Accession Protein Name Gene symbol MW [Da] Protein Score Match of sequences Bait CHTOP_HUMAN Chromatin target of PRMT1 protein CHTOP 26380 709 8 SMN binding proteins SMN_HUMAN Survival motor neuron protein SMN 32285 255 3 GEMI2_HUMAN Gem-associated protein 2 GEMIN2 32021 102 2 DDX20_HUMAN Probable ATP-dependent RNA helicase DDX20 DDX20 92981 293 9 GEMI6_HUMAN Gem-associated protein 6 GEMIN6 18983 41 1 GEMI8_HUMAN Gem-associated protein 8 GEMIN8 28904 54 2 STRAP_HUMAN Serine-threonine kinase receptor-associated protein STRAP 38756 121 4 FMR1_HUMAN Fragile X mental retardation protein 1 FMR1 71473 265 9 Protein arginine N-methyltransferases (PRMTs) and related proteins ANM1_HUMAN Protein arginine N-methyltransferase 1 PRMT1 42059 648 8 ANM5_HUMAN Protein arginine N-methyltransferase 5 PRMT5 73322 90 4 Zinc finger proteins KHDR1_HUMAN KH domain-containing, RNA-binding, signal transductionassociated protein 1 KHDR1 48311 290 7 ZC3HE_HUMAN Zinc finger CCCH domain-containing protein 14 ZC3HE 83793 210 5 ZC11A_HUMAN Zinc finger CCCH domain-containing protein 11A ZC11A 89931 66 2 Transcription related proteins CIZ1_HUMAN Cip1-interacting zinc finger protein CIZ1 101066 396 8 P53_HUMAN Cellular tumor antigen p53 TP53 44196 216 6 ERH_HUMAN Enhancer of rudimentary homolog ERH 12422 180 3 TR150_HUMAN Thyroid hormone receptor-associated protein 3 THRAP3 108658 85 2 SAFB2_HUMAN Scaffold attachment factor B2 SAFB2 107921 78 3 YLPM1_HUMAN YLP motif-containing protein 1 YLPM1 220077 53 2 MATR3_HUMAN Matrin-3 MATR3 95078 52 2 snRNA binding proteins U5S1_HUMAN 116 kDa U5 small nuclear ribonucleoprotein component EFTUD2 110336 105 3 RU17_HUMAN U1 small nuclear ribonucleoprotein 70 kDa SNRNP70 51583 74 2 mRNA splicing factors C1QBP_HUMAN Complement component 1 Q subcomponent-binding protein, mitochondrial C1QBP 31742 591 5 IF4A3_HUMAN Eukaryotic initiation factor 4A-III EIF4A3 47126 227 2 PABP2_HUMAN Polyadenylate-binding protein 2 PABPN1 32843 161 2 SRSF6_HUMAN Serine/arginine-rich splicing factor 6 SRSF6 39677 74 2 hnRNPs and RNA helicases HNRH1_HUMAN Heterogeneous nuclear ribonucleoprotein H HNRNPH1 49484 142 3 HNRPC_HUMAN Heterogeneous nuclear ribonucleoproteinsC1/C2 HNRNPC 33707 143 3 HNRPF_HUMAN Heterogeneous nuclear ribonucleoprotein F HNRNPF 45985 113 2 DX39A_HUMAN ATP-dependent RNA helicase DDX39A DDX39A 49611 78 2 Chaperons &Cytoskeltons LBR_HUMAN Lamin-B receptor LBR 71057 1134 14 ACTA_HUMAN Actin, aortic smooth muscle ACTA2 42381 97 4 HSP71_HUMAN Heat shock 70 kDa protein 1A/1B HSPA1A 70294 743 13 HSP7C_HUMAN Heat shock cognate 71 kDa protein HSPA8 71082 371 9 Others           NPM_HUMAN Nucleophosmin NPM1 32726 127 3 PNMA2_HUMAN Paraneoplastic antigen Ma2 PNMA2 41711 117 3 VIME_HUMAN Vimentin VIM 53676 54 2

Table 1: Identification of proteins associated with the nuclear HB-FOP by LC-MS/MS analysis. The Nuclear HB-FOP -associated proteins containig SMN complex are indicated. Proteins are classified into functional groups based on SwissProt classification. Proteins were identified by Q-Tof2 as described in Supplementary Tables II. Proteins detected in mock are not listed in this table. Uniprot accession, protein name, gene symbol as well as molecular weight are shown. we added GEMIN6 to the identification list by the confirmation of the asscociation of GEMIN6 with HB-FOP using western blot analyis.