@article{2230a0c7f6fa425687336f1eb1f582f1,
title = "Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance",
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",
author = "Nahid Iglesias and Paulo, {Joao A.} and Antonis Tatarakis and Xiaoyi Wang and Edwards, {Amanda L.} and Bhanu, {Natarajan V.} and Garcia, {Benjamin A.} and Wilhelm Haas and Gygi, {Steven P.} and Danesh Moazed",
note = "Funding Information: We are grateful to Zarmik Moqtaderi and Ruby Yu for Python scripts, Larissa Grolimund for helpful discussion on protein purifications, the Nikon Imaging Center at HMS for advice and access to microscopes, Gergana Shipkovenska, Juntao Yu, and Chen Zhou for comments on the manuscript, and members of the Moazed lab for discussion. This work was supported by an EMBO long-term fellowship and a Swiss National Science Foundation postdoctoral fellowship (N.I.), K01 DK098285 (J.A.P.), NIH GM110174 and CA196539 (B.A.G.), and NIH RO1 GM072805 (D.M.). D.M. is a Howard Hughes Medical Institute Investigator. N.I. and D.M. conceived the study and designed experiments. N.I. carried out mutagenesis, strain construction, protein purifications, western blot, ChIP-seq, ChIP-qPCR, RT-qPCR, and silencing assays and analyzed the data. N.I. analyzed sequencing libraries. J.A.P. A.L.E. N.V.B. and W.H. performed mass spectrometry. A.T. carried out microscopy experiments and analyzed the data. X.W. performed strain construction, ChIP-qPCR, and silencing assay for Figures S5H–S5L and analyzed the data. N.I. A.T. X.W. and D.M. interpreted data. B.A.G. W.H. S.P.G. and D.M. supervised research. N.I. A.T. X.W. and D.M. prepared figures. N.I. and D.M. wrote the manuscript. All authors discussed the results and commented on the manuscript. The authors declare no competing interests. Funding Information: We are grateful to Zarmik Moqtaderi and Ruby Yu for Python scripts, Larissa Grolimund for helpful discussion on protein purifications, the Nikon Imaging Center at HMS for advice and access to microscopes, Gergana Shipkovenska, Juntao Yu, and Chen Zhou for comments on the manuscript, and members of the Moazed lab for discussion. This work was supported by an EMBO long-term fellowship and a Swiss National Science Foundation postdoctoral fellowship (N.I.), K01 DK098285 (J.A.P.), NIH GM110174 and CA196539 (B.A.G.), and NIH RO1 GM072805 (D.M.). D.M. is a Howard Hughes Medical Institute Investigator . Publisher Copyright: {\textcopyright} 2019 Elsevier Inc.",
year = "2020",
month = jan,
day = "2",
doi = "10.1016/j.molcel.2019.10.018",
language = "English",
volume = "77",
pages = "51--66.e8",
journal = "Molecular Cell",
issn = "1097-2765",
number = "1",
}