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Mol Cell. 2019 Nov 7. pii: S1097-2765(19)30796-8. doi: 10.1016/j.molcel.2019.10.018. [Epub ahead of print]

Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance.

Author information

1
Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
2
Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
3
Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, MA, USA.
4
Department of Biochemistry and Biophysics, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
5
Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, MA, USA.
6
Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA. Electronic address: danesh@hms.harvard.edu.

Abstract

Spatially and functionally distinct domains of heterochromatin and euchromatin play important roles in the maintenance of chromosome stability and regulation of gene expression, but a comprehensive knowledge of their composition is lacking. Here, we develop a strategy for the isolation of native Schizosaccharomyces pombe heterochromatin and euchromatin fragments and analyze their composition by using quantitative mass spectrometry. The shared and euchromatin-specific proteomes contain proteins involved in DNA and chromatin metabolism and in transcription, respectively. The heterochromatin-specific proteome includes all proteins with known roles in heterochromatin formation and, in addition, is enriched for subsets of nucleoporins and inner nuclear membrane (INM) proteins, which associate with different chromatin domains. While the INM proteins are required for the integrity of the nucleolus, containing ribosomal DNA repeats, the nucleoporins are required for aggregation of heterochromatic foci and epigenetic inheritance. The results provide a comprehensive picture of heterochromatin-associated proteins and suggest a role for specific nucleoporins in heterochromatin function.

KEYWORDS:

Bdf1; Clr4; H3K9me; HP1; INM proteins; NPC; SUV39H; Swi6; epigenetic inheritance; nucleoporins

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