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Supporting Material

Notes to Tables S1–S3. The protein composition of spliceosomal or snRNP complexes as determined by mass spectrometry. ¹Complexes analyzed are as follows: Spl1 (Zhou et al. 2002) and Spl2 (Rappsilber et al. 2002) are a mixture of human spliceosomal complexes (plus mRNPs) isolated from HeLa nuclear extract under low salt conditions in the absence of heparin; A indicates the human spliceosomal A complex (Hartmuth et al. 2002), and 35S is the human 35S U5 snRNP (Makarov et al. 2002), both isolated from HeLa nuclear extract under moderate salt in the absence of heparin. BDU1 (Makarova et al. 2004), B* (Makarov et al. 2002), and C (Jurica et al. 2002) indicate the human pre-catalytic B complex, catalytically activated B* complex, and catalytically active C complex, respectively. These complexes were purified from HeLa nuclear extract under stringent conditions (i.e., in the presence of heparin). S.c. indicates a putative yeast postspliceosomal complex (Ohi et al. 2002), and Penta indicates the yeast penta-snRNP (Stevens et al. 2002), both isolated from Saccharomyces cerevisiae total cell extracts under low salt conditions. The presence of a given protein in a particle complex is indicated by a black dot; an open dot indicates that the protein is likely to be present in low amounts, based on the number of peptides identified and the percentage of sequence coverage. ²Abbreviations: RRM, RNA recognition motif; RS, region rich in arg/ser dipeptides; ZnF, zinc finger; Ser-rich, serine rich; SURP, also known as SWAP, Suppressor-of-White-Apricot; UBQ, ubiquitin family; CPSF A, cleavage and polyadenylation specificity factor A; DnaJ, molecular chaperone dnaj domain; HEAT; derived from Huntingtin protein, Elongation factor 3, the Alpha regulatory subunit of protein phosphatase 2A and the yeast PI3-kinase TOR1; HMG, high-mobility-group; SAP, after SAF-A/B, Acinus and PIAS motif; DEXH/DEAD, Asp- box of RNA helicase family; TPR, tetratricopeptide repeat; PWI, proline-tryptophan-isoleucine motif; PPIase, peptidyl-prolyl isomerase; WW, tryptophan–tryptophan domain; HAT, histone acetyltransferase; KH, hnRNP K homology domain; helicase SF, helicase super family; DEATH, domain found in proteins involved in cell death; DSRM, double-stranded RNA binding motif; SFM, splicing factor motif in Prp18; Ubox, modified RING finger domain; SH2, Src homology domain; CSP, cold shock protein; DZF, Domain found in DSRM or ZnF-containing proteins; SMC-N, RecF/RecN/SMC N-terminal domain; MIF4G; middle domain of eukaryotic initiation factor; PTPc, protein tyrosine phosphatase; bdg, binding. ³The genename of the S. cerevisiae homolog is given. *Also functions in transcription. **93 proteins identified only by Rappsilber et al. 2002, and 37 yeast proteins found by Ohi et al. 2002 and Stevens et al. 2002 are not included in Table 1 and Tables S1-S3. These tables were kindly prepared by Reinhard Rauhut.

Jurica M.S., Licklider L.J., Gygi S.R., Grigorieff N., and Moore M.J. 2002. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. RNA 8: 426–439.

Makarov E.M., Makarova O.V., Urlaub H., Gentzel M., Will C.L., Wilm M., and Lührmann R. 2002. Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome. Science 298: 2205–2208.

Makarova O.V., Makarov E.M., Urlaub H., Will C.L., Gentzel M., Wilm M., and Lührmann R. 2004. A subset of human 35S U5 proteins, including Prp19, function prior to catalytic step 1 of splicing. EMBO J. 23: 2381–2391.

Ohi M.D., Link A.J., Ren L., Jennings J.L., McDonald W.H., and Gould K.H. 2002. Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs. Mol. Cell. Biol. 22: 2011–2024.

Rappsilber J., Ryder U., Lamond A.I., and Mann M. 2002. Large-scale proteomic analysis of the human spliceosome. Genome Res. 12: 1231–1245.

Stevens S.W., Ryan D.E., He H.Y., Moore R.E., Young M.K., Lee T.D., and Abelson J. 2002. Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol. Cell 9: 31–44.

Zhou Z., Licklider L.J., Gygi S.P., and Reed R. 2002. Comprehensive proteomic analysis of the human spliceosome. Nature 419: 182–185.

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