4598 Nucleic Acids Research, 2006, Vol. 34, No. 16 Table 1. Putative NOP132-, DDX47-, and DDX18-associated proteins Putative ribosome biogenesis proteins DDX47, FBL, GRWD1, NCL, NPM1, WDR57, NOP254/C21orf108 Putative function NOP132/NOL8-associating proteins DDX47-asssociating proteins DDX18-associating proteins BMS1L, BOP1, BXDC2, C4orf9, C20orf6, CIRH1A, DDX10, DDX24, DDX27, DDX47, EBNA1BP2, FBL, FLJ12949, FTSJ3, GNL2, GNL3, GTPBP4, GRWD1, HEATR1, HRB2, KIAA0179, KIAA0690, MKI67IP, MPHOSPH10, NCL, NOC2L, NOC3L, NOL1, NOL5A, NOP5, NOP254/C21orf108, NPM1, PDCD11, PES1, PPAN, RBM28, RRS1, RSL1D1, SART3, SDAD1, TBL3, WDR46, XRN2 RPLP0, RPL3, RPL3L, RPL4, RPL6, RPL7, RPL7A, RPL7L, RPL7L1, WUGSC:H_RG054D04.1, RPL8, RPL10, RPL10A, RPL13, RPSA, RPS2, RPS3, RPS3A, LOC146053, RPS4, RPS6, RPS8, MRPS2,MRPS9, MRPS22, MRPS28, MRPS29, MRPS34 DHX15, HNRPAB, HNRPA0, HNRPA3, HNRPC, HNRPCL1, HNRPF, HNRPM, HNRPR, HNRPU, PRPF31, RBM10, SF3B1, SFRS10, SNRPA1, SNRPB2, SNRP70 HSPA1L, HSPA6, HSPA9B, HSPD1 H1FX, H1F0, HIST1H1C, H2AFY, H2AFY2 AATF, ABT1, BCLAF1, C1orf107, CEBPZ, CSDA, CTCF, DHX9, FLJ10774, ILF2, MYBBP1A, PURA, PWP1, RARA, YBX1, ZFR DDX21, DDX50, EIF3S10, EIF4B, IMP1IGF2BP1, IGF2BP2IMP2, IGF2BP3IMP3, IGF2BP4IMP4, LARP1, PABPC4 FLNA KPNA2 FAF-X, FAF-Y, UBR2 C14orf120, FLJ20758, HP1BP3, KIAA0020, LYAR, MATR3, MOV10, NOL10, SLC25A6, PABPC1 DDX18, DDX47, FBL, FLJ12949, GNL3, GTPBP4, HRB2, NCL, NOL1, NPM1, RSL1D1 RPLA0, RPL3, RPL4, RPL6, RPL7, RPL7A, RPL8, RPL10A, RPL13, RPL14, RPL19, RPS2, RPS3, RPS3A, RPS4, RPS6, RPS8 CDC5L, DHX15, HNRPAB, HNRPA2B1, HNRPD, HNRPF, HNRPH1, HNRPH2, HNRPM, HNRPR, HNRPQ, HNRPU, HNRPUL1, IVNS1ABP, PRPF31, RBM10, SF3B1, SF3B3, SNRPN, U2AF2 HSPA1L, HSPA5, HSPA6, HSPA9B, HSPCA, HSPD1 H1FX, HIST1H1C CENTB2-ARF GAP. MAP3K7, MAP3K7IP1. DHX9, MYBBP1A, ILF3, SSB, YBX1 GRSF1, DDX21, EIF2B, EIF4B TUBB, TUBA3, TUBB2C PRPSAP2, ANKFY1, LOC144097, OTUD4, PABPC1 Ribosome subunits Putative mRNA splicing factors Heat shock Chromatin binding Transcription Translation Filament Transport Protein degradation Others and unknown RPLP0, RPL3, PRL3L, RPL4, RPL6, RPL7, RPL7A, RPL8, RPL10A, RPL13, RPL14, RPS2, RPS3, RPS3A, RSP4RPS4, RPS6, RPS8, RPSA, RSMB ASCC3L1, CDC5L, DHX15, HNRPA0, HNRPA1, HNRPD, HNRPF, HNRPH1, HNRPH2, HNRPU, IVNS1ABP, RBMX, PRPF31, PTBP1, RBM10, SF3B1, SF3B3, SF3B4 CCT6A, CDC37, DNAJA1, HSPA1L, HSPA2, HSPA4, HSPA4L, HSPA5, HSPA6, HSPCA, HSPD1, HSPH1 HIST1H1C CSDA, DHX9, E2F7, ILF3, P53, SSB, TAF4 DDX21, EEF1A , EEF1G, EIF4B, WARS ACTS, CLASP2, TUBA1, TUBA6, TUBB TUBB2A, TUBB4, TUBB6, VIM KPNA3, KPNA4, KPNB1 ANKFY1, FHL2, KIAA0133, LOC144097, C14orf150 Signal transduction JAK1, MAP3K7IP1 Gene names according to HUGO nomenclature. DDX47- and DDX18-associated proteins that were also identified in FLAG-NOP132-associated complexes are underlined. DDX18-associated proteins that were also identified in FLAG-DDX47-associated complexes are in bold. Supplementary Table 1) (4,30,32). In addition, the FLAG immunoprecipitates in FLAG-NOP132-expresssing cells con- tained many splicing factors, suggesting that NOP132 might also be involved in pre-mRNA splicing. This is consistent with our previous observation that NOP132 co-localizes with proteins such as Clk-1 and RNPS1 located in nuclear speckles (15). P53, a tumor suppressor, was repeatedly iden- tiﬁed in NOP132 complexes (Table 1 and Supplementary Table 1) and was also detected in NOP132 complex by west- ern blotting (data not shown). RRAG A was not detected in the NOP132 complex, however. This ﬁnding might be the result of a transient interaction or because RRAG A is a minor component of the NOP132 complex and consequently below the limit of detection of this experiment. Among the proteins identiﬁed, DDX47, which was repeat- edly identiﬁed, and DDX18, which was identiﬁed once but belongs to a group of proteins similar to DDX47, were used for reciprocal immunoprecipitation experiments. The associated proteins were identiﬁed from SDS–PAGE gels as described above (Figures 1b, c and 2b) and are summarized in Table 1. One hundred and eight proteins associated with DDX18 and 119 proteins associated with DDX47 were iden- tiﬁed by nano-LC-MS/MS analysis after Lys-C digestion (Supplementary Table 1). Analysis of these proteins indicated that the two complexes share 37 large subunit ribosomal proteins, 23 small subunit ribosomal proteins, and 41 non- ribosomal proteins in common, demonstrating their similarity in protein composition. DDX47 was found in the DDX18