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Mammalian genomes undergo pervasive transcription in both genic and intergenic regions. Trimethylation of histone H3 lysine 4 (H3K4me3) is a deeply conserved and functionally important histone modification enriched at transcriptionally active promoters, where it facilitates RNA polymerase activity. H3K4me3 is also commonly found in intergenic regions, where its role is poorly understood. We interrogated the role of H3K4me3 at intergenic regulatory elements by using epigenetic editing to efficiently deposit H3K4me3 at intergenic loci. We found that H3K4me3 amplifies RNA polymerase activity and is actively remodeled at intergenic regions, shedding light on these important but poorly understood regions of the genome.
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http://dx.doi.org/10.1101/gad.352841.125 | DOI Listing |
Physiol Plant
September 2025
Department of Plant Physiology, Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
Several genes in the mitochondria of angiosperms are interrupted by introns, and their posttranscriptional excision involves numerous nucleus-encoded auxiliary factors. Most of these factors are of eukaryotic origin, among them members of the pentatricopeptide-repeat (PPR) family of RNA-binding proteins. This family divides into the PLS and P classes, with PLS-class proteins typically participating in C-to-U mRNA editing and P-class members contributing to transcript stabilization and intron splicing.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
September 2025
School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
Two yeast strains, PYCC 10015 and PYCC 10016, were isolated from soil from an Irish forest. Sequence analysis of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) of the rRNA gene repeat, and the D1/D2 domain of the LSU rRNA gene, showed that they belong to the and genera of the order , but they did not exactly match any known species.
View Article and Find Full Text PDFNucleic Acids Res
September 2025
School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, No. 100 Waihuanxi Road, Guangzhou 510006, China.
The 5' untranslated region (5'UTR) plays a crucial regulatory role in messenger RNA (mRNA), with modified 5'UTRs extensively utilized in vaccine production, gene therapy, etc. Nevertheless, manually optimizing 5'UTRs may encounter difficulties in balancing the effects of various cis-elements. Consequently, multiple 5'UTR libraries have been created, and machine learning models have been employed to analyze and predict translation efficiency (TE) and protein expression, providing insights into critical regulatory features.
View Article and Find Full Text PDFPLoS Biol
September 2025
Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, United States of America.
Despite the success of antiretroviral therapy in suppressing plasma viremia in people living with human immunodeficiency virus type-1 (HIV-1), persistent viral RNA expression in tissue reservoirs is observed and can contribute to HIV-1-induced immunopathology and comorbidities. Infection of long-lived innate immune cells, such as tissue-resident macrophages and microglia may contribute to persistent viral RNA production and chronic inflammation. We recently reported that de novo cytoplasmic expression of HIV-1 intron-containing RNA (icRNA) in macrophages and microglia leads to MDA5 and MAVS-dependent innate immune sensing and induction of type I IFN responses, demonstrating that HIV icRNA is a pathogen-associated molecular pattern (PAMP).
View Article and Find Full Text PDFAgeing Res Rev
September 2025
Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy; Department of Medicine and Surgery, LUM University, Casamassima, Italy. Electronic address: