EpigenomesPub Date : 2025-12-13DOI: 10.3390/epigenomes9040051
Stefano Amatori
{"title":"The Evolutionary Misfit: Evolution, Epigenetics, and the Rise of Non-Communicable Diseases.","authors":"Stefano Amatori","doi":"10.3390/epigenomes9040051","DOIUrl":"10.3390/epigenomes9040051","url":null,"abstract":"<p><p>Human life expectancy has risen dramatically in the last century, but this demographic triumph has come at the cost of an explosion of non-communicable diseases (NCDs), threatening the sustainability of healthcare systems in aging, low-fertility societies. Evolutionary medicine provides a framework to understand, at least in part, this paradox. Many vulnerabilities to disease are not failures of design but the predictable outcomes of evolutionary trade-offs, constraints, and mismatches. Evolutionary mismatch theory explains how traits once advantageous in ancestral environments become maladaptive in modern contexts of abundance, sedentarism, and urbanization. The developmental origins of health and disease (DOHaD) concept describes how epigenetic plasticity in early life can buffer or amplify these mismatches, depending on whether adult environments align with developmental forecasts. Transgenerational epigenetic inheritance, even if still debated in humans, may further influence phenotypic plasticity, increasing or mitigating the mismatch. In evolutionary terms, the theories of mutation accumulation, antagonistic pleiotropy, and the disposable soma explain why longer lifespans, and ecological and social conditions profoundly different from those in which we developed, increase the likelihood that these costs are expressed clinically. Because most NCDs can be prevented and effectively controlled but not cured, efforts should prioritize quality of life for people, families, and communities. At the individual level, aligning lifestyles with evolved biology can mitigate risk, but the greatest leverage lies in population-level interventions. Urban health strategies represent a forward-looking attempt to realign modern environments with human biology. In this way, the concept of the evolutionary misfit becomes not just a diagnosis of maladaptation, but a guide for building healthier, more sustainable societies.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 4","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12731877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomesPub Date : 2025-12-08DOI: 10.3390/epigenomes9040050
Abhishu Chand, Kyoungtae Kim
{"title":"The Epigenomic Impact of Quantum Dots: Emerging Biosensors and Potential Disruptors.","authors":"Abhishu Chand, Kyoungtae Kim","doi":"10.3390/epigenomes9040050","DOIUrl":"10.3390/epigenomes9040050","url":null,"abstract":"<p><p>Quantum dots (QDs) have emerged as powerful tools in biomedical applications due to their unique optical and fluorescent properties which enable highly sensitive and multiplexed detection of biomolecules. Particularly in the field of epigenetic research, QDs are utilized as biosensors for monitoring changes in DNA methylation, microRNA (miRNA) expression, and histone modifications, providing a viable alternative to conventional assays. However, increasing evidence also suggests that QDs act as an epigenetic disruptor, altering epigenetic mechanisms and downstream cellular processes. This dual role raises important questions about the safety, reliability, and translational potential of QDs in clinical usage. Therefore, in this commentary we critically evaluate the advances of QD-based epigenetic sensing platforms while also providing insights into QD-based epigenetic dysregulation. We further discuss the current limitations and provide future directions to gain a better understanding of how QDs function to bridge the gap between their diagnostic potential and clinical integration.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12731947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomesPub Date : 2025-12-05DOI: 10.3390/epigenomes9040049
Edward A Ruiz-Narváez
{"title":"Introducing the EpG<sup>2</sup> System: Epigenomic Processes and the Emergent Genome.","authors":"Edward A Ruiz-Narváez","doi":"10.3390/epigenomes9040049","DOIUrl":"10.3390/epigenomes9040049","url":null,"abstract":"<p><p><b>Background/Objectives:</b> Current genomics research equates the genome with DNA sequence and treats the epigenome as a regulatory layer. This DNA-centric view obscures the fact that genomic identity arises through epigenomic processes. The objective of this article is to reinterpret published findings into a new theoretical framework: the EpG<sup>2</sup> (Epigenome-Genome) system. <b>Methods:</b> This work develops a new conceptual framework by integrating published evidence from diverse domains-including enhancer biology, overlapping genomic functions, alternative coding frames, zygotic genome activation, and disease-associated loci-and reinterpreting these findings through the lens of epigenomic processes. <b>Results:</b> Evidence shows that enhancers emerge only through the interplay of sequence, transcription factors, and chromatin environment. At fertilization, paternal and maternal genomes remain separate, and a new genome emerges through coordinated epigenomic reprogramming or zygote genome emergence (ZGE). DNA sequence risk variants illustrate the concept of contextual risk alleles, whose effects shift across tissues and developmental stages as epigenomic contexts change. <b>Conclusions:</b> The EpG<sup>2</sup> system reframes the genome as a processual, emergent entity generated and regulated by epigenomic processes, offering a paradigm for understanding genomic variation beyond DNA sequence.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12731938/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomesPub Date : 2025-11-27DOI: 10.3390/epigenomes9040048
Alexandra L Nowak, Marvin A Schilt-Solberg, Xiaoyu Liang, Fabiola Magaña, Dawn P Misra, Carmen Giurgescu
{"title":"Adverse Childhood Experiences, DNA Methylation, and Depressive Symptoms in Black Pregnant Women.","authors":"Alexandra L Nowak, Marvin A Schilt-Solberg, Xiaoyu Liang, Fabiola Magaña, Dawn P Misra, Carmen Giurgescu","doi":"10.3390/epigenomes9040048","DOIUrl":"10.3390/epigenomes9040048","url":null,"abstract":"<p><strong>Background: </strong>Prenatal depression, affecting up to a quarter of all pregnancies in the United States, contributes to morbidity and mortality and is associated with increased risk of adverse birth and long-term mental health outcomes. Adverse childhood experiences (ACEs, or experiences of abuse, neglect, or family dysfunction experienced prior to age 18) are a strong predictor of adult depression and adverse health outcomes. The present study investigated whether epigenetic modification in the form of DNA methylation (DNAm) of four stress-related, glucocorticoid pathway genes (<i>CRH</i>, <i>CRHR1</i>, <i>FKBP5</i>, <i>NR3C1</i>) mediates associations between ACEs and depressive symptoms among Black pregnant women.</p><p><strong>Methods: </strong>Using a cross-sectional design, we examined the mediating role of DNAm on the relationship between depressive symptoms (Center for Epidemiologic Studies Depression Scale (CES-D)) and ACEs (Centers for Disease Control and Prevention 10-item questionnaire), in a subsample (<i>n</i> = 61) of Black pregnant women who were participants of the Biosocial Impacts of Black Births (BIBB) study.</p><p><strong>Results: </strong>A significant association was found between ACEs and depressive symptoms scores (TE α_X = 2.29 with p_TE = 6.60 × 10<sup>5</sup>). DNAm on five CpG sites within two genes significantly mediated the relationship between ACEs and depressive symptoms (cg03238273 on <i>CRHR1</i>, and cg08845721, cg16594263, cg19820298, and cg23430507 on <i>NR3C1</i>).</p><p><strong>Conclusions: </strong>This study provides evidence that DNAm partially mediated the association of ACEs and depressive symptoms during pregnancy among Black pregnant women. Understanding the molecular pathways underlying the mediating effect of ACEs on depressive symptoms among Black pregnant women can illuminate biological markers that help identify and treat pregnant women who are at an increased risk for depression following childhood trauma.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12731584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"CircRNAs-Potential Diagnostic Biomarkers and Therapeutic Targets for Receptive and Cancerous Endometrium.","authors":"Antoan Milov, Maria Nikolova, Stoilka Mandadzhieva, Nina Doncheva, Nadezhda Milova, Angel Yordanov","doi":"10.3390/epigenomes9040047","DOIUrl":"10.3390/epigenomes9040047","url":null,"abstract":"<p><p>Circular RNAs (circRNAs) are small, non-coding RNAs in which the 5' and 3' ends are linked covalently by back-splicing of exons from a single pre-mRNA. More and more scientific evidence is gathered for their wide distribution in the animal world, playing the role of regulators for biological processes, being cell- and tissue-specific. They can influence cellular physiology by various molecular mechanisms, finally modulating gene expression. CircRNAs are believed nowadays to be expressed in both receptive and cancerous endometrium. Due to their abundant expression in the endometrial tissue and their small size and stability, they have been considered potential diagnostic markers and treatment targets for endometrial-related diseases. The regulation of proliferation and differentiation is essential for the formation of receptive endometrium and for endometrial cancer emergence and progression. The receptive endometrium can be regarded as the most highly differentiated state of the endometrium. In contrast, the cancerous endometrium is characterized by a high level of proliferation and the lowest degree of differentiation. These endometria could be conditionally considered opposites. We are investigating the circRNA-miRNA-mRNA regulatory networks that can promote or suppress the proliferation and differentiation of endometrial cells by activating specific signaling pathways in both receptive and cancerous endometria. It could be worth knowing whether there are universal endometrial switches responsible for proliferation and differentiation processes that can alter the balance between them. We are interested in their clinical application as biomarkers and therapeutic targets for both endometrial receptivity issues and EC cases, particularly in diagnosis, progression assessment, and outcome prediction.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12641921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomesPub Date : 2025-11-16DOI: 10.3390/epigenomes9040046
Emanuela Talarico, Eleonora Greco, Francesco Guarasci, Fabrizio Araniti, Adriana Chiappetta, Leonardo Bruno
{"title":"Epigenetic Regulation of Salt Stress Responses in Rice: Mechanisms and Prospects for Enhancing Tolerance.","authors":"Emanuela Talarico, Eleonora Greco, Francesco Guarasci, Fabrizio Araniti, Adriana Chiappetta, Leonardo Bruno","doi":"10.3390/epigenomes9040046","DOIUrl":"10.3390/epigenomes9040046","url":null,"abstract":"<p><p>Rice (<i>Oryza sativa</i> L.) is a staple food for over half the global population and a model organism for monocot plant research. However, it is susceptible to salinity, with most cultivated varieties showing reduced growth at salt levels above 3 dS/m. Despite numerous efforts to improve its salt tolerance, little progress has been made. A promising area of research lies in the study of epigenetic regulation, which encompasses DNA methylation, histone modifications, and chromatin remodelling. These processes play a crucial role in mediating how plants respond to salt stress by modulating gene expression. This often results in heritable changes that can be used as molecular markers. Studies in rice and other cereals have demonstrated a clear association between histone alterations, shifts in DNA methylation patterns, and the expression of salt-responsive genes. Furthermore, epigenetic mechanisms contribute to the development of stress memory, enabling plants to respond more effectively to recurring stressful conditions. Understanding these regulatory pathways offers new opportunities for breeding or engineering salt-tolerant rice varieties, potentially leading to improved crop resilience and productivity under saline conditions.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12641941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomesPub Date : 2025-11-11DOI: 10.3390/epigenomes9040045
Sebastian Gaston Alvarado, Annaliese Chang, Maral Tajerian
{"title":"Convergent Evolution and the Epigenome.","authors":"Sebastian Gaston Alvarado, Annaliese Chang, Maral Tajerian","doi":"10.3390/epigenomes9040045","DOIUrl":"10.3390/epigenomes9040045","url":null,"abstract":"<p><strong>Background: </strong>Trait convergence or parallelism is widely seen across the animal and plant kingdoms. For example, the evolution of eyes in cephalopods and vertebrate lineages, wings in bats and insects, or shark and dolphin body shapes are examples of convergent evolution. Such traits develop as a function of environmental pressures or opportunities that lead to similar outcomes despite the independent origins of underlying tissues, cells, and gene transcriptional patterns. Our current understanding of the molecular processes underlying these phenomena is gene-centric and focuses on how convergence involves the recruitment of novel genes, the recombination of gene products, and the duplication and divergence of genetic substrates.</p><p><strong>Scope: </strong>Despite the independent origins of a given trait, these model organisms still possess some form of epigenetic processes conserved in eukaryotes that mediate gene-by-environment interactions. These traits evolve under similar environmental pressures, so attention should be given to plastic molecular processes that shape gene function along these evolutionary paths. Key Mechanisms: Here, we propose that epigenetic processes such as histone-modifying machinery are essential in mediating the dialog between environment and gene function, leading to trait convergence across disparate lineages. We propose that epigenetic modifications not only mediate gene-by-environment interactions but also bias the distribution of de novo mutations and recombination, thereby channeling evolutionary trajectories toward convergence. An inclusive view of the epigenetic landscape may provide a parsimonious understanding of trait evolution.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12641935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Exploring the Impact of Nanotherapeutics on Histone H3 and H4 Acetylation Enrichment in Cancer Epigenome: A Systematic Scoping Synthesis.","authors":"Milad Shirvaliloo, Sepideh Khoee, Samideh Khoei, Roghayeh Sheervalilou, Parisa Mohammad Hosseini, Reza Afzalipour, Sakine Shirvalilou","doi":"10.3390/epigenomes9040044","DOIUrl":"10.3390/epigenomes9040044","url":null,"abstract":"<p><p><b>Background/Objectives</b>: Histone acetylation regulates gene expression and plays a key role in cancer pathophysiology. Nanotherapeutics are known to modulate histone acetylation and influence cancer progression. This systematic scoping review examines the effects of nanotherapeutics on histone acetylation enrichment across multiple cancers. <b>Methods</b>: A systematic search of Embase, PubMed/MEDLINE, Scopus, and Web of Science was conducted in accordance with the PRISMA 2020 statement. A total of 13 studies were included. Data were analyzed and visualized in R, and risk of bias was assessed with ToxRTool (OSF Registration: 10.17605/OSF.IO/E643S). <b>Results</b>: Nanotherapeutics were most commonly evaluated against breast (21.4%), prostate (21.4%), pancreatic (14.3%), and bladder (14.3%) cancers. Primary nanomaterials used in the synthesis of nanotherapeutics included poly(lactic-co-glycolic acid) (25.0%), gold (21.4%) and arsenic oxide (21.4%) nanoparticles. Studied histone acetylation marks included H3K9ac, H3K14ac, H3K27ac and H4K16ac. Treatment with nanotherapeutics increased histone H3 and H4 acetylation enrichment, particularly H3K14ac in colorectal and prostate cancers and H4K16ac in ovarian cancer. Conversely, gold-based nanotherapeutics decreased H3K9ac and H3K14ac enrichment in breast cancer. The optimal concentration for most nanotherapeutics was ≤25 µM, with PpIX-FFYSV showing the strongest anticancer effect (viability <25%). Across four preclinical studies (<i>n</i> = 58), treatment with the nanotherapeutics reduced tumor size to less than 50% of control in 64% of animals (95% CI: 21-92%, I<sup>2</sup> = 63.8%). Altered histone acetylation was associated with differential expression of <i>CDKN1A</i>, <i>HSPA1</i>, <i>SREBF2</i> and <i>TGFB</i>. <b>Conclusions</b>: The evidence demonstrates that nanotherapeutics can alter histone acetylation patterns by modulating EP300/CBP, GCN5 and HDAC, preventing cancer progression and invasion.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12641773/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomesPub Date : 2025-11-02DOI: 10.3390/epigenomes9040043
Eleonora Greco, Emanuela Talarico, Francesco Guarasci, Marina Camoli, Anna Maria Palermo, Alice Zambelli, Adriana Chiappetta, Fabrizio Araniti, Leonardo Bruno
{"title":"Epigenetic Mechanisms of Plant Adaptation to Cadmium and Heavy Metal Stress.","authors":"Eleonora Greco, Emanuela Talarico, Francesco Guarasci, Marina Camoli, Anna Maria Palermo, Alice Zambelli, Adriana Chiappetta, Fabrizio Araniti, Leonardo Bruno","doi":"10.3390/epigenomes9040043","DOIUrl":"10.3390/epigenomes9040043","url":null,"abstract":"<p><p>Heavy metal and metalloid stress, particularly from toxic elements like cadmium (Cd), poses a growing threat to plant ecosystems, crop productivity, and global food security. Elevated concentrations of these contaminants can trigger cytotoxic and genotoxic effects in plants, severely impairing growth, development, and reproduction. In recent years, epigenetic mechanisms have emerged as crucial regulators of plant responses to heavy metal stress, offering novel insights and strategies for enhancing plant resilience in contaminated environments. This review synthesises current advances in the field of plant epigenetics, focusing on key modifications such as DNA methylation, histone acetylation and remodelling, chromatin dynamics, and small RNA-mediated regulation. These processes not only influence gene expression under metal-induced stress but also hold promise for long-term adaptation through transgenerational epigenetic memory. Recent developments in high-throughput sequencing and functional genomics have accelerated the identification of epigenetic markers associated with stress tolerance, enabling the integration of these markers into breeding programs and targeted epigenome editing strategies. Special attention is given to cadmium stress responses, where specific epigenetic traits have been linked to enhanced tolerance. As plant epigenomic research progresses, its application in sustainable agriculture becomes increasingly evident offering environmentally friendly solutions to mitigate the impact of heavy metal pollution. This review provides a foundation for future research aimed at leveraging epigenetic tools to engineer crops capable of thriving under metal stress, thereby contributing to resilient agricultural systems and sustainable food production.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12641728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
EpigenomesPub Date : 2025-10-15DOI: 10.3390/epigenomes9040041
Mullen Boulter, Ryan Collins, Kyle K Biggar
{"title":"Exploration into the MLL4/WRAD Enzyme-Substrate Network: Systematic In Vitro Identification of CFP1 as a Potential Non-Histone Substrate of the MLL4 Lysine Methyltransferase.","authors":"Mullen Boulter, Ryan Collins, Kyle K Biggar","doi":"10.3390/epigenomes9040041","DOIUrl":"10.3390/epigenomes9040041","url":null,"abstract":"<p><p>Lysine methylation is a critical post-translational modification catalyzed by lysine methyltransferases (KMTs), originally characterized in the regulation of histones. However, the breadth of non-histone targets remains largely unexplored. Here, we used a systematic peptide array-based approach to define a substrate preference motif for the SET-domain-containing KMT MLL4 (KMT2D), a member of the COMPASS complex and a known H3K4 methyltransferase. Using this motif, we identified CXXC finger protein 1 (CFP1), a core component of Setd1A/B complexes, as a putative MLL4 substrate. In vitro methyltransferase assays confirmed robust methylation of CFP1 by an MLL4-WRAD complex. Surprisingly, while initial predictions implicated K328, array-based methylation profiling revealed multiple lysine residues within CFP1's lysine-rich basic domain as methylation targets, including K331, K335, K339, and K340. We further demonstrated that CFP1 methylation likely modulates its interaction with MLL4's PHD cassettes and facilitates binding to Setd1A. Binding preferences of MLL4's PHD1-3 and PHD4-6 domains varied with methylation state and site, suggesting non-histone methyl mark recognition by these cassettes. Pulldown assays confirmed that methylated, but not unmethylated, CFP1 binds Setd1A, supporting a potential methyl-switch mechanism. Together, our findings propose CFP1 as a potential non-histone substrate of MLL4 and suggest that MLL4 may regulate Setd1A/B function indirectly via CFP1 methylation. This study expands the substrate landscape of MLL4 and lays the groundwork for future investigations into non-histone methylation signaling in chromatin regulation.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":"9 4","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12551112/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145356825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}