Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programs and repeats in pluripotent cells

  • bioRxiv. 2024 Sep 16:2024.09.16.613328. doi: 10.1101/2024.09.16.613328.
Jingchao Zhang  1  2  3 ,  Greg Donahue  1  2  3 ,  Michael B Gilbert  2  4 ,  Tomer Lapidot  5  6 ,  Dario Nicetto  1  2  3 ,  Kenneth S Zaret  1  2  3
Affiliations
  • 1. Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
  • 2. Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
  • 3. Dept. Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
  • 4. Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
  • 5. Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
  • 6. Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
PMID: 39345615 DOI: 10.1101/2024.09.16.613328
Abstract

H3K9me3-heterochromatin, established by lysine methyltransferases (KMTs) and compacted by HP1 isoforms, represses alternative lineage genes and DNA repeats. Our understanding of H3K9me3-heterochromatin stability is presently limited to individual domains and DNA repeats. We engineered Suv39h2 KO mouse embryonic stem cells to degrade remaining two H3K9me3-KMTs within one hour and found that both passive dilution and active removal contribute to H3K9me3 decay within 12-24 hours. We discovered four different H3K9me3 decay rates across the genome and chromatin features and transcription factor binding patterns that predict the stability classes. A "binary switch" governs heterochromatin compaction, with HP1 rapidly dissociating from heterochromatin upon KMTs' depletion and a particular threshold level of HP1 limiting pioneer factor binding, chromatin opening, and exit from pluripotency within 12 hr. Unexpectedly, receding H3K9me3 domains unearth residual HP1β peaks enriched with heterochromatin-inducing proteins. Our findings reveal distinct H3K9me3-heterochromatin maintenance dynamics governing gene networks and repeats that together safeguard pluripotency.

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