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Developmentally linked human DNA hypermethylation is associated with down-modulation, repression, and upregulation of transcription

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Epigenetics and its role in effecting agronomical traits

Gupta, C., & Salgotra, R. K. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.925688 · Cited by 43 · see citing works

Dnmt1, Dnmt3a and Dnmt3b cooperate in photoreceptor and outer plexiform layer development in the mammalian retina

Singh, R. K., Mallela, R. K., Moye, A. R., Dunham, N. R., Hedden, M., Enke, R. A., Fariss, R. N., Sternberg, H., West, M. D., & Nasonkin, I. O. (2016) · Experimental Eye Research · doi:10.1016/j.exer.2016.11.014 · Cited by 42 · see citing works

Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development

Yang, X., Hu, B., Liao, J., Qiao, Y., Chen, Y., Qian, Y., Feng, S., Yu, F., Dong, J., Hou, Y., et al. (2019) · Cell Research · doi:10.1038/s41422-019-0234-8 · Cited by 40 · see citing works

A novel bivalent chromatin associates with rapid induction of camalexin biosynthesis genes in response to a pathogen signal in Arabidopsis

Zhao, K., Kong, D., Jin, B., Smolke, C. D., & Rhee, S. Y. (2021) · eLife · doi:10.7554/elife.69508 · Cited by 39 · see citing works

Lsh/HELLS regulates self-renewal/proliferation of neural stem/progenitor cells

Han, Y., Ren, J., Lee, E. Y., Xu, X., Yu, W., & Muegge, K. (2017) · Scientific Reports · doi:10.1038/s41598-017-00804-6 · Cited by 38 · see citing works

Tissue-Specific Epigenetics of Atherosclerosis-Related ANGPT and ANGPTL Genes

Ehrlich, K. C., Lacey, M. R., & Ehrlich, M. (2019) · Epigenomics · doi:10.2217/epi-2018-0150 · Cited by 38 · see citing works

Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs

Zhu, Y., Zhou, Z., Huang, T., Zhang, Z., Li, W., Ling, Z., Jiang, T., Yang, J., Yang, S., Xiao, Y., et al. (2022) · Science China Life Sciences · doi:10.1007/s11427-021-2034-5 · Cited by 38 · see citing works

Are there specific readers of oxidized 5‐methylcytosine bases?

Song, J., & Pfeifer, G. P. (2016) · BioEssays · doi:10.1002/bies.201600126 · Cited by 35 · see citing works

The Dynamics of Histone Modifications during Mammalian Zygotic Genome Activation

Lugo, F. S., Barrameda, N. I., Castillo‐Aleman, Y. M., Hernández, I. C., Valverde, C. A. V., Bencomo‐Hernandez, A. A., Ventura‐Carmenate, Y., & Jimenez, R. A. R. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25031459 · Cited by 34 · see citing works

Extraordinary Cancer Epigenomics: Thinking Outside the Classical Coding and Promoter Box

Murtha, M. J., & Esteller, M. (2016) · Trends in cancer · doi:10.1016/j.trecan.2016.08.004 · Cited by 30 · see citing works

Early-life DNA methylation profiles are indicative of age-related transcriptome changes

Hadad, N., Masser, D. R., Blanco-Berdugo, L., Stanford, D. R., & Freeman, W. M. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0306-5 · Cited by 29 · see citing works

Exposure to extracellular vesicles from Pseudomonas aeruginosa result in loss of DNA methylation at enhancer and DNase hypersensitive site regions in lung macrophages

Lee, M. K., Armstrong, D. A., Hazlett, H. F., Dessaint, J. A., Mellinger, D., Aridgides, D. S., Christensen, B. C., & Ashare, A. (2020) · Epigenetics · doi:10.1080/15592294.2020.1853318 · Cited by 28 · see citing works

Dual detection of chromatin accessibility and DNA methylation using ATAC-Me

Guerin, L. N., Barnett, K. R., & Hodges, E. C. (2021) · Nature Protocols · doi:10.1038/s41596-021-00608-z · Cited by 28 · see citing works

Recent Advances in DNA Methylation and Their Potential Breeding Applications in Plants

Shaikh, A., Chachar, S., Chachar, M., Ahmed, N., Guan, C., & Zhang, P. (2022) · Horticulturae · doi:10.3390/horticulturae8070562 · Cited by 28 · see citing works

DNA Hypomethylation in Intragenic and Intergenic Enhancer Chromatin of Muscle-Specific Genes Usually Correlates with their Expression.

Ehrlich, K. C., Paterson, H. L., Lacey, M. R., & Ehrlich, M. (2016) · Europe PMC (PubMed Central) · Cited by 28 · see citing works

MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis

Tong, Y., Sun, J., Wong, C. F., Kang, Q., Ru, B., Wong, C. N., Chan, A., Leung, S. Y., & Zhang, J. (2018) · Genome biology · doi:10.1186/s13059-018-1442-0 · Cited by 28 · see citing works

The Role of DNA Methylation and DNA Methyltransferases in Cancer

Weisenberger, D. J., Lakshminarasimhan, R., & Liang, G. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11454-0_13 · Cited by 27 · see citing works

Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies

Son, K. H., Aldonza, M. B. D., Nam, A.-R., Lee, K.-H., Lee, J.-W., Shin, K.-J., Kang, K., & Cho, J. (2023) · Science Advances · doi:10.1126/sciadv.ade3399 · Cited by 27 · see citing works

STAT5 Regulation of Sex-Dependent Hepatic CpG Methylation at Distal Regulatory Elements Mapping to Sex-Biased Genes

Hao, P., & Waxman, D. J. (2020) · Molecular and Cellular Biology · doi:10.1128/mcb.00166-20 · Cited by 27 · see citing works

Regulation of histone H3K27 methylation in inflammation and cancer

Ma, J., Zhang, Y., Li, J., Dang, Y., & Hu, D. (2025) · Molecular Biomedicine · doi:10.1186/s43556-025-00254-x · Cited by 25 · see citing works

Histone modifications and DNA methylation act cooperatively in regulating symbiosis genes in the sea anemone Aiptasia

Nawaz, K., Cziesielski, M. J., Mariappan, K. G., Cui, G., & Aranda, M. (2022) · BMC Biology · doi:10.1186/s12915-022-01469-y · Cited by 25 · see citing works

Analysis of KLF4 regulated genes in cancer cells reveals a role of DNA methylation in promoter- enhancer interactions

Oyinlade, O., Wei, S., Kammers, K., Liu, S., Wang, S., Ma, D., Huang, Z., Qian, J. X., Zhu, H., Wan, J., et al. (2018) · Epigenetics · doi:10.1080/15592294.2018.1504592 · Cited by 24 · see citing works

Epigenetic Regulation of β-Globin Genes and the Potential to Treat Hemoglobinopathies through Epigenome Editing

Fontana, L., Alahouzou, Z., Miccio, A., & Antoniou, P. (2023) · Genes · doi:10.3390/genes14030577 · Cited by 24 · see citing works

Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation

Sklias, A., Halaburková, A., Vanzan, L., Jimenez, N. F., Cuenin, C., Bouaoun, L., Cahais, V., Ythier, V., Sallé, A., Renard, C., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab697 · Cited by 21 · see citing works

Relationship of DNA methylation to mutational changes and transcriptional organization in fusion‐positive and fusion‐negative rhabdomyosarcoma

Sun, W., Chatterjee, B., Shern, J. F., Patidar, R., Song, Y., Wang, Y., Walker, R. L., Pawel, B., Linardic, C. M., Houghton, P. J., et al. (2018) · International Journal of Cancer · doi:10.1002/ijc.32006 · Cited by 21 · see citing works

DNA Glycosylases Define the Outcome of Endogenous Base Modifications

Lirussi, L., & Nilsen, H. L. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241210307 · Cited by 20 · see citing works

Genome-wide allele-specific methylation is enriched at gene regulatory regions in a multi-generation pedigree from the Norfolk Island isolate

Benton, M. C., Lea, R. A., Macartney-Coxson, D. P., Sutherland, H. G. E., White, N. M., Kennedy, D. W., Mengersen, K. L., Haupt, L. M., & Griffiths, L. R. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0304-7 · Cited by 20 · see citing works

Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification

Guerin, L. N., Scott, T. J., Yap, J. A., Johansson, A., Puddu, F., Charlesworth, T., Yang, Y., Simmons, A. J., Lau, K. S., Ihrie, R. A., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115680 · Cited by 19 · see citing works

Upregulation of Thymidylate Synthase Induces Pemetrexed Resistance in Malignant Pleural Mesothelioma

Sato, Y., Tomita, M., Soga, T., Ochiai, A., & Makinoshima, H. (2021) · Frontiers in Pharmacology · doi:10.3389/fphar.2021.718675 · Cited by 19 · see citing works

Epigenomic alterations in cancer: mechanisms and therapeutic potential

Gray, J. S., Wani, S. A., & Campbell, M. J. (2022) · Clinical Science · doi:10.1042/cs20210449 · Cited by 19 · see citing works

Relevance of DNA methylation at enhancers for the acquisition of cell identities

Kreibich, E., & Krebs, A. R. (2023) · FEBS Letters · doi:10.1002/1873-3468.14686 · Cited by 18 · see citing works

DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency

Albert, J. R., Urli, T., Monteagudo, A., Breton, A. L., Sultanova, A., David, A., Scarpa, M., Schulz, M., & Greenberg, M. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01405-4 · Cited by 18 · see citing works

Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer

Flam, E. L., Danilova, L., Kelley, D. Z., Stavrovskaya, E. D., Guo, T. W., Considine, M., Qian, J. X., Califano, J. A., Favorov, A. V., Fertig, E. J., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-51018-x · Cited by 17 · see citing works

Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced somatic mutation rates in survival outliers of glioblastoma

Hwang, T., Mathios, D., McDonald, K., Daris, I., Park, S.-H., Burger, P., Kim, S., Dho, Y.-S., Carolyn, H., Bettegowda, C., et al. (2019) · Acta Neuropathologica Communications · doi:10.1186/s40478-019-0744-0 · Cited by 13 · see citing works

HIST1H1C Regulates Interferon-β and Inhibits Influenza Virus Replication by Interacting with IRF3

Liu, X., Yang, C., Hu, Y., Lei, E., Lin, X., Zhao, L., Zou, Z., Zhang, A., Zhou, H., Chen, H., et al. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00350 · Cited by 16 · see citing works

Deciphering the Epigenetic Code in Embryonic and Dental Pulp Stem Cells.

Bayarsaihan, D. (2016) · Europe PMC (PubMed Central) · Cited by 14 · see citing works

Harnessing targeted DNA methylation and demethylation using dCas9

Pflueger, C., Swain, T., & Lister, R. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190029 · Cited by 14 · see citing works

DNA Promoter Methylation and ERG Regulate the Expression of CD24 in Prostate Cancer

Tolkach, Y., Zarbl, R., Bauer, S., Ritter, M., Ellinger, J., Hauser, S., Hüser, L., Klauck, S. M., Altevogt, P., Sültmann, H., et al. (2021) · American Journal Of Pathology · doi:10.1016/j.ajpath.2020.12.014 · Cited by 13 · see citing works

Interleukin-1 receptor associated kinase 1 (IRAK1) is epigenetically activated in luminal epithelial cells in prostate cancer

Schagdarsurengin, U., Breiding, V., Loose, M., Wagenlehner, F. R. A., & Dansranjav, T. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.991368 · Cited by 13 · see citing works

Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers

Bhandari, Y. R., Krishna, V., Powers, R., Parmar, S., Thursby, S.-J., Gupta, E., Kulak, O., Gokare, P. R., Reumers, J., Wesenbeeck, L. V., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2301536120 · Cited by 14 · see citing works

Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation

Edrei, Y., Levy, R., Kaye, D., Marom, A., Radlwimmer, B., & Hellman, A. (2023) · Genome biology · doi:10.1186/s13059-023-03094-6 · Cited by 12 · see citing works

Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters

Stefanova, M. E., Ing‐Simmons, E., Stefanov, S. R., Flyamer, I. M., García, H. D., Schöpflin, R., Henssen, A. G., Vaquerizas, J. M., & Mundlos, S. (2023) · Cells · doi:10.3390/cells12152001 · Cited by 12 · see citing works

MethylationToActivity: a deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors

Williams, J. S., Xu, B., Putnam, D. K., Thrasher, A., Li, C., Yang, J., & Chen, X. '. (2021) · Genome biology · doi:10.1186/s13059-020-02220-y · Cited by 12 · see citing works

Immunohistochemical Detection of 5-Methylcytosine and 5-Hydroxymethylcytosine in Developing and Postmitotic Mouse Retina

Singh, R. K., Diaz, P. E., Binette, F., & Nasonkin, I. O. (2018) · Journal of Visualized Experiments · doi:10.3791/58274 · Cited by 12 · see citing works

Analysis of expression of FLI1 and MMP1 in American cutaneous leishmaniasis caused by Leishmania braziliensis infection

de Almeida, L. D. S., Silva, J., Andrade, V. M., Machado, P. R. L., Jamieson, S. E., Carvalho, E. M., Blackwell, J. M., & Castellucci, L. C. (2017) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2017.01.018 · Cited by 10 · see citing works

Primetime for Learning Genes

Keifer, J. (2017) · Genes · doi:10.3390/genes8020069 · Cited by 10 · see citing works

Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress

Xu, Q., Huang, S., Guo, G., Yang, C., Wang, M., Zeng, X., & Wang, Y. (2022) · BMC Genomics · doi:10.1186/s12864-022-09070-x · Cited by 9 · see citing works

DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape

Gehrs, S., Gu, Z., Hey, J., Weichenhan, D., Buckwalter, N., Jakab, M., Hotz‐Wagenblatt, A., Breuer, K., Prada, M. L., Hübschmann, D., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf435 · Cited by 8 · see citing works

DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era

MacPhillamy, C., Chen, T., Hiendleder, S., Williams, J. L., Alinejad‐Rokny, H., & Low, W. Y. (2024) · GigaScience · doi:10.1093/gigascience/giae061 · Cited by 8 · see citing works

DNA methylation and chromatin modifications

Sepehri, Z., Beacon, T. H., Osman, F. D. S., Jahan, S., & Davie, J. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-816843-1.00002-3 · Cited by 8 · see citing works

A competition model of multilineage priming and cell-fate decisions

Steinschaden, T., Faure, L., Soldatov, R., & Adameyko, I. I. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116690 · Cited by 7 · see citing works

Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells

Mantsoki, A., Parussel, K., & Joshi, A. (2021) · Bioinformatics and Biology Insights · doi:10.1177/1177932220974623 · Cited by 7 · see citing works

Modified Forms of Cytosine in Eukaryotes: DNA (De)methylation and Beyond

Eleftheriou, M., & Ruzov, A. S. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0876-0_1 · Cited by 7 · see citing works

The Potential Role of Epigenetics in Aquaculture

Wang, H., & Shen, Z. (2023) · Wiley eBooks · doi:10.1002/9781119821946.ch1 · Cited by 7 · see citing works

The Distinct Role of the HDL Receptor SR-BI in Cholesterol Homeostasis of Human Placental Arterial and Venous Endothelial Cells

Strahlhofer-Augsten, M., Schliefsteiner, C., Cvitic, S., George, M., Lang, I., Hirschmugl, B., Marsche, G., Lang, U., Novakovic, B., Saffery, R., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23105364 · Cited by 6 · see citing works

Super-enhancer DNA methylation in cancer: the mechanism of action and therapeutic directions

Bi, Y., Zou, K., & Wang, K. (2025) · Frontiers in Oncology · doi:10.3389/fonc.2025.1610579 · Cited by 4 · see citing works

Challenges and Opportunities of Genomic Approaches in Therapeutics Development.

Gray, J. S., & Campbell, M. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0849-4_7 · Cited by 2 · see citing works

STXBP6, reciprocally regulated with autophagy, reduces triple negative breast cancer aggressiveness

Lenka, G., Shan, J., Halabi, N. M., Abuaqel, S. W. J., Goswami, N., Schmidt, F., Zaghlool, S. B., Romero, A. R., Subramanian, M., Boujassoum, S., et al. (2020) · Clinical and Translational Medicine · doi:10.1002/ctm2.147 · Cited by 4 · see citing works

DNA methylation and hydroxymethylation dynamics in the aging brain and its impact on ischemic stroke

Arruri, V. K., Joshi, P., & Vemuganti, R. (2025) · Neurochemistry International · doi:10.1016/j.neuint.2025.106007 · Cited by 3 · see citing works

Association of Intergenic and Intragenic MGMT Enhancer Methylation with MGMT Promoter Methylation, MGMT Protein Expression and Clinical and Demographic Parameters in Glioblastoma

Pühringer, K., Czarda, P., Iluca, S., Zappe, K., Weis, S., Spiegl‐Kreinecker, S., & Cichna‐Markl, M. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26073390 · Cited by 2 · see citing works

A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome

Liu, H., Jiang, T., Wang, S., Chen, X. '., Jin, X., Wang, Q., Li, X., Yin, J., Shao, T., Li, Y., et al. (2019) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2019.00427 · Cited by 2 · see citing works

Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies

Kanapeckaitė, A., Burokienė, N., Mažeikienė, A., Cottrell, G. S., & Widera, D. (2021) · Biophysical Reports · doi:10.1016/j.bpr.2021.100028 · Cited by 2 · see citing works

Coloured noise induces phenotypic diversity with energy dissipation

Chen, L., Wang, Y., Liu, J., & Wang, H. (2022) · Biosystems · doi:10.1016/j.biosystems.2022.104648 · Cited by 2 · see citing works

Transition Yet Energy Consuming for Tumor Growth Regulated by the Colored Microenvironment

Chen, L., Wang, Y., Li, Q., & Wang, H. (2023) · Complexity · doi:10.1155/2023/5557123 · Cited by 2 · see citing works

Enhancer dynamics and cellular architecture in the human spinal cord

Kandror, E. K., Wang, A., Carriere, M., Peterson, A., Liao, W., Tjärnberg, A., Fung, J. H., Mahbubani, K. T. A., Loper, J., Pangburn, W., et al. (2026) · Neuron · doi:10.1016/j.neuron.2025.12.035 · Cited by 1 · see citing works

Interplay of the Genetic Variants and Allele Specific Methylation in the Context of a Single Human Genome Study

Voronina, M. D., Zayakina, O. V., Deinichenko, K. A., Shingalieva, O. S., Tsimmer, O. Y., Tarasova, D. A., Grebnev, P. A., Snigir, E. A., Игоревич, М. С., Yudin, V. S., et al. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26199641 · Cited by 1 · see citing works

Analyses of Genome-Wide Histone Modifications in the Mammalian Genome

Tian, S., Slager, S. L., Gaonkar, K. S., & Yan, H. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-805388-1.00010-9 · Cited by 1 · see citing works

Epigenetic disruption of the RARγ complex impairs its function to bookmark AR enhancer interactions required for enzalutamide sensitivity in prostate cancerPreprint

Wani, S. A., Hussain, S., Gray, J. S., Nayak, D., Tang, H., Perez, L. M., Long, M. D., Manjunath, S., McCabe, C. J., Sucheston‐Campbell, L. E., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.15.571947 · Cited by 1 · see citing works

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism

Sharifi‐Zarchi, A., Daniela Gerovska, D., Adachi, K., Totonchi, M., Pezeshk, H., Taft, R. J., Schöler, H. R., Chitsaz, H., Sadeghi, M., Baharvand, H., et al. (2017) · BMC Genomics · doi:10.1186/s12864-017-4353-7 · Cited by 123 · see citing works

The DNA Methylation Landscape of Enhancers in The Guinea Pig Hippocampus

Boureau, L., Constantinof, A., Moisiadis, V. G., Matthews, S. G., & Moshe Szyf, A. (2018) · Epigenomics · doi:10.2217/epi-2017-0064 · Cited by 5 · see citing works

Causal role of histone acetylations in enhancer function

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Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation

Kreibich, E., Kleinendorst, R., Barzaghi, G., Kaspar, S., & Krebs, A. R. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.01.017 · Cited by 97 · see citing works

DNA methylation patterns expose variations in enhancer-chromatin modifications during embryonic stem cell differentiation

Alajem, A., Roth, H., Ratgauzer, S., Bavli, D., Motzik, A., Lahav, S., Peled, I., & Ram, O. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009498 · Cited by 21 · see citing works