Supplementary Figure 1. Importance of Exon numbers for transcript downregulation by CPT Numbers of down-regulated genes for four groups of comparable size genes, differing only by the number of exons. Supplementary Figure 2. CPT up-regulates the p53 signaling pathway genes A, List of the GO categories for the up-regulated genes in CPT-treated HCT116 cells (p<0.05). In bold: GO category also present for the genes that are up-regulated in CPT- treated MCF7 cells. B, List of the up-regulated genes in both CPT-treated HCT116 cells and CPT-treated MCF7 cells (CPT 4 h). C, RT-PCR showing the effect of CPT on JUN and H2AFJ transcripts. Control cells were exposed to DMSO. β2 microglobulin (β2) mRNA was used as control. Supplementary Figure 3. Down-regulation of RNA degradation-related genes after CPT treatment A, “RNA degradation” pathway from KEGG. The genes with “red stars” were down- regulated genes after CPT treatment. B, Affy Exon array data for the “CNOT” genes. The log2 difference for the “CNOT” genes expression depending on CPT treatment was normalized to the untreated controls. C, RT-PCR showing the effect of CPT on “CNOT” genes down-regulation. HCT116 cells were treated with CPT (10 µM, 20 h) and CNOT6L, CNOT2, CNOT4 and CNOT6 mRNA were analysed by RT-PCR. Control cells were exposed to DMSO. β2 microglobulin (β2) mRNA was used as control. D, CNOT6L down-regulation after CPT treatment. CNOT6L transcript was analysed by Q- PCR. Supplementary Figure 4. Down-regulation of ubiquitin-related genes after CPT treatment A, “Ubiquitin-mediated proteolysis” pathway from KEGG. The genes with “red stars” were down-regulated genes after CPT treatment. B, Affy Exon array data for ubiquitin- related genes. The log2 difference for the “ubiquitin” genes expression depending on CPT treatment normalized to the untreated controls. C, RT-PCR showing the effect of CPT on ubiquitin-related genes down-regulation. CUL1, CUL3, CUL5 and UBE2W mRNA were analysed by RT-PCR. Control cells were exposed to DMSO. β2 microglobulin (β2) mRNA was used as control. D, CUL1 down-regulation after CPT treatment. CUL1 transcript was analysed by Q-PCR. Supplementary Figure 5. Top1 down-regulation does not impacts gene expression for CUL5 and UBE2W HCT116 cells were transfected with negative control siRNA or siRNA against Top1. A, Western blotting showing the efficiency of Top1 down-regulation by siRNA. Top1 was analysed by Western blotting. GAPDH was used as loading control. B, CUL5 and UBE2W mRNA were analysed by RT-PCR. β2 microglobulin (β2) mRNA was used as - Ct control. C, CUL5 and UBE2W mRNA were analysed by Q-RT-PCR (2 ΔΔ ± standard deviation). A 120 100 80 60 Viability (%) Viability 40 20 0 Negative Control siRNA hsa-miR-142-3p B control si BCL2L1 si-Qiagen BCL2L1si-Ambion ~25$fold) Viability (%) Viability CPT (Log M) C control si MAP3K7IP2 si-Qiagen MAP3K7IP2 si-Ambion Viability (%) Viability ~25$fold) CPT (Log M) Supplementary Figure 6. miR-142-3p decreases cell survival, and down-regulation of its target genes BCL2L1 and MAP3K7IP2 sensitize to CPT A, Overexpression of miR-142-3p decreases cell survival. MDA-MB-231 cells were transfected with hsa-miR-142-3p mimic or negative control siRNA. Viability assays were performed 5 days post-transfection. Y-axes represent cell viability (% of controls). B & C, Down-regulation of two target genes of miR-142-3p sensitizes to CPT. MDA-MB-231 cells were transfected with siRNAs against BCL2L1 (B) or MAP3K7IP2 (C), and full CPT concentration responses performed. X-axes indicate CPT concentration (Log M) and Y-axes represent cell viability (%). oligonucleotide name sequence (5' to 3') β2 s CTCACGTCATCCAGCAGAGA β2 as TCTTTTTCAGTGGGGGTGAA CNOT2 1680s AGCAGAGACAGACCCAGGAA CNOT2 1982as CGGTTAAAAAGCTCCACTGC CNOT4 1555s TCGAAAAGCCTTAGCAGACC CNOT4 1847as TGATGCTATTGCGTGGAAAG CNOT6 1374s CGTCTGGAAAGCCACATCTT CNOT6 1729as TCCATTGGTGGTTCCATTCT CNOT6L 8343s CATCCCTGGAGAAAGTGGTT CNOT6L 8727as AGGTGCAAGGAAACAAGCAT CUL1 1399s CAGCCATTGAAAAGTGTGGA CUL1 1880 as GTCTTGAAACATGCGCTGAA CUL3 1180s AGGGAACTCATTTCCAAGCA CUL3 1591as GCCCTTTGACTCCCTTTTTC CUL5 1840s GAAGGGGGTGGGATTAAAAA CUL5 2337as TCCGGTATCAAGTCCTCCAG H2AFJ 1943s GTGAATGAGGCCAACCAGAT H2AFJ 2432as TTGTTCCACTGACCCCAAGT JUN 768s AGTGAGTGACCGCGACTTTT JUN 1163as CAGGGTCATGCTCTGTTTCA UBE2W 173s CATGGAAGGTGCACCAGGTA UBE2W 428as TGGTCGTCTCTTTTCCTTGC Supplementary Table 1. List of primers gene name AADAC AADAT AARS AASDH AASDHPPT AASS AATF ABCA11P ABCA5 ABCB1 ABCB7 ABCC1 ABCC2 ABCC4 ABCC5 ABCD3 ABCE1 ABCF1 ABHD10 ABHD5 ABHD6 ABI1 ABI2 ABL1 ACAA2 ACACA ACAD11 ACAP2 ACAT2 ACBD6 ACER3 ACLY ACN9 ACOXL ACP6 ACPL2 ACSL1 ACSL3 ACSL4 ACTL6A ACTR10 ACTR3 ACTR3B ACTR8 ACVR1 ACVR2A ACVR2B ADAL ADAM10 ADAM17 ADAM19 ADAM22 ADAMTS14 ADAR ADCY3 ADD3 ADIPOR2 ADNP ADNP2 ADORA2B ADRBK2 ADSS AEBP2 AFAP1 AFF1 AFF4 AFG3L2 AFTPH AGAP1 AGFG1 AGGF1 AGK AGL AGPAT5 AGPAT9 AGPS AGTPBP1 AHCTF1 AHCYL2 AHI1 AHNAK AHR AHSA2 AIG1 AIM1 AK3L1 AKAP1 AKAP10 AKAP11 AKAP12 AKAP13 AKAP9 AKT3 AKTIP ALAS1 ALCAM ALDH3A2 ALG11 ALG13 ALG14 ALG6 ALKBH8 ALMS1 ALOX12P2 ALPK1 ALS2 ALS2CR4 AMD1 AMOTL1 ANAPC1 ANAPC10 ANAPC13 ANAPC4 ANGEL2 ANKFY1 ANKH ANKHD1 ANKIB1 ANKMY2 ANKRD12 ANKRD13C ANKRD17 ANKRD22 ANKRD26 ANKRD27 ANKRD28 ANKRD32 ANKRD36 ANKRD36B ANKRD50 ANKS1A ANLN ANO10 ANO5 ANO6 ANP32A ANP32B ANP32E ANTXR2 ANUBL1 ANXA10 AP1AR AP1G1 AP1S3 AP3B1 AP3M2 AP3S1 AP4E1 AP4S1 APAF1 APBB2 APC APH1B API5 APIP APOOL APPBP2 APPL1 APPL2 AQR ARAP2 ARCN1 AREG ARF6 ARFGEF1 ARFGEF2 ARFIP1 ARGLU1 ARHGAP10 ARHGAP11A ARHGAP12 ARHGAP18 ARHGAP19 ARHGAP21 ARHGAP24 ARHGAP26 ARHGAP29 ARHGAP5 ARHGEF10 ARHGEF11 ARHGEF12 ARHGEF2 ARHGEF3 ARHGEF5L ARHGEF7 ARID1A ARID1B ARID2 ARID4A ARID4B ARID5B ARIH1 ARL1 ARL13B ARL15 ARL4A ARL4C ARL5A ARL6 ARL8B ARMC1 ARMC10 ARMC4 ARMC8 ARMC9 ARNT ARNTL ARNTL2 ARRB1 ARRDC1 ARRDC3 ARSK ASAP1 ASAP2 ASCC1 ASCC3 ASF1A ASH1L ASH2L ASPM ASXL1 ASXL2 ATAD1 ATAD2 ATAD2B ATAD5 ATE1 ATF1 ATF2 ATF6 ATF7IP ATG10 ATG16L1 ATG3 ATG4A ATG4C ATG5 ATG7 ATL2 ATM ATP10D ATP11A ATP11B ATP11C ATP13A3 ATP1B1 ATP1B3 ATP2A2 ATP2B1 ATP2B4 ATP2C1 ATP6AP1L ATP6V0A2 ATP6V1A ATP6V1B2 ATP6V1C1 ATP6V1H ATP7A ATP8B1 ATP8B2 ATP9A ATPBD4 ATR ATRN ATRX ATXN2 ATXN3 ATXN7 AUH AURKA AVL9 AZI2 AZIN1 B3GALNT1 B3GALT1 B3GALTL B3GNT2 B3GNT5 B4GALT4 B4GALT5 BACH1 BAG2 BAG4 BAIAP2L1 BARD1 BAT2D1 BAT2L BAZ1A BAZ1B BAZ2B BBS10 BBS2 BBS7 BBS9 BBX BCAP29 BCAR3 BCAS2 BCAS3 BCKDHB BCL2L1 BCL9 BCLAF1 BCO2 BCOR BDNF BDP1 BEND3 BEND6 BICD1 BIRC2 BIRC6 BIVM BLID BLM BLVRA BLZF1 BMI1 BMP2K BMP4 BMPR1A BMPR2 BMS1 BNIP2 BNIP3L BOD1L BPTF BRAF BRAP BRCA1 BRCA2 BRCC3 BRD7 BRE BRI3BP BRIP1 BRIX1 BRP44 BRWD1 BRWD2 BRWD3 BTAF1 BTBD10 BTBD3 BTBD7 BTBD8 BTBD9 BTF3L4 BTN3A1 BTN3A2 BTRC BUB1 BUB1B BUB3 BZW2 C10orf118 C10orf119 C10orf12 C10orf18 C10orf28 C10orf4 C10orf46 C10orf76 C11orf30 C11orf49 C11orf54 C11orf60 C11orf73 C11orf74 C12orf11 C12orf23 C12orf27 C12orf30 C12orf35 C12orf4 C12orf48 C12orf51 C13orf23 C13orf27 C13orf34 C14orf106 C14orf126 C14orf133 C14orf135 C14orf145 C15orf23 C15orf29 C15orf41 C15orf42 C15orf44 C16orf52 C16orf63 C16orf87 C17orf75 C17orf85 C17orf95 C18orf25 C18orf45 C18orf54 C18orf8 C19orf2 C19orf61 C1GALT1 C1orf103 C1orf112 C1orf135 C1orf163 C1orf198 C1orf201 C1orf25 C1orf26 C1orf27 C1orf58 C1orf71 C1orf83 C1orf9 C20orf94 C21orf63 C21orf66 C21orf82 C21orf91 C22orf30 C2CD3 C2orf29 C2orf3 C2orf34 C2orf43 C2orf56 C2orf63 C2orf65 C2orf67 C3orf17 C3orf23 C3orf26 C3orf31 C3orf33 C3orf52 C3orf59 C3orf63 C3orf64 C3orf67 C4orf21 C4orf27 C4orf29 C4orf41 C4orf43 C5orf22 C5orf25 C5orf28 C5orf30 C5orf33 C5orf34 C5orf36 C5orf37 C5orf42 C5orf43 C5orf44 C5orf51 C6orf106 C6orf115 C6orf130 C6orf145 C6orf153 C6orf162 C6orf163 C6orf167 C6orf170 C6orf182 C6orf192 C6orf211 C6orf70 C6orf72 C7orf30 C7orf44 C7orf54 C7orf60 C7orf66 C8orf37 C8orf41 C8orf83 C9orf102 C9orf21 C9orf41 C9orf72 C9orf82 C9orf85 C9orf93 CA13 CAB39 CACHD1 CACYBP CAD CADPS2 CALCOCO2 CALM2 CALU CAMK1D CAMK2D CAMK4 CAMSAP1 CAMSAP1L1 CAND1 CAP2 CAPN7 CAPRIN1 CAPRIN2 CAPS2 CAPZA2 CARS CASC4 CASC5 CASD1 CASK CASP2 CASP4 CASP6 CASP8 CASP8AP2 CASP9 CAST CATSPER3 CAV1 CBFB CBL CBLB CBWD2 CBWD5 CBX3 CBX6 CC2D2A CCAR1 CCBL2 CCDC104 CCDC109A CCDC109B CCDC111 CCDC112 CCDC12 CCDC125 CCDC126 CCDC132 CCDC138 CCDC14 CCDC146 CCDC150 CCDC18 CCDC21 CCDC25 CCDC28A CCDC29 CCDC41 CCDC46 CCDC50 CCDC52 CCDC55 CCDC58 CCDC59 CCDC6 CCDC66 CCDC68 CCDC77 CCDC82 CCDC88A CCDC91 CCDC93 CCDC99 CCNA2 CCNB1 CCNB2 CCNC CCNE2 CCNF CCNG2 CCNH CCNT2 CCNYL1 CCPG1 CCT6A CD109 CD164 CD2AP CD46 CD47 CD58 CD97 CDC123 CDC14A CDC16 CDC2 CDC20 CDC23 CDC25A CDC25B CDC25C CDC27 CDC2L5 CDC2L6 CDC40 CDC42BPA CDC42BPB CDC42SE2 CDC5L CDC6 CDC7 CDC73 CDCA2 CDCA3 CDCA7 CDCA7L CDCA8 CDCP1 CDK5RAP2 CDK6 CDK7 CDK8 CDKAL1 CDKN3 CDON CDS1 CDS2 CDYL CEBPZ CENPC1 CENPE CENPF CENPI CENPJ CENPK CENPO CENPQ CEP110 CEP120 CEP135 CEP152 CEP170 CEP192 CEP290 CEP350 CEP55 CEP57 CEP63 CEP70 CEP78 CEP97 CEPT1 CETN3 CFL2 CHAC2 CHAF1A CHAF1B CHCHD3 CHD1 CHD1L CHD2 CHD4 CHD6 CHD7 CHD8 CHD9 CHEK1 CHEK2 CHKA CHM CHML CHMP2B CHN1 CHORDC1 CHRNA5 CHUK CIRH1A CISD2 CIT CKAP2 CKAP2L CKAP5 CKLF CLASP1 CLASP2 CLCC1 CLCN3 CLCN4 CLCN5 CLDN12 CLDN4 CLDND1 CLINT1 CLIP1 CLIP2 CLIP4 CLOCK CLPB CLPX CLSPN CLTC CLUAP1 CMAS CMC1 CMTM4 CMTM7 CMTM8 CNKSR3 CNNM2 CNOT1 CNOT10 CNOT2 CNOT4 CNOT6 CNOT6L CNOT7 CNOT8 CNTLN CNTNAP3 COG2 COG3 COG5 COG6 COL12A1 COL4A3BP COMMD1 COMMD10 COMMD2 COMMD8 COPB1 COPB2 COPG2 COPS2 COPS4 COQ5 COQ7 CORIN COX10 CP110 CPD CPNE3 CPNE8 CPOX CPS1 CPSF2 CPSF3 CPSF6 CPT1A CRBN CRCP CREB1 CREB3L2 CREBBP CRIM1 CRIPT CRKRS CRLF3 CRNDE CRTC3 CRY1 CRYBG3 CRYZ CSE1L CSNK1A1 CSNK1G1 CSNK1G3 CSNK2A1 CSNK2A2 CSPP1 CSRP2BP CSTF2 CSTF3 CTBP2 CTBS CTCF CTDSPL2 CTH CTNNB1 CTNND1 CTPS CTPS2 CTR9