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In mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation.
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http://dx.doi.org/10.1073/pnas.2009316117 | DOI Listing |
Epigenomics
September 2025
College of Physical Education, Yangzhou University, Yangzhou, China.
Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder lacking objective biomarkers for early diagnosis. DNA methylation is a promising epigenetic marker, and machine learning offers a data-driven classification approach. However, few studies have examined whole-blood, genome-wide DNA methylation profiles for ASD diagnosis in school-aged children.
View Article and Find Full Text PDFTree Physiol
September 2025
Pollen Biotechnology of Crop Plants Group, Margarita Salas Center of Biological Research, CIB-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.
Somatic embryogenesis (SE) is an in vitro mass propagation system widely employed in plant breeding programs. However, its efficiency in many forest species remains limited due to their recalcitrance. SE relies on the induction of somatic cell reprogramming into embryogenic pathways, a process influenced by transcriptomic changes regulated, among other factors, by epigenetic modifications such as DNA methylation, histone methylation, and histone acetylation.
View Article and Find Full Text PDFNucleic Acids Res
September 2025
School of Microbiology, University College Cork, Cork, T12 Y337, Ireland.
The genomes of 43 distinct lactococcal strains were reconstructed by a combination of long- and short-read sequencing, resolving the plasmid complement and methylome of these strains. The genomes comprised 43 chromosomes of approximately 2.5 Mb each and 269 plasmids ranging from 2 to 211 kb (at an average occurrence of 6 per strain).
View Article and Find Full Text PDFJ Investig Med
September 2025
Unidad de Investigación Biomédica, Delegación Durango, Instituto Mexicano del Seguro Social, Durango, México.
It has been reported that DNA methylation in the epigenetic profile of the genes LEP and ADIPOQ is associated with obesity. To the best of our knowledge, there are no previous reports assessing the methylation of the LEP, LEPR, and ADIPOQ genes in subjects with metabolically healthy obesity (MHO). Therefore, the aim of this study was to determine the association between methylation of the LEP, LEPR, and ADIPOQ genes with the MHO phenotype.
View Article and Find Full Text PDFBioimpacts
August 2025
Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Ankara 06330, Türkiye.
Colorectal cancer (CRC) constitutes a significant global health challenge, accounting for a considerable proportion of cancer cases and associated mortality. Projections indicate a potential increase in new cases by 2040, attributed to demographic factors such as aging and population growth. Although advancements in the understanding of CRC pathophysiology have broadened treatment options, challenges such as drug resistance and adverse effects persist, highlighting the necessity for enhanced diagnostic methodologies.
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