Supporting Information

Lock et al. 10.1073/pnas.1405507111 SI Text AAACAGCAAATCAACAAAAAGGCGTGGGCTTTGCCACTA- GGCAGGTGGGAAATGTGACCAAACCAACGGTAATTA- 1. Candidate Function Synopsis TCAGTCAAGAAGGAGACAAAGTGGTCATCAGGACTCT- Microfibrillar Associated Protein 5. The microfibrillar associated CAGCACATTCAAGAACACGGAGATTAGTTTCCAGCTG- protein 5 (MFAP5, also known as MAGP2) gene encodes a GGAGAAGAGTTTGATGAAACCACTGCAGATGATAGAA- 25-kDa microfibril-associated glycoprotein (1) that can activate ACTGTAAGTCTGTTGTTAGCCTGGATGGAGACAAACTT- Notch signaling (2) and has been shown to negatively affect se- GTTCACATACAGAAATGGGATGGCAAAGAAACAAATT- rous ovarian cancer patient survival (3). However, this gene or TTGTAAGAGAAATTAAGGATGGCAAAATGGTTATGAC- gene product has not previously been described in association CCTTACTTTTGGTGATGTGGTTGCTGTTCGCCACTATG- with lymphoma. AGAAGGCATAA In the red LTR2 sequence, light blue shows splice junctions, Dermatan Sulfate Proteoglycan 3 Precursor. The dermatan sulfate splicing into exon 2, then 3 and 4. In green, ATG is present in the proteoglycan 3 precursor (EPYC) gene encodes a member of the alternative first exon. Bold type represents the translated portion small leucine-rich repeat proteoglycan family (epiphycan) and of the first exon, specific to chimeric mRNA. regulates fibrillogenesis by interacting with collagen fibrils and other extracellular matrix proteins; hence, it is involved in bone MER57B-ALDH1L1. Karpas 422 cell-line (DLBCL) RACE sequence formation and also in establishing the ordered structure of car- (GenBank accession no. KM111187) tilage through matrix organization. Increased EPYC mRNA CTGGnGTCTCTCTGATCTGCTGTGATTCTGAGGGCT- expression has been observed in patients with invasive pancreatic GCCCAATTTGTGAATCGTTCATTGCTCAATTAAACTTT- ductal adenocarcinoma, compared with normal pancreatic tissues TTTAAATTTAATTTGGCTGAAGTTTTTCTTTTAACATGG- (4), but has not previously been associated with blood cancers. TGTCAGAAGCGGGATCCAAAGTACAGCTTCTAGCGAC- CCCCAGGAGTACTGAGTGAACAAGCAAGGTCCTTCCA- Protein Tyrosine Phosphatase, Receptor Type F. Protein tyrosine ACCCTCCTGCTACCATGAAGATTGCAGTGATTGGACAG- phosphatase, receptor type F (PTPRF, or LAR) protein is AGCCTGTTTGGCCAGGAAGTTTACTGCCACCTGAGGAA member of the protein tyrosine phosphatase family of signaling The MER57B sequence is shown in red; light blue is the splice molecules that regulate a variety of cellular processes including junction, splicing into exon 2. cell growth, differentiation, cell cycle, and oncogenic trans- IM9 cell line RACE sequence (GenBank accession no. formation. Two alternatively spliced transcript variants of this KM111188) gene, which encode distinct proteins, have been reported. PTPRF TTTGTGAATCGTTGATTGCTCAATTAAACTTTTTTAA- possesses an intrinsic protein tyrosine phosphatase activity ATTTAATTTGGCTGAAGTTTTTCTTTTAACATGGTGTC- (5). PTPRF expression is significantly increased in thyroid car- AGAAGCGGGATCCAAAGTACAGCTTCTAGCGACCCCC- cinomas (6) and breast cancer (7). AGGAGTACTGAGTGAACAAGCAAGGTCCTTCCAACCC- TCCTGCTACCATGAAGATTGCAGTGATTGGACAGAGC- 1 Family, Member L1. Aldehyde de- CTGTTTGGCCAGGAAGTTTACTGCCACCTGAGGAAGG- hydrogenase 1 family, member L1 (ALDH1L1, or FDH) protein AGGGCCACGAAGTGGTGGGTGTGTTCACTGTTCCAGA- encoded by this gene belongs to the aldehyde dehydrogenase CAAGGATGGAAAGGCCGACCCCCTGGGTCTGGAAGC- family and catalyzes the conversion of 10-formyltetrahydrofolate, TGAGAAGGATGGAGTGCCGGTATTCAAGTACTCCCG- + NADP , and water to tetrahydrofolate, NADPH, and CO2 (8). GTGGCGTGCAAAAGGACAGGCTTTGCCTGATGTGGT- Alternative splicing results in multiple transcript variants (9). GGCAAAATACCAGGCTTTGGGGGCCGAGCTCAACGTC- Loss of function or expression of ALDH1L1 is associated with CTGCCCTTCTGCAGCCAATTCATCCCCATGGAGATAAT- decreased apoptosis, increased cell motility, and cancer pro- CAGTGCCCCCCGGCATGGCTCCATCATCTATCACCCGT- gression. ALDH1L1 is expressed in normal adult liver and down- CACTGCTCCCTAGGCACCGAGGGGCCTCGGCCATCA- regulated in liver cancer (10). ACTGGACCCTCATTCACGGAGATAAGAAAGGGGGG- TTTTCCATCTTCTGGGCGGATGATGGTCTGGACACC- Fatty Acid-Binding Protein 7. Brain fatty acid-binding protein GGAGACCTGCTGCTGCAGAAGGAGTGTGAGGTGCTCC- (FABP7, or BLBP) is a member of the FABP family of lipid CGGACGACACCGTGAGCACGCTGTACAACCGCTTCCT- chaperones that are involved in the uptake, storage, and in- CTTCCCTGAAGGCATCAAAGGGATGGTGCAGGCCGTG- tracellular trafficking of fatty acids (11). FABP7 is expressed AGGCTGATCGCTGAGGGCAAAGCCCCCAGACTCCCTC- in normal brain and is up-regulated in various solid cancers, AGCCTGAGGAAGGAGCCACCTATGAGGGGATTCAGA- including glioma (12), melanoma (13), renal cell carcinoma (14), AGAAGGAGACAGCCAAG and aggressive triple negative breast cancer (15) and is associ- The MER57B sequence is shown in red; light blue shows splice ated with poor prognosis. FABP7 has not been associated with junctions, splicing into the second exon, then the third, fourth, blood cancers before this report, to our knowledge, and the and fifth. ATG present in exon 2 is shown in green. native FABP7 promoter is not functional in normal blood cells. THE1A-MFAP5. NUDUL1 cell line (DLBCL) RT-PCR sequence 2. Transposable Element-Gene Chimeric Sequences from (GenBank accession no. KM111189) RACE or RT-PCR TAAGGTCTCCCCAGCCATGTGAAACTCCTCATTGTA- LTR2-FABP7. SUDHL4 cell-line [diffuse large B-cell lymphoma ACACACATTCTACGCCTAGCCTGGCTTTCTTGCTCTCCC- (DLBCL)] RT-PCR sequence (GenBank accession no. KM111186) TCATCTCATTGTTTCAGCGGAGGCCAAATCTGAAGTCC- ACTTCTTTCTTTGGAGGCAAAAATTGGGTATAAGAC- TTTCCAGGGAGTGGCTCTGTTCATCTTATTCGCCAGCC- AATATGAGGGGTGGTCTCCTCCCTTAAACCTGGTGGA- AAAGTAGGAACAGCGTAAGAGGAGAGAGACACATTC- ATGCAACTGAAGGAGAAGGATTGGAGATCTGCACTTATCA- AGCAGCCAAAGGACTCGGTGGAAAGAGCAGAACACC-

Lock et al. www.pnas.org/cgi/content/short/1405507111 1of10 ATAGACAATATGTCGCTCTTGGGACCCAAGGTGCTGC- AAGGAGACAGCCACGCAAATATCTGGGAAAAGAG- TGTTTCTTGCTGCAT CTCCAGGTGCCATAGGAGGAGCGGCGTCAGAAGGG- The THE1A sequence is shown in red; light blue shows splice ACTGATGACTGATTGGACAGTGGTGCAGGAGGGAAG- junctions, splicing into the eighth base of exon 1. ATG present in GTCTCTGCATGTCAGTGATTAAATTGCTGAAGATGCCA- exon 2 is shown in green. CTGCCTGAGACGGGCAGTATTGAAGGAAGGAGTGGAG- GCCCTGGTGCCCGGCCCTTGGTGCTGAGTATCCAGCAA L2-EPYC. OCL-Ly3 cell line (DLBCL) RT-PCR sequence (Gen- L2 is shown in red; light blue shows splice junctions, splicing Bank accession no. KM111190) into an intronic region then into exon 2. ATG was present in exon GCCAACCAACCACCACTTTGAAAGGACTGCAGAGG- 3 but not sequenced. AAAACCTTTGTCAGGAGACAGCCAGATTCTTTTAAGG- ATG AAAGCTTGAAAA AAGACATTAGCAGGACTTGTTC- 3. Native FABP7 Amino Acid Sequence Compared with TGGGACTTGTCATCTTTGATGCTGCTGTGACTGCCCCA- Chimeric FABP7 Amino Acid Sequence ACTCTAGAGTCCATCAACTATGACTCAGAAACATATGA- Native FABP7 amino acid sequence: MVEAFCATWKLTN- TGCCACCTTAGAAGACCTGGATAATTTGTACAACTATG- SQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGDKVVIR- AAAACATACCTGTTGATAAAGTTGAGATTGAAATAGC- CACAGTGATGCCTTCAGGGAACAGAGAGCTCCTCACT- TLSTFKNTEISFQLGEEFDETTADDRNCKSVVSLDGDKLVH- CCACCCCCACAGCCTGAGAAGGCCCAGGAAGAGGAAG- IQKWDGKETNFVREIKDGKMVMTLTFGDVVAVRHYEKA AGGAGGAGGAATCTACTCCCAGGCTGATTGATGGCTC- Chimeric FABP7 predicted amino acid sequence derived from TTCTCCCCAGGAGCCTGAATTCACAGGGGTTCTGGGG- SUDHL-4 amplification and sequencing: CCACACACAAATGAAGACTTTCCAACCTGTCTTTTGTG- MQLKEKDWRSALIKTANQQKGVGFATRQVGNVTKP- TACTTGTATAAGTACCACCGTGTACTGTGATGACCATG- TVIISQEGDKVVIRTLSTFKNTEISFQLGEEFDETTADDRN- AACTTGATGCTATTCCTCCGCTGCCAAAGAA CKSVVSLDGDKLVHIQKWDGKETNFVREIKDGKMVMT- The L2a sequence is shown in red; light blue shows splice junc- LTFGDVVAVRHYEKA tions, splicing into exon 2. ATG present in exon 2 is shown in green. In the underlined sequence, different first exons result in different amino acid sequences. Red highlighting shows that the LTR16A1-L2-PTPRF. L591 cell line (HL) RT-PCR sequence (Gen- conserved nuclear localization sequence [conserved K (lysine)] is Bank accession no. KM111191) missing in chimeric FABP7.

1. Penner AS, Rock MJ, Kielty CM, Shipley JM (2002) Microfibril-associated glycoprotein- 8. Krupenko SA (2009) FDH: an aldehyde dehydrogenase fusion in folate 2 interacts with fibrillin-1 and fibrillin-2 suggesting a role for MAGP-2 in elastic fiber metabolism. Chem Biol Interact 178(1-3):84–93. assembly. J Biol Chem 277(38):35044–35049. 9. Black WJ, et al. (2009) Human aldehyde dehydrogenase : Alternatively spliced 2. Miyamoto A, Lau R, Hein PW, Shipley JM, Weinmaster G (2006) Microfibrillar proteins transcriptional variants and their suggested nomenclature. Pharmacogenet Genomics MAGP-1 and MAGP-2 induce Notch1 extracellular domain dissociation and receptor 19(11):893–902. activation. J Biol Chem 281(15):10089–10097. 10. Chen XQ, He JR, Wang HY (2012) Decreased expression of ALDH1L1 is associated with 3. Mok SC, et al. (2009) A gene signature predictive for outcome in advanced ovarian a poor prognosis in hepatocellular carcinoma. Med Oncol 29(3):1843–1849. cancer identifies a survival factor: Microfibril-associated glycoprotein 2. Cancer Cell 11. Feng L, Hatten ME, Heintz N (1994) Brain lipid-binding protein (BLBP): A novel 16(6):521–532. signaling system in the developing mammalian CNS. Neuron 12(4):895–908. 4. Buchholz M, et al. (2005) Transcriptome analysis of microdissected pancreatic 12. Liang Y, et al. (2005) profiling reveals molecularly and clinically distinct intraepithelial neoplastic lesions. Oncogene 24(44):6626–6636. subtypes of glioblastoma multiforme. Proc Natl Acad Sci USA 102(16):5814–5819. 5. Chagnon MJ, Uetani N, Tremblay ML (2004) Functional significance of the LAR 13. Slipicevic A, et al. (2008) The fatty acid binding protein 7 (FABP7) is involved in receptor protein tyrosine phosphatase family in development and diseases. Biochem proliferation and invasion of melanoma cells. BMC Cancer 8:276. Cell Biol 82(6):664–75. 14. Seliger B, et al. (2005) Identification of fatty acid binding proteins as markers associated 6. Konishi N, et al. (2003) Overexpression of leucocyte common antigen (LAR) P-subunit with the initiation and/or progression of renal cell carcinoma. Proteomics 5(10): in thyroid carcinomas. Br J Cancer 88(8):1223–1228. 2631–2640. 7. Yang T, Zhang JS, Massa SM, Han X, Longo FM (1999) Leukocyte common antigen- 15. Liu RZ, et al. (2012) A fatty acid-binding protein 7/RXRβ pathway enhances survival related tyrosine phosphatase receptor: increased expression and neuronal-type and proliferation in triple-negative breast cancer. J Pathol 228(3):310–321. splicing in breast cancer cells and tissue. Mol Carcinog 25(2):139–149.

Lock et al. www.pnas.org/cgi/content/short/1405507111 2of10 A Scale 10 kb hg18 chr1: 43,765,000 43,770,000 43,775,000 43,780,000 43,785,000 43,790,000 Control 5 _ RPKM library 0.051094 _ Chimeric paired-end reads 4.04996 _ RPKM DLBCL library

0.0826523 _ Chimeric paired-end reads

CpG Islands RefSeq Genes PTPRF PTPRF Transposable elements SINE LINE LTR DNA

B Scale 10 kb hg18 chr12: 89,900,000 89,905,000 89,910,000 89,915,000 89,920,000 89,925,000 No data _ RPKM Control library No data _ Chimeric paired-end reads 12.3203 _ RPKM DLBCL library 0.205338 _ Chimeric paired-end reads

CpG Islands RefSeq Genes EPYC Transposable elements SINE LINE LTR DNA

C Scale 10 kb hg18 chr12: 8,695,000 8,700,000 8,705,000 8,710,000 8,715,000 20 _ Control RPKM library 0.051094 _ Chimeric paired-end reads 20.4234 _ RPKM DLBCL library 0.153559 _ Chimeric paired-end reads

CpG Islands RefSeq Genes MFAP5 Transposable elements SINE LINE LTR DNA

Fig. S1. (Continued)

Lock et al. www.pnas.org/cgi/content/short/1405507111 3of10 D Scale 10 kb hg18 chr3: 127,360,000 127,365,000 127,370,000 127,375,000 127,380,000 127,385,000 127,390,000 127,395,000 127,400,000 Control 5 _ RPKM library 0.051094 Chimeric paired-end reads 5.03207 _ RPKM DLBCL library

0.102695 _ Chimeric paired-end reads

CpG Islands RefSeq Genes ALDH1L1 ALDH1L1 ALDH1L1 ALDH1L1 ALDH1L1-AS2 Transposable elements SINE LINE LTR DNA

E Scale 10 kb hg18 chr6: 123,115,000 123,120,000 123,125,000 123,130,000 123,135,000 123,140,000 123,145,000 5 _ Control RPKM library 0.128912 _ Chimeric paired-end reads 5.2836 _ RPKM DLBCL library 0.0800546 _ Chimeric paired-end reads

CpG Islands RefSeq Genes FABP7 Repeating Elements by RepeatMasker SINE LINE LTR DNA

Fig. S1. Human hg18 UCSC genome browser screenshots for the five transposable element (TE)-gene chimeric candidates modified to show only paired-end reads verified to be chimeric (one read located in a TE sequence). RPKM tracks are computed with all paired-end reads including reads mapping to multiple locations but where mates are uniquely mapped. TEs acting as promoters are depicted in red or pink and the sense of gene transcription is showed as a blue arrow on top of each gene: (A) PTPRF,(B) EPYC,(C) MFAP5,(D) ALDH1L1,and(E) FABP7. The DLBCL library depicted in the FABP7 screenshot is different from in Fig. 1A to show different libraries for this example.

Lock et al. www.pnas.org/cgi/content/short/1405507111 4of10 Primer locations

12910 11121345687

Primer walking RT-PCR result

Fig. S2. Primer walking for LTR2-FABP7. Hg18 UCSC genome browser screenshot of the LTR2 upstream of FABP7 putatively acting as a promoter showing the peak of reads for one DLBCL sample. Note that the mappability of the region around the localized transcription start site is low, resulting in a lack of reads mapping closer to it. The RT-PCR product obtained to confirm presence of LTR2-FABP7 chimera is shown along with all of the primers used for primer walking in the Blat track. On the RT-PCR gel, a 100-bp ladder is shown and numbers correspond to primer names in the genome browser screenshot.

LTR2 FABP7 (HERV-E) ~30 Kb 5’ ATG 3’

SUDHL9

TSS

Fig. S3. Bisulfite sequencing of native and TE promoters for FABP7 in the SUDHL9 DLBCL cell line. Gene scheme is the same as in Fig. 1B; filled circles represent methylated CpGs, empty circles represent unmethylated CpGs, and each row represents an independent clone. The localization of CpGs relative to the DNA sequence is shown with colored lines. This cell line was inconsistently positive for the chimeric transcript by RT-PCR but negative for expression from the native promoter, and protein expression was not detectable (Fig. 3A).

Lock et al. www.pnas.org/cgi/content/short/1405507111 5of10 i.S4. Fig. oke al. et Lock hlodn(ci) AP niois ra g oto,a pcfe,adDP ula ti.FB7lclzto a sesdb ofclmicrosco confocal by ( units. assessed arbitrary was A.U., localization given. cell. is FABP7 DB cells single stain. DB a nuclear 30 of DAPI least diameter at the and from across specified, intensity intensity as staining fluorescence control, DAPI FABP7 and intensity/perinuclear IgG FABP7 an of or data Representative antibodies, FABP7 (Actin), phalloidin ( A www.pnas.org/cgi/content/short/1405507111 21clso ( or cells U251 ) B Bclswr rae ihBA(vehicle), BSA with treated were cells DB ) B A DB : AA DB : DHA DB : BSA U251: IgG control C D Staining intensity (A.U) 100 150 200

Nucelar intensity / 250 50 0

perinuclear 0.0025 intensity 0.002 0.0015 0.001 0.0005 0 (Mean ± SEM) 0.5 Actin Actin 1 0 Distance (µM) Distance DB: BSA DB: DHA DB: AA DB: DHA DB: BSA DB: S DHA BSA NS DB NS Nuclei Nuclei 100 150 200 250 50 0 AA .05001001 .0 0.0025 0.002 0.0015 0.001 0.0005 0 ω 3dcshxeocai DA,or (DHA), acid -3-docosahexaenoic Distance (µM) Distance (µM) Distance (µM) Distance IgG control FABP7 100 150 200 250 50 0 .05001001 .0 0.0025 0.002 0.0015 0.001 0.0005 0 ω 6aahdncai A) ie,adsandwith stained and fixed, (AA), acid -6-arachidonic Merge Merge D enncerFB7fluorescence FABP7 nuclear Mean ) FABP7 Nuclei y ( py. 6of10 C ) Fig. S5. cDNAs encoding native or chimeric FABP7 were cloned into the pCMV-3Tag (Flag) expression vector (Agilent), transfected into HEK293 cells by calcium phosphate precipitation, and treated with BSA (vehicle), DHA, or AA as previously. Transfected FABP7-Flag localization was assessed by Flag immu- nofluorescence.

30

0.0245* 20

10 %BrdUpositive

0 Scrambled 745 FABP7 RNAi

Fig. S6. SUDHL4 were stably transfected with RNAi vectors targeting FABP7 (745) or a scrambled control and subjected to BrdU incorporation assay, assessed by FACS analysis. Representative of two independent experiments.

Lock et al. www.pnas.org/cgi/content/short/1405507111 7of10 Scale 20 kb hg18 chr3: 127,360,000 127,365,000 127,370,000 127,375,000 127,380,000 127,385,000 127,390,000 127,395,000 127,400,000 5.03207 _ RPKM

HS1458_DLBCL_ABC

0.102695 _ Chimeric paired-end reads

Tophat junctions HS1458 DLBCL JUNC00114486 JUNC00114487 JUNC00114488 JUNC00114489 JUNC00114490 JUNC00114492 JUNC00114491 JUNC00114493 Cufflinks transcripts HS1458 DLBCL CUFF.1849305.1 CUFF.1849313.1 CUFF.1849317.1 CUFF.1849323.1 15.5306 _ RPKM

HS1975_DLBCL_ABC

0.0800546 _ Chimeric paired-end reads

Tophat junctions HS1975 DLBCL JUNC00124868 JUNC00124869 JUNC00124870 JUNC00124871 JUNC00124872 JUNC00124874 JUNC00124873 Cufflinks transcripts HS1975 DLBCL CUFF.1966547.1 CUFF.1966551.1 CUFF.1966553.1 RefSeq Genes ALDH1L1 ALDH1L1 ALDH1L1 ALDH1L1 ALDH1L1-AS2 Transposable elements SINE LINE LTR DNA

Fig. S7. Example of our paired-end chimeric read analysis compared with ab initio transcript assembly using Tophat/Cufflinks. Human hg18 UCSC genome browser screenshots for the ALDH1L1 gene region in two DLBCL libraries. For each library, the tracks show reads per kilobase of transcript per million reads mapped (RPKM), chimeric paired-end reads found by our analysis in red as well the result of ab initio transcript assembly using split read junctions in green (Tophat) and assembled Cufflinks transcripts in black. The LTR acting as the promoter is highlighted in red in the transposable element (RepeatMasker) track and the sense of gene transcription is showed as a blue arrow above the Refseq track. The LTR-initiated transcript is not detected by ab initio assembly in the upper library.

Lock et al. www.pnas.org/cgi/content/short/1405507111 8of10 Table S1. Primers used in this study: 5′ RACE ALDH1L1 Primer sequence

RLM 5′RACE inner primer CGCGGATCCGAACACTGCGTTTGCTGGCTTTGATG ALDH1L1 exon 2 forward CCTCAGGTGGCAGTAAACTTC

Table S2. Primers used in this study: RT-PCR Target Forward Reverse

GABPDH CATGAGAAGTATGACAACAGCCTC GTTGCTGTAGCCAAATTCGTTGTC FABP7 native GCTACCTGGAAGCTGACCA CTGAAGAGCTCTTCCAAGCC FABP7 chimera TGGAATGCAACTGAAGGAGA CTGAAGAGCTCTTCCAAGCC FABP7 total TGGATGGAGACAAACTTGTTCA TATGCCTTCTCATAGTGGCGA EPYC native GCTCTGCATCCTCAGTCACT TTCTTTGGCAGCGGAGGAAT EPYC chimera GCCAACCAACCACCACTTTG TTCTTTGGCAGCGGAGGAAT EPYC total ATTCCTCCGCTGCCAAAGAA GTGGCAGAGGGATGTGGTC PTPRF native TGGGTTCTCCTGTAGCTTGG GCAGAGGAGTGGGAGCAG PTPRF chimera GGGAAACCTGACCTAACACAGA TGCTGGATACTCAGCACCAA PTPRF total GAGGACCAGACTGGGCTGT GAACGCAGCTGCTTGATG ALDH1L1 native AGTGAACACACCCACCACTTC GGTCTGCACCAACCTCAGTT ALDH1L1 chimera AGTGAACACACCCACCACTTC TTGTGAATCGTTCATTGCTC ALDH1L1 total TAACTCCAGGCCATCACACA AGAGGCCATTCACAACTGGA MFAP5 native GTGCAATATCAGCCAAA ATTCCAGCCTCATTG MFAP5 chimera ATGCAGCAAGAAACAGCAGC TAAGGTCTCCCCAGCCATGT MFAP5 total AAGGAAGACTTGCCAGGCAA CGGCCGGTTAAACAATGCAT

Table S3. Primers used in this study: Bisulfite analysis Gene promoter Primer sequence Primer sequence

MFAP5 native, first round MFAP5 BIS-S1 MFAP5 BIS-AS1 TTTAGGGTTTTAGGTAATTAAATAATTTAT ACAAAAAAAATCTAAATATATAAATCAAAA MFAP5 native, second round MFAP5 BIS-S1 MFAP5 BIS-AS5 TTTAGGGTTTTAGGTAATTAAATAATTTAT AATCACATCATTACACTCCAACCTA MFAP5 LTR, first round MFAP5 BIS-S2 MFAP5 BIS-AS3 TTTAATTTTTGTTTGTTATTTAGTTTTAAA AAAACAAAACAAAAACAAACCATTC MFAP5 LTR, second round MFAP5 BIS-S2 MFAP5 BIS-AS4 TTTAATTTTTGTTTGTTATTTAGTTTTAAA AAAATCATCTTTCCCATACTATTCTC FABP7 native, first round FABGeneBisulF FABGeneBisulR1 GGGGTTTTTATTTGTGATTAGTTTT TTATTACCTACCTAAAACCTTCATATACTC FABP7 native, second round FABGeneBisulF FABGeneBisulR2 GGGGTTTTTATTTGTGATTAGTTTT CTCATCAAAATTCTAACTATTAATCAACTT FABP7 LTR, first round FABLTRBisulF FABLTRBisulR1 TTGGTTAGAGTTTTTTGTAGGGATG TTCAATTACATTCCACCAAATTTAAA FABP7 LTR, second round FABLTRBisulF FABLTRBisulR2 TTGGTTAGAGTTTTTTGTAGGGATG AAAAAAAACCACCCCTCATATTATC ALDH1L1 native, first round ALDH1L1geneF1 ALDH1L1geneF2 GGGTAGGTTAGATTTTTGTGAGT GAAATTGAGGTTGGTGTAGATT ALDH1L1 native, second round ALDH1L1geneF1 ALDH1L1geneR GGGTAGGTTAGATTTTTGTGAGT AAAAACCAAAAACTATTTTTCTCTC ALDH1L1 LTR, first round ALDH1L1LTRF1 ALDH1L1LTRF2 TTATTTTGAGAGATTAATGGATATAAATAG TTTGATATTATGTTAAAAGAAAAATTTTAG ALDH1L1 LTR, second round ALDH1L1LTRF1 ALDH1L1LTRR TTATTTTGAGAGATTAATGGATATAAATAG ACAAAAACTAAAACAAACAAAAAAC

Lock et al. www.pnas.org/cgi/content/short/1405507111 9of10 Table S4. Primers used in this study: Primer walking Primer Sequence

Reverse primer orfF4Rev CTGAAGAGCTCTTCCAAGCC Forward primers FABP7 pw-1 TGCCTGACCCATATTTCCTC FABP7-pw2 AATCACCACGTTTCCTGGTC FABP7-pw3 GGGTTGTCTGCTTGTGGATT FABP7 pw4 TGAGCAATTCCTGTCCCTTT FABP7 pw5 AGGGTCGTGATTGATTGAGC FABP7 pw6 CAAGCAGGGGGTACATGACT FABP7 pw7 CCAATTAGGTCAGGGGTTGA FABP7 pw8 CAGGGATTTTCACAGTGCTTT FABP7 pw9 GGAACCAAGAAATGTAGCAGGA FAPB7 pw10 GACAAGCCGCAGACAAAACC FABP7 pw11 GCAGACAAAACCCCTCAGAC FABP7 pw12 GTTTATTCCACCGGGAGCAT FABP7 pw13 GGAGCATCAGCAAGACTCCT

Dataset S1. Bioinformatics pipeline output of the 98 chimeric genes where the gene is silent in normal (RPKM <1) and the following criteria are met in at least two DLBCL libraries: (i) presence of at least three chimeric reads and (ii) expression in DLBCL libraries (RPKM ≥1)

Dataset S1

All of the different RefSeq symbols with the number of chimeric reads and RPKM for each library where the parameters are met are shown. Each Refseq gene name is shown by alternating colors.

Lock et al. www.pnas.org/cgi/content/short/1405507111 10 of 10