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

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. • Strategy for affinity purification of native chromatin fragments • Heterochromatin and euchromatin have overlapping and non-overlapping proteomes • The heterochromatin proteome includes inner nuclear membrane proteins and nucleoporins • Inner-ring nucleoporins are required for clustering and maintenance of heterochromatin Iglesias et al. describe a strategy for identification of proteins associated with native heterochromatin and euchromatin DNA domains. In addition to previously identified proteins, the heterochromatin-specific proteome contains inner nuclear membrane proteins and a specific subset of nucleoporins, some of which function in epigenetic inheritance and clustering together of distal heterochromatic regions. [ABSTRACT FROM AUTHOR]