HDAC11 functional interaction network analysis identifies components of snRNP biogenesis complexes. HDAC11 functional interaction network analysis identifies.

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HDAC11 functional interaction network analysis identifies components of snRNP biogenesis complexes. HDAC11 functional interaction network analysis identifies components of snRNP biogenesis complexes. (A) Cytoscape interaction network of putative HDAC11 interactions. 124 SAINT‐filtered proteins co‐isolated with HDAC11 were grouped by subcellular localizations. Proteins were color coded by biological processes. Circle‐shaped nodes indicate previously unreported interactions. (B) GO biological process (GO BP) network comparing classifications of HDAC11 versus the HDAC1–10 interactome data set. GO BP terms, assigned by the ClueGO Cytoscape plugin, depict functions that are (1) common (white circles, 33–66% of HDAC11 genes), (2) enriched in HDAC11 (red circles, >66% of HDAC11 genes), or (3) enriched in the HDAC1–10 interactome (green circles, <33% of HDAC11 genes). For clarity, a subset of GO BP term labels relating to detailed RNA metabolic processes were removed (see Supplementary Figure S6A). (C) STRING functional network of prominent candidate HDAC11 interactions visualized in Cytoscape. Nodes were color coded by biological processes indicated in (A). Node size was expressed as an enrichment index, which is the protein's normalized spectral abundance factor (NSAF) relative to its estimated cellular abundance in the PAX database, normalized to SUGT1 set at an arbitrary value of one. (D) Validation of selected HDAC11 interactions by reciprocal isolations and immunopurification of endogenous HDAC11 (eHDAC11). IgG was used as a control. Left, immunoaffinity purifications of endogenous SMN1, Gemin3, Gemin4, or Dicer1, and detection of complex members by western blot. Right, immunoaffinity purification of eHDAC11. (E) Splicing defects in the ATXN10 U12‐type intron 10 upon knockdown of HDAC11 in WT CEM T cells. RNA levels upon treatment with HDAC11 siRNA or a scrambled control were quantified by qRT–PCR (n=3). A representative agarose gel is shown to visualize the levels of indicated PCR products. Left, mRNA of GAPDH (GAP) and snRNA of U2, U12, U4 and U4atac. Right, mRNA of ATXN10, ATXN10_intron, and HDAC11. Preeti Joshi et al. Mol Syst Biol 2013;9:672 © as stated in the article, figure or figure legend