ArticleNature communications2022
DNA sequence-dependent formation of heterochromatin nanodomains.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 58 citations in OpenAlex.
- SLX4IP limits replication stress globally and at ALT telomeres.The EMBO journal · 2026Article
- A preliminary investigation into the etiology of agar-like zona pellucida in human oocytes.Journal of assisted reproduction and genetics · 2026Article
- A kinetic proofreading argument to understand the role of H3K9 trimethylation in phase-separated chromatin states.Biophysical journal · 2026Article
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- Scaling and self-similarity in the formation of the embryonic epigenome.Nature physics · 2026Article
- A Biophysics of Epigenetic Rejuvenation.Cells · 2025Article
- CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation.Nucleic acids research · 2025Article
- Heterochromatin de novo formation and maintenance in Plasmodium falciparum.PLoS pathogens · 2025Article
- ADNP is essential for sex-dependent hippocampal neurogenesis, through male unfolded protein response and female mitochondrial gene regulation.Molecular psychiatry · 2025Article
- The chromatin remodeler ADNP regulates neurodevelopmental disorder risk genes and neocortical neurogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- PhpCNature communications · 2025Article
- Single-housing-induced islet epigenomic changes are related to polymorphisms in diabetic KK mice.Life science alliance · 2024Article
- Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus.Physical review. E · 2024Article
- ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice.Genes & development · 2024Article
- Clinical impact and in vitro characterization of ADNP variants in pediatric patients.Molecular autism · 2024Article
- Divergent phenotypes in constitutive versus conditional mutant mouse models of Sifrim-Hitz-Weiss syndrome.Human molecular genetics · 2023Article
- Cryoelectron tomography reveals the multiplex anatomy of condensed native chromatin and its unfolding by histone citrullination.Molecular cell · 2023Article
- Article
- The molecular basis of heterochromatin assembly and epigenetic inheritance.Molecular cell · 2023Review
- Epigenetic signals that direct cell type-specific interferon beta response in mouse cells.Life science alliance · 2023Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
The mammalian epigenome contains thousands of heterochromatin nanodomains (HNDs) marked by di- and trimethylation of histone H3 at lysine 9 (H3K9me2/3), which have a typical size of 3-10 nucleosomes. However, what governs HND location and extension is only partly understood. Here, we address this issue by introducing the chromatin hierarchical lattice framework (ChromHL) that predicts chromatin state patterns with single-nucleotide resolution. ChromHL is applied to analyse four HND types in mouse embryonic stem cells that are defined by histone methylases SUV39H1/2 or GLP, transcription factor ADNP or chromatin remodeller ATRX. We find that HND patterns can be computed from PAX3/9, ADNP and LINE1 sequence motifs as nucleation sites and boundaries that are determined by DNA sequence (e.g. CTCF binding sites), cooperative interactions between nucleosomes as well as nucleosome-HP1 interactions. Thus, ChromHL rationalizes how patterns of H3K9me2/3 are established and changed via the activity of protein factors in processes like cell differentiation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.