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Notch signalling patterns retinal composition by regulating atoh7 during post-embryonic growth

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DNA methylation changes in cystic fibrosis: Cause or consequence?

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Directed Evolution of an Enhanced POU Reprogramming Factor for Cell Fate Engineering

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PCSK9 genetic (rs11591147) and epigenetic (DNA methylation) modifications associated with PCSK9 expression and serum proteins in CAD patients

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An in vitro chronic damage model impairs inflammatory and regenerative responses in human colonoid monolayers

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Cis-regulatory elements: systematic identification and horticultural applications

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Deciphering a TB-related DNA methylation biomarker and constructing a TB diagnostic classifier

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Context-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38

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Tet2 regulates Sin3a recruitment at active enhancers in embryonic stem cells

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Extensive DNA methylome rearrangement during early lamprey embryogenesis

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DNMT3A loss drives a HIF-1-dependent synthetic lethality to HDAC6 inhibition in non-small cell lung cancer

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Capturing functional epigenomes for insight into metabolic diseases

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Clinical and genetic characterization of nephropathy in patients with nail-patella syndrome

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Identification of atypical mitogen-activated protein kinase MAPK4 as a novel regulator in acute lung injury

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DNA methylation changes in metabolic and immune-regulatory pathways in blood and lymph node CD4 + T cells in response to SIV infections

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RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF

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Cell identity bookmarking through heterogeneous chromatin landscape maintenance during the cell cycle

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DNA methylation profiling allows for characterization of atrial and ventricular cardiac tissues and hiPSC-CMs

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Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO2 Levels

Corbett, R. J., PAS, M. F. W. T., van den Brand, H., Groenen, M. A. M., Crooijmans, R. P. M. A., Ernst, C. W., & Madsen, O. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.558189 · Cited by 16

Hypoxia Affects HIF-1/LDH-A Signaling Pathway by Methylation Modification and Transcriptional Regulation in Japanese Flounder (Paralichthys olivaceus)

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Methylation and transcriptomic profiling reveals short term and long term regulatory responses in polarized macrophages

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Maternal Inulin Supplementation Alters Hepatic DNA Methylation Profile and Improves Glucose Metabolism in Offspring Mice

Zhang, Q., Xiao, X., Zheng, J., Li, M., Yu, M., Ping, F., Wang, T., & Wang, X. (2020) · Frontiers in Physiology · doi:10.3389/fphys.2020.00070 · Cited by 16

Whole genome bisulfite sequencing of sperm reveals differentially methylated regions in male partners of idiopathic recurrent pregnancy loss cases

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Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly ( Vanessa cardui )

Boman, J., Zhu, Y., Höök, L., Vila, R., Talavera, G., & Backström, N. (2023) · Molecular Ecology · doi:10.1111/mec.16957 · Cited by 15

Elevated Expression of Two Pore Potassium Channel THIK-1 in Alzheimer’s Disease: An Inflammatory Mechanism

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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

An aggregated mitochondrial distribution in preimplantation embryos disrupts nuclear morphology, function, and developmental potential

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Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia

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Targeting DNA Methylation Machinery in Pediatric Solid Tumors

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

Cadmium exposure and its association with oxidative stress, MT1A methylation, and idiopathic male infertility in Egypt: A case-control study

Hassan, J., Elmetwalli, A., Helal, M., Munajer, E. A. A., Hussien, T. M., Saad, A. A., & Sikaily, A. E. (2024) · Food and Chemical Toxicology · doi:10.1016/j.fct.2024.114925 · Cited by 15

Ageing, Drosophila melanogaster and Epigenetics

Halim, M. A., Tan, F. H. P., Azlan, A., Rasyid, I. I., Rosli, N., Shamsuddin, S., & Azzam, G. (2020) · Malaysian Journal of Medical Sciences · doi:10.21315/mjms2020.27.3.2 · Cited by 17

The ubiquitous transcriptional protein ZNF143 activates a diversity of genes while assisting to organize chromatin structure

Huning, L., & Kunkel, G. R. (2020) · Gene · doi:10.1016/j.gene.2020.145205 · Cited by 13

Insights from multidimensional analyses of the pan‐cancer DNA methylome heterogeneity and the uncanonical CpG–gene associations

Liu, Y., Huang, R., Liu, Y., Song, W., Wang, Y., Yang, Y., Dong, S., & Yang, X. (2018) · International Journal of Cancer · doi:10.1002/ijc.31810 · Cited by 16

The role of noncoding mutations in blood cancers

Rahman, S., & Mansour, M. R. (2019) · Disease Models & Mechanisms · doi:10.1242/dmm.041988 · Cited by 16

Clinical implications of chromatin accessibility in human cancers

Liu, Y. (2020) · Oncotarget · doi:10.18632/oncotarget.27584 · Cited by 15

Unveiling the regulatory potential of the non-coding genome: Insights from the human genome project to precision medicine

Ruffo, P., Traynor, B. J., & Conforti, F. L. (2025) · Genes & Diseases · doi:10.1016/j.gendis.2025.101652 · Cited by 15

Distinctive aspects of the placental epigenome and theories as to how they arise

Pastor, W. A., & Kwon, S. Y. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-022-04568-9 · Cited by 15

Unanticipated broad phylogeny of BEN DNA-binding domains revealed by structural homology searches

Pan, A., Zeng, Y., Liu, J., Zhou, M., Lai, E. C., & Yu, Y. (2023) · Current Biology · doi:10.1016/j.cub.2023.05.011 · Cited by 14

Pancreatic cancer acquires resistance to MAPK pathway inhibition by clonal expansion and adaptive DNA hypermethylation

Godfrey, L., Förster, J., Liffers, S., Schröder, C., Köster, J., Henschel, L., Ludwig, K. U., Laehnemann, D., Trajkovic‐Arsic, M., Behrens, D., et al. (2024) · Clinical Epigenetics · doi:10.1186/s13148-024-01623-z · Cited by 15

DNA methylation-environment interactions in the human genome

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Specificity landscapes of 40 R2R3‐MYBs reveal how paralogs target different cis‐elements by homodimeric binding

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Nucleic Acid Aptamers Targeting Epigenetic Regulators: An Innovative Therapeutic Option

Catuogno, S., Esposito, C. L., Ungaro, P., & de Franciscis, V. (2018) · Pharmaceuticals · doi:10.3390/ph11030079 · Cited by 14

A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences

Nikolova, E. N., Stanfield, R. L., Dyson, H. J., & Wright, P. E. (2020) · Biochemistry · doi:10.1021/acs.biochem.0c00253 · Cited by 16

Regulation of Gene Expression and the Elucidative Role of CRISPR-Based Epigenetic Modifiers and CRISPR-Induced Chromosome Conformational Changes

Martella, A., & Fisher, D. I. (2021) · The CRISPR Journal · doi:10.1089/crispr.2020.0108 · Cited by 14

Charting differentially methylated regions in cancer with Rocker-meth

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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

Conflicts of CpG density and DNA methylation are proximally and distally involved in gene regulation in human and mouse tissues

Chen, F., Zhang, Q., Deng, X., Zhang, X., Chen, C., Lv, D., Li, Y., Li, D., Zhang, Y., Li, P., et al. (2018) · Epigenetics · doi:10.1080/15592294.2018.1500057 · Cited by 13

Organ-specific expression and epigenetic traits of genes encoding digestive enzymes in the lance-leaf sundew (Drosera adelae)

Arai, N., Ohno, Y., Jumyo, S., Hamaji, Y., & Ohyama, T. (2020) · Journal of Experimental Botany · doi:10.1093/jxb/eraa560 · Cited by 13

Silencing of MBD2 and EZH2 inhibits the proliferation of colorectal carcinoma cells by rescuing the expression of SFRP

Xie, Y., Wang, F., Yu, J. Q., Zhang, J., Liu, Y., Li, M., & Qi, J. (2021) · Oncology Reports · doi:10.3892/or.2021.8201 · Cited by 13

RNA-Seq and WGBS Analyses During Fruit Ripening and in Response to ABA in Sweet Cherry (Prunus avium) Reveal Genetic and Epigenetic Modulation of Auxin and Cytokinin Genes

Kühn, N., Arellano, M., Ponce, C., Christian Hodar, Q., Correa, F., Multari, S., Martens, S., Carrera, E., Donoso, J. M., & Meisel, L. A. (2024) · Journal of Plant Growth Regulation · doi:10.1007/s00344-024-11340-9 · Cited by 15

Identification of Eleutherococcus senticosus NAC transcription factors and their mechanisms in mediating DNA methylation of EsFPS, EsSS, and EsSE promoters to regulate saponin synthesis

Dong, J., Zhao, X., Song, X., Wang, S., Zhao, X., Liang, B., Long, Y., & Xing, Z. (2024) · BMC Genomics · doi:10.1186/s12864-024-10442-8 · Cited by 13

Skin Rejuvenation by Modulation of DNA Methylation

Grönniger, E., Max, H., & Lyko, F. (2024) · Experimental Dermatology · doi:10.1111/exd.70005 · Cited by 13

Origin, fate and function of extraembryonic tissues during mammalian development

Thowfeequ, S., Hanna, C. W., & Srinivas, S. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00809-w · Cited by 16

DNA 5mC methylation inhibits the formation of G-quadruplex structures in the genome

Niu, K., Xiang, L., Zhang, X., Li, X., Yao, T., Li, J., Zhang, C., Liu, J., Peng, Y., Xu, G., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03678-4 · Cited by 13

RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF

Rozenberg, J. M., Taylor, J. M., & Mack, C. P. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky617 · Cited by 13

Inhibition of PHLDA2 transcription by DNA methylation and YY1 in goat placenta

Wang, R., Su, L., Yu, S., Ma, X., Jiang, C., & Yu, Y. (2020) · Gene · doi:10.1016/j.gene.2020.144512 · Cited by 13

Identifying molecular targets for reverse aging using integrated network analysis of transcriptomic and epigenomic changes during aging

Lee, H.-Y., Jeon, Y., Kim, Y. K., Jang, J. Y., Cho, Y. S., Bhak, J., & Cho, K. (2021) · Scientific Reports · doi:10.1038/s41598-021-91811-1 · Cited by 13

SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes

Mulugeta, T. D., Nome, T., To, T., Gundappa, M. K., Macqueen, D. J., Våge, D. I., Sandve, S. R., & Hvidsten, T. R. (2019) · BMC Genomics · doi:10.1186/s12864-019-6051-0 · Cited by 13

A genome-wide analysis of DNA methylation identifies a novel association signal for Lp(a) concentrations in the LPA promoter

Coassin, S., Hermann‐Kleiter, N., Haun, M., Wahl, S., Wilson, R., Paulweber, B., Kunze, S., Meitinger, T., Strauch, K., Peters, A., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0232073 · Cited by 13

Folate deficiency disturbs PEG10 methylation modifications in human spina bifida

Lü, X., Yang, S., Jie, M., Wang, S., Sun, C., Wu, L., Chang, S., Pei, P., Wang, S., Zhang, T., et al. (2021) · Pediatric Research · doi:10.1038/s41390-021-01908-6 · Cited by 13

DNA methylation insulates genic regions from CTCF loops near nuclear specklesPreprint

Roseman, S. A., Siegenfeld, A. P., Lee, C., Lue, N. Z., Waterbury, A. L., & Liau, B. B. (2024) · eLife · doi:10.7554/elife.102930 · Cited by 15

Molecular mechanisms of estrogen action in female genital tract development

Alderman, M. H., & Taylor, H. S. (2021) · Differentiation · doi:10.1016/j.diff.2021.01.002 · Cited by 14

The circadian demethylation of a unique intronic deoxymethylCpG-rich island boosts the transcription of its cognate circadian clock output gene

Misra, N., Damara, M., Ye, T., & Chambon, P. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2214062120 · Cited by 13

Involvement of CCCTC-binding factor in epigenetic regulation of cancer

Bose, S., Saha, S., Goswami, H., Shanmugam, G., & Sarkar, K. (2023) · Molecular Biology Reports · doi:10.1007/s11033-023-08879-3 · Cited by 13

Hsa_circ_0020134 promotes liver metastasis of colorectal cancer through the miR-183-5p-PFN2-TGF-β/Smad axis

Yu, J.-H., Tan, J.-N., Zhong, G., Zhong, L., Hou, D., Ma, S., Wang, P., Zhang, Z., Lu, X.-Q., Yang, B., et al. (2023) · Translational Oncology · doi:10.1016/j.tranon.2023.101823 · Cited by 13

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

Early developmental carry‐over effects on exploratory behaviour and DNA methylation in wild great tits (Parus major)

Sepers, B., Verhoeven, K. J. F., & van Oers, K. (2024) · Evolutionary Applications · doi:10.1111/eva.13664 · Cited by 11

Dynamic DNA methylation modifications in the cold stress response of cassava

Yu, G., Zhang, B., Chen, Q., Huang, Z., Zhang, B., Wang, K., & Han, J. (2024) · Genomics · doi:10.1016/j.ygeno.2024.110871 · Cited by 12

Deciphering the dynamic code: DNA recognition by transcription factors in the ever-changing genome

Yao, Y. M., Miodownik, I., O’Hagan, M., Jbara, M., & Afek, A. (2024) · Transcription · doi:10.1080/21541264.2024.2379161 · Cited by 12

Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models

Laufer, B. I., Hasegawa, Y., Zhang, Z., Hogrefe, C. E., Rosso, L. A. D., Haapanen, L. A. D., Hwang, H., Bauman, M. D., de Water, J. V., Taha, A. Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33162-7 · Cited by 12

Proteins That Read DNA Methylation

Liu, K., Shimbo, T., Song, X., Wade, P. A., & Min, J. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11454-0_11 · Cited by 13

The MECP2‐TRD domain interacts with the DNMT3A‐ADD domain at the H3 ‐tail binding site

Kunert, S., Linhard, V. L., Weirich, S., Choudalakis, M., Osswald, F., Krämer, L., Köhler, A., Bröhm, A., Wollenhaupt, J., Schwalbe, H., et al. (2022) · Protein Science · doi:10.1002/pro.4542 · Cited by 12

Age‐ and quality‐dependent DNA methylation correlate with melanin‐based coloration in a wild bird

Soulsbury, C. D., Lipponen, A., Wood, K., Mein, C. A., Hoffman, J. I., & Lebigre, C. (2018) · Ecology and Evolution · doi:10.1002/ece3.4132 · Cited by 12

Transcriptional Landscape of PARs in Epithelial Malignancies

Nag, J. K., & Bar‐Shavit, R. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19113451 · Cited by 12

Pilocytic astrocytoma demethylation and transcriptional landscapes link bZIP transcription factors to immune response

Aichmüller, C., Iskar, M., Jones, D., Korshunov, A., Radlwimmer, B., Kool, M., Ernst, A., Pfister, S. M., Lichter, P., & Zapatka, M. (2020) · Neuro-Oncology · doi:10.1093/neuonc/noaa035 · Cited by 12

DNMT3A and TET2 mutations reshape hematopoiesis in opposing ways

López-Moyado, I. F., & Rao, A. (2020) · Nature Genetics · doi:10.1038/s41588-020-0641-2 · Cited by 12

Evolution of Developmental GATA Factors in Nematodes

Eurmsirilerd, E., & Maduro, M. (2020) · Journal of Developmental Biology · doi:10.3390/jdb8040027 · Cited by 12

The non-coding genome in genetic brain disorders: new targets for therapy?

Salsench, E. M., Karkala, F., Lanko, K., & Barakat, T. S. (2021) · Essays in Biochemistry · doi:10.1042/ebc20200121 · Cited by 11

Promoter Hypermethylation Promotes the Binding of Transcription Factor NFATc1, Triggering Oncogenic Gene Activation in Pancreatic Cancer

Wu, Y., Kröller, L., Miao, B., Boekhoff, H., Bauer, A. S., Büchler, M. W., Hackert, T., Giese, N. A., Taipale, J., & Hoheisel, J. D. (2021) · Cancers · doi:10.3390/cancers13184569 · Cited by 12

Comparison of Genome-Wide DNA Methylation Profiles of Human Fetal Tissues Conceived by in vitro Fertilization and Natural Conception

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Notch Controls Multiple Pancreatic Cell Fate Regulators Through Direct Hes1-mediated RepressionPreprint

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