Exon 2 Exon 3 STOP K8β intron Figure S1 …acacaagacagcugcagcag GUAUAGACGGGAAACAGGUGUCUAUCUUGGCCGGCUGGUUACUCAAAUGGGAACAAUGGCGCCACCUUGCUGUCUUUGUAG gcauuagaagaaaaggaugc…

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Exon 2 Exon 3 STOP K8β intron Figure S1 …acacaagacagcugcagcag GUAUAGACGGGAAACAGGUGUCUAUCUUGGCCGGCUGGUUACUCAAAUGGGAACAAUGGCGCCACCUUGCUGUCUUUGUAG gcauuagaagaaaaggaugc… 5’ss 3’ss oVM241 oVM242 oVM243 oVM244 oVM245 oVM246

K8β 1234 K8  - -++ORF57 RBM CNCNRNA CNCN GAPDH U6 -- -- K8 Figure S2

Figure S3 A B RBM15 SRSF3 ORF β-tubulin ORF57 DNA (ng) HEK293 - full - cleaved VA (h) BCBL RBM15 SRSF3 β-tubulin ORF57 - full - cleaved SRSF3/RBM15 (%)

Sample 1 Peptide Mass Peptide SequenceSequence Header EVSFQSTGESEWK MSGGWELELNGTEAK ITVTFNINNSIPPTFDGEEEPSQG QK AFVDFLSDEIKEER VEEQEPELTSTPNFVVEVIK >gi| |ref|NP_ | complement component 1, q subcomponent binding protein precursor [Homo sapiens]gi|730772|sp|Q |C1QBP_HUMAN RecName: Full=Complement component 1 Q subcomponent-binding protein, mitochondrial; AltName: Full=Glycoprot IYVGNLPTDVR GSPHYFSPFRPY EKDLEDLFYK HGLVPFAFVR >gi| |ref|NP_ | splicing factor, arginine/serine-rich 9 [Homo sapiens]gi| |ref|XP_ | PREDICTED: splicing factor, arginine/serine-rich 9 isoform 2 [Pan troglodytes]gi| |sp|Q |SFRS9_HUMAN RecName: Full=Splic LTPEEEEILNK ISSLLEEQFQQGK IIDVVYNASNNELVR QWYESHYALPLGR >gi| |ref|NP_ | ribosomal protein S8 [Homo sapiens]gi| |ref|NP_ | ribosomal protein S8 [Mus musculus]gi| |ref|NP_ | ribosomal protein S8 [Rattus norvegicus]gi| |ref|NP_ | ribosomal protein S ELLTLDEKDPR LFEGNALLR KQVVNIPSFIVR QVVNIPSFIVR >gi| |ref|NP_ | ribosomal protein S9 [Homo sapiens]gi| |ref|NP_ | ribosomal protein S9-like [Mus musculus]gi| |ref|NP_ | ribosomal protein S9 [Rattus norvegicus]gi| |ref|NP_ | ribosomal VRVELSNGEK AFGYYGPLR NPPGFAFVEFEDPR NPPGFAFVEFEDPRDAADAVR >gi| |ref|NP_ | splicing factor, arginine/serine-rich 3 [Homo sapiens]gi| |ref|NP_ | splicing factor, arginine/serine-rich 3 (SRp20) [Mus musculus]gi| |ref|NP_ | splicing factor, arginine/serine-rich 3 [Bo AQQNNVEHKVETFSGVYK AIIIFVPVPQLK TLTAVHDAILEDLVFPSEIVGK >gi| |ref|NP_ | ribosomal protein S7 [Homo sapiens]gi| |ref|NP_ | ribosomal protein S7 [Mus musculus]gi| |ref|NP_ | ribosomal protein S7 [Felis catus]gi| |ref|NP_ | ribosomal protein S FSGSGSGTDFTLK DSTYSMSSTLTLTKDEYER >gi| |pdb|1FLR|L Chain L, Fab Fragment VWLDPNETNEIANANSR >gi| |ref|NP_ | ribosomal protein L19 [Homo sapiens]gi| |ref|NP_ | ribosomal protein L19 [Rattus norvegicus]gi| |ref|NP_ | ribosomal protein L19 [Bos taurus]gi| |ref|NP_ | ribosomal pro TAVVVGTITDDVR >gi| |ref|NP_ | ribosomal protein L18 [Homo sapiens]gi| |ref|XP_ | PREDICTED: similar to ribosomal protein L18 [Macaca mulatta]gi|548749|sp|Q |RL18_HUMAN RecName: Full=60S ribosomal protein L18gi| |sp|Q GLDVDSLVIEHIQVNK >gi| |gb|AAH | Ribosomal protein L17 [Homo sapiens] VLEQLTGQTPVFSK >gi|495126|emb|CAA | ribosomal protein L11 [Homo sapiens] Sample EVSFQSTGESEWK MSGGWELELNGTEAK AFVDFLSDEIKEER VEEQEPELTSTPNFVVEVIK >gi| |ref|NP_ | complement component 1, q subcomponent binding protein precursor [Homo sapiens]gi|730772|sp|Q |C1QBP_HUMAN RecName: Full=Complement component 1 Q subcomponent-binding protein, mitochondrial; AltName: Full=Glycoprot LTPEEEEILNK ISSLLEEQFQQGK IIDVVYNASNNELVR QWYESHYALPLGR >gi| |ref|NP_ | ribosomal protein S8 [Homo sapiens]gi| |ref|NP_ | ribosomal protein S8 [Mus musculus]gi| |ref|NP_ | ribosomal protein S8 [Rattus norvegicus]gi| |ref|NP_ | ribosomal protein S FSGSGSGTDFTLK QNGVLNSWTDQDSK DSTYSMSSTLTLTKDEYER >gi| |pdb|1FLR|L Chain L, Fab Fragment FEDPRDAEDAIYGR IYVGNLPTDVR GSPHYFSPFRPY >gi| |ref|NP_ | splicing factor, arginine/serine-rich 9 [Homo sapiens]gi| |ref|XP_ | PREDICTED: splicing factor, arginine/serine-rich 9 isoform 2 [Pan troglodytes]gi| |sp|Q |SFRS9_HUMAN RecName: Full=Splic VWLDPNETNEIANANSR >gi| |ref|NP_ | ribosomal protein L19 [Homo sapiens]gi| |ref|NP_ | ribosomal protein L19 [Rattus norvegicus]gi| |ref|NP_ | ribosomal protein L19 [Bos taurus]gi| |ref|NP_ | ribosomal pro QVVNIPSFIVR >gi| |ref|NP_ | ribosomal protein S9 [Homo sapiens]gi| |ref|NP_ | ribosomal protein S9-like [Mus musculus]gi| |ref|NP_ | ribosomal protein S9 [Rattus norvegicus]gi| |ref|NP_ | ribosomal TAVVVGTITDDVR >gi| |ref|NP_ | ribosomal protein L18 [Homo sapiens]gi| |ref|XP_ | PREDICTED: similar to ribosomal protein L18 [Macaca mulatta]gi|548749|sp|Q |RL18_HUMAN RecName: Full=60S ribosomal protein L18gi| |sp|Q GLDVDSLVIEHIQVNK >gi| |gb|AAH | Ribosomal protein L17 [Homo sapiens] NPPGFAFVEFEDPRDAADAVR >gi| |ref|NP_ | splicing factor, arginine/serine-rich 3 [Homo sapiens]gi| |ref|NP_ | splicing factor, arginine/serine-rich 3 (SRp20) [Mus musculus]gi| |ref|NP_ | splicing factor, arginine/serine-rich 3 [Bos taurus] Supplementary Table S1: Peptides and corresponding proteins associated with KSHV ORF57 in THE absence (Fig 2A, sample 1) or presence (Fig 2A, sample 2) of ectopically expressed RBM15. The peptides and proteins were identified with LC-MS/MS.

OligoSequencePosition KSHV oVM241 5'-Biotin-rArCrArCrArArGrArCrArGrCrUrGrCrArGrCrArGrGrUrArUrAdTdT-3' oVM242 5'-Biotin-rGrUrArUrArGrArCrGrGrGrArArArCrArGrGrUrGrUrCrUrArUdTdT-3' oVM243 5'-Biotin-rUrCrUrArUrCrUrUrGrGrCrCrGrGrCrUrGrGrUrUrArCrUrCrAdTdT-3' oVM244 5'-Biotin-rArCrUrCrArArArUrGrGrGrArArCrArArUrGrGrCrGrCrCrArCdTdT-3' oVM245 5'-Biotin-rGrCrCrArCrCrUrUrGrCrUrGrUrCrUrUrUrGrUrArGrGrCrArUdTdT-3' oVM246 5'-Biotin-rUrGrUrArGrGrCrArUrUrArGrArArGrArArArArGrGrArUrGrCdTdT-3' HPV16 oJR9 (wt) 5′-Biotin-rCrCrArGrArCrArCrCrGrGrArArArCrCrCrCrUrGrCrCrArCrArCrCrArC-3′ oJR10 (mt) 5′-Biotin-rCrCrArGrArUrGrUrCrGrGrArArArCrCrUrCrUrGrCrUrGrUrGrCrUrGrU-3′ SUPPLEMENTARY TABLE S2. Biotinylated RNA oligos from the KSHV K8β intron region and the HPV16 ESE used in RNA pulldowns. Underlined are point mutations.

Supplementary Table S3: Primers used for RT-PCR and Northern Blotting. T7, T7 promoter; U1bs, U1 binding site OligoSequenceTargetPosition oST15'-TAATACGACTCACTATAGGG /ACCACCAAGAGGACCACACATTTC-3' T7/KSHV K8 (exon 1) oST35'-GTACTCACCCC/CACACAAA GTCTGGCATGGTTCTCCC-3' U1bs/ KSHV K8 (exon 3) oVM2135'-CCCGGGATCCACCGGTCGCCACCA-3'BamHI/GFP oVM1625'-GGTTCAGGGGGAGGTGTGG-3'GFP oZMZ2465’-CAATGGGACGCGTGCAAAGC-3’BPV-1 (Pr1) oZMZ2495’-TAATACGACTCACTATAGGGA/ CAGTATTTGTGCTTGTCCTT-3’ T7/BPV-1 (Pr2) oXFL0495’-TAATACGACTCACTATAGG /TTTAATGCTTTGCTTGATGC-3’ T7/BPV-1 (Pr3) oXFL0465’-CATATCCCCATCTTCTATGTGC-3’BPV-1 (Pr4) oSB235’-TATTAGGCAGCACTTGGC-3’HPV16 (Pr1) oXHW415’-CAACATATTCATCCGTGCTTACAAC-3’HPV16 (Pr2) oST2855’-TGGCTTTGGTGCTATGGACT-3’HPV16 (Pr3) oYL95’-GAAGTAGATATGGCAGCACA-3’HPV16 (Pr4) oZMZ2695'-GTCATCAATGGAAATCCCATCACC-3'GAPDH oZMZ2705'-TGAGTCCTTCCACGATACCAAA-3'GAPDH oST32CGGACGACGGCACAACCAKSHV K8 (exon 3) oST197AAAATATGGAACGCTTCACGAU