ArticleNature genetics2022
Prediction of histone post-translational modification patterns based on nascent transcription data.
Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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70 citing papers in PubMed.
- RNA-independent cis-autoregulatory circuits within bidirectional gene pairs control metabolism.Science advances · 2026Article
- Analysis of host and viral nascent and steady-state RNA levels in a human neuronal model of herpes simplex virus 1 infection.PLoS pathogens · 2026Article
- Improved spike-in normalization clarifies the relationship between active histone modifications and transcription.Nature genetics · 2026Article
- Accurate de novo transcription unit annotation from run-on and sequencing data.PLoS computational biology · 2026Article
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- Transcriptomic and epigenomic profiling datasets of murine HL-1 cardiomyocytes.Data in brief · 2026Article
- RNA polymerase II transcription initiation with and without XPB translocase activity.Communications biology · 2026Review
- An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation.Nature communications · 2026Article
- Unraveling the complexity of the histone code: implications for gene regulation and disease.Genome biology · 2026Review
- KMT2C and KMT2D amplify GRHL2-driven enhancer activation.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic editing: from concept to clinic.Nature reviews. Drug discovery · 2026Review
- Crosstalk between EZH2 and DNA methylation mediates neuroendocrine prostate cancer lineage plasticity.Nature communications · 2026Article
- Modeling nascent transcription from chromatin landscape and structure with CLASTER.Genome biology · 2026Article
- Evolution of promoter-proximal pausing enabled a new layer of transcription control.Nature structural & molecular biology · 2026Article
- mwHIT: accelerated and accurate histone modification imputation using multi-scale window attention.Frontiers in genetics · 2026Article
- HK2 drives synaptic dysfunction in fragile X syndrome via epigenetic regulation of H3K18 lactylation.Frontiers in pharmacology · 2026Article
- H3K4me3 amplifies transcription at intergenic active regulatory elements.Genes & development · 2025Article
- Broad H3K4me3 domains support oocyte genome silencing and maturation but are dispensable for repression in early embryos.Development (Cambridge, England) · 2025Article
- A PHF19-YTHDC1 condensate switches EZH2-mediated gene suppression to activation for prostate cancer progression.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer.Nature genetics · 2025Article
10 more citing papers are in PubMed but not listed here.
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Abstract
The role of histone modifications in transcription remains incompletely understood. Here, we examine the relationship between histone modifications and transcription using experimental perturbations combined with sensitive machine-learning tools. Transcription predicted the variation in active histone marks and complex chromatin states, like bivalent promoters, down to single-nucleosome resolution and at an accuracy that rivaled the correspondence between independent ChIP-seq experiments. Blocking transcription rapidly removed two punctate marks, H3K4me3 and H3K27ac, from chromatin indicating that transcription is required for active histone modifications. Transcription was also required for maintenance of H3K27me3, consistent with a role for RNA in recruiting PRC2. A subset of DNase-I-hypersensitive sites were refractory to prediction, precluding models where transcription initiates pervasively at any open chromatin. Our results, in combination with past literature, support a model in which active histone modifications serve a supportive, rather than an essential regulatory, role in transcription.
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