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Particular chromatin modifications are associated with different states of gene transcription, yet our understanding of which modifications are causal 'drivers' in promoting transcription is incomplete. Here, we discuss new developments describing the ordered, mechanistic role of select histone marks occurring during distinct steps in the RNA polymerase II (Pol II) transcription cycle. In particular, we highlight the interplay between histone marks in specifying the 'next step' of transcription. While many studies have described correlative relationships between histone marks and their occupancy at distinct gene regions, we focus on studies that elucidate clear functional consequences of specific histone marks during different stages of transcription. These recent discoveries have refined our current mechanistic understanding of how histone marks promote Pol II transcriptional progression.
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http://dx.doi.org/10.1016/j.tibs.2017.10.004 | DOI Listing |
Elife
September 2025
Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States.
Human cytomegalovirus (HCMV) infects up to 80% of the world's population. Here, we show that HCMV infection leads to widespread changes in human chromatin accessibility and chromatin looping, with hundreds of thousands of genomic regions affected 48 hr after infection. Integrative analyses reveal HCMV-induced perturbation of Hippo signaling through drastic reduction of TEAD1 transcription factor activity.
View Article and Find Full Text PDFEMBO Rep
September 2025
Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287, Darmstadt, Germany.
The flexibility of the spatio-temporal genome replication program during development and disease highlights the regulatory role of plastic epigenetic mechanisms over genetic determinants. Histone post-translational modifications are broadly implicated in replication timing control, yet the specific mechanisms through which individual histone marks influence replication dynamics, particularly in heterochromatin, remain unclear. Here, we demonstrate that H3K36me3 dynamically enriches at pericentromeric heterochromatin, composed of major satellite DNA repeats, prior to replication during mid S phase in mouse embryonic stem cells.
View Article and Find Full Text PDFZool Res
September 2025
MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong 266003, China.
Bivalve mollusks represent a taxonomically and economically significant clade within Mollusca. However, the regulatory mechanisms governing their embryonic development remain poorly characterized. The dwarf surf clam ( ), characterized by a short generation time and high fecundity, has recently gained recognition as an ideal model system for bivalve embryological research.
View Article and Find Full Text PDFNAR Mol Med
July 2025
Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada.
Advanced maternal age increases the risk of pregnancy complications due, in part, to changes in the uterine environment. Here, we show that uterine aging in mice is associated with a progressive increase in transcriptional variation, accompanied by a notable accumulation of activating histone marks at multiple genomic loci. Importantly, the transcriptional signatures of uterine aging differ substantially from senescence markers associated with organismal aging.
View Article and Find Full Text PDFJ Biol Chem
September 2025
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. Electronic address:
Posttranslational modifications (PTMs) of proteins are efficient biological mechanisms for expanding the genetic code and for regulating cellular physiology. However, there have been no systematic approaches to profile all the PTMs critical for autoreactive neoantigen production or the etiology and pathology of autoimmune diseases. In the present study, to gain insight into protein PTMs associated with systemic lupus erythematosus (SLE), we applied a mass spectrometry-based method for the comprehensive analysis of modified amino acids ("adductome").
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