DNA sequence-dependent formation of heterochromatin nanodomains
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 is...
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| Hauptverfasser: | , , , , , , |
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| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
06 April 2022
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| In: |
Nature Communications
Year: 2022, Jahrgang: 13, Pages: 1-13 |
| ISSN: | 2041-1723 |
| DOI: | 10.1038/s41467-022-29360-y |
| Online-Zugang: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1038/s41467-022-29360-y Verlag, lizenzpflichtig, Volltext: https://www.nature.com/articles/s41467-022-29360-y 
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| Verfasserangaben: | Graeme J. Thorn, Christopher T. Clarkson, Anne Rademacher, Hulkar Mamayusupova, Gunnar Schotta, Karsten Rippe & Vladimir B. Teif |
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| 520 | |a 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. | ||
| 650 | 4 | |a Biological physics | |
| 650 | 4 | |a Epigenomics | |
| 650 | 4 | |a Gene regulation | |
| 650 | 4 | |a Gene silencing | |
| 650 | 4 | |a Histone post-translational modifications | |
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| 700 | 1 | |a Teif, Vladimir B. |e VerfasserIn |4 aut | |
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