body CpG methylation are valuable prognostic biomarkers for laryngeal squamous cell carcinoma

Liang, F., Zhang, A., & Deng, P. (2019) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2019.109174 · Cited by 14

Integrated Genome-Wide DNA Methylation and RNAseq Analysis of Hippocampal Specimens Identifies Potential Candidate Genes and Aberrant Signalling Pathways in Patients with Hippocampal Sclerosis

Dixit, A., Chandra, P., Srivastava, A., Sharma, D., Tripathi, M., Paul, D., Lalwani, S., Doddamani, R. S., Sharma, M., & Banerjee, J. (2020) · Neurology India · doi:10.4103/0028-3886.280649 · Cited by 14

Comparative genome‐wide methylation analysis of longissimus dorsi muscles in Yorkshire and Wannanhua pigs

Li, X. ‐., Liu, L. ‐., Dong, H., Yang, J. ‐., Wang, W. ‐., Zhang, Q.-K., Wang, C. ‐., Zhou, J., & Chen, H. (2020) · Animal Genetics · doi:10.1111/age.13029 · Cited by 14

Genomic and epigenomic biomarkers in colorectal cancer: From diagnosis to therapy

Bañobre, J. R., & Goel, A. (2021) · Advances in cancer research · doi:10.1016/bs.acr.2021.02.008 · Cited by 15

Analysis of the Prognostic Value and Gene Expression Mechanism of SHOX2 in Lung Adenocarcinoma

Li, N., Zeng, Y., Tai, M., Lin, B., Zhu, D., Luo, Y., Ren, X., Zhu, X., Li, L., Wu, H., et al. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.688274 · Cited by 14

Charting differentially methylated regions in cancer with Rocker-meth

Benelli, M., Franceschini, G. M., Magi, A., Romagnoli, D., Biagioni, C., Migliaccio, I., Malorni, L., & Demichelis, F. (2021) · Communications Biology · doi:10.1038/s42003-021-02761-3 · Cited by 14

DNA Methyltransferase 3B–Mediated Intratumoral Heterogeneity and Therapeutic Targeting in Breast Cancer Recurrence and Metastasis

So, J. Y., Yang, H. H., Park, W. Y., Skrypek, N., Ishii, H., Chen, J. M., Lee, M. P., & Li, Y. (2022) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-21-0887 · Cited by 14

DNA Methyltransferase Inhibitors

Raynal, N. J. ‐., & Issa, J. J. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-802208-5.00007-2 · Cited by 14

Tumor-augmenting effects of gestational arsenic exposure on F1 and F2 in mice

Nohara, K., Suzuki, T., Okamura, K., Matsushita, J., & Takumi, S. (2017) · Genes and Environment · doi:10.1186/s41021-016-0069-1 · Cited by 15

Competition between DNA Methylation, Nucleotide Synthesis, and Antioxidation in Cancer versus Normal Tissues

Cao, S., Zhu, X., Zhang, C., Qian, H., Schüttler, H.-B., Gong, J., & Xu, Y. (2017) · Cancer Research · doi:10.1158/0008-5472.can-17-0262 · Cited by 14

Epigenetic modulation of vascular diseases: Assessing the evidence and exploring the opportunities

Schiattarella, G. G., Madonna, R., Linthout, S. V., Thum, T., Schulz, R., Ferdinándy, P., & Perrino, C. (2018) · Vascular Pharmacology · doi:10.1016/j.vph.2018.02.009 · Cited by 14

Bayesian Negative Binomial Mixture Regression Models for the Analysis of Sequence Count and Methylation Data

Li, Q., Cassese, A., Guindani, M., & Vannucci, M. (2018) · Biometrics · doi:10.1111/biom.12962 · Cited by 14

Ranking genomic features using an information-theoretic measure of epigenetic discordance

Jenkinson, G., Abante, J., Koldobskiy, M. A., Feinberg, A. P., & Goutsias, J. I. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2777-6 · Cited by 13

Harnessing targeted DNA methylation and demethylation using dCas9

Pflueger, C., Swain, T., & Lister, R. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190029 · Cited by 18

A Novel Model of Pancreatic Cancer Dormancy Reveals Mechanistic Insights and a Dormancy Gene Signature with Human RelevancePreprint

Dudgeon, C., Harris, C. R., Chen, Y., Ghaddar, B., Sharma, A., Shah, M. M., Roberts, A. I., Casabianca, A., Collisson, E. A., Balachandran, V. P., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.13.037374 · Cited by 15

Aberrant DNA methylation as a key modulator of cell death pathways: insights into cancer progression and other diseases

Zahoor, A., Khazer, R., Mehraj, I., Gani, U., Fayaz, F., Khanday, F. A., & Saleem, S. (2025) · Functional & Integrative Genomics · doi:10.1007/s10142-025-01552-x · Cited by 13

Gene Body Methylation Confers Transcription Robustness in Mangroves During Long-Term Stress Adaptation

Wang, Y., Dai, A., Chen, Y., & Tang, T. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.733846 · Cited by 14

The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity

Ohnmacht, A. J., Rajamani, A., Avar, G., Kutkaite, G., Gonçalves, E., Saur, D., & Menden, M. P. (2023) · Communications Biology · doi:10.1038/s42003-023-05198-y · Cited by 12

Functional significance of DNA methylation: epigenetic insights into Sjögren’s syndrome

Wang, Y., Riaz, F., Wang, W., Pu, J., Liang, Y., Wu, Z., Pan, S., Song, J., Yang, L., Zhang, Y., et al. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1289492 · Cited by 16

Triphenyl Phosphate Alters Methyltransferase Expression and Induces Genome-Wide Aberrant DNA Methylation in Zebrafish Larvae

Negi, C. K., Bláhová, L., Phan, A., Bajard, L., & Bláha, L. (2024) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.4c00223 · Cited by 13

Abstract B56: DNA demethylation in gene bodies is of therapeutic significance

Zhang, H. H., Yang, X., Carvalho, D. D. D., Jones, P. A., & Liang, G. (2013) · Cancer Research · doi:10.1158/1538-7445.cec13-b56 · Cited by 1

Up and down for DNA methylation inhibitors

Burgess, D. J. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3845 · Cited by 2

5-Aza-CdR Delivers a Gene Body Blow

Kasinathan, S., & Henikoff, S. (2014) · Cancer Cell · doi:10.1016/j.ccell.2014.09.004 · Cited by 11

Putative promoters within gene bodies control exon expression via TET1‐mediated H3K36 methylation

Ma, L., Muhammad, T., Wang, H., Du, G., Sakhawat, A., Wei, Y., Khan, A. A., Cong, X., & Huang, Y. (2020) · Journal of Cellular Physiology · doi:10.1002/jcp.29566 · Cited by 3

Combination Treatment of AML Cells with Dnmt and HDAC Inhibitors: Synergistic Target Gene Downregulation Associated with Gene Body Demethylation

Blagitko‐Dorfs, N., Schlosser, P., Pfeifer, D., & Lübbert, M. (2015) · Blood · doi:10.1182/blood.v126.23.2432.2432