Supplementary Figure legends Figure S1. The molecular weight of proteins encoded by genes in each sub-region of Chr.20 Figure S2. The hydrophobicity of proteins encoded by genes in each sub-region of Chr.20 Figure S3. The sequence alignment of defensin protein family using CLUSTAL 2.1 Figure S4. The substitution types of nucleic acids at mutation sites Figure S5. The MS/MS spectra of all the identified mutated peptides Figure S6. The MRM signals of validated mutated peptides Supplementary Tables Table S1. The liver cancer related variations. Table S2. The expression signals of defensin genes on Chr.20 Table S3. The differentially expressed Chr.20 genes at mrna, RNC-mRNA and protein Table S4. The mutated Chr.20 genes in three liver cancer cell lines identified at mrna and RNC-mRNA
Figure S1
Figure S2
chr4_sp P59861 DB131_HUMAN chr20_sp Q5J5C9 DB121_HUMAN chr20_sp Q8N688 DB123_HUMAN chr20_sp Q96PH6 DB118_HUMAN chr20_sp Q7Z7B7 DB132_HUMAN chr6_sp Q30KQ1 DB133_HUMAN chr8_sp Q8NG35 D105A_HUMAN chr8_sp Q8N104 D106A_HUMAN chr8_sp Q30KP9 DB135_HUMAN chr20_sp Q8NES8 DB124_HUMAN chr20_sp Q9H1M4 DB127_HUMAN chr20_sp Q7Z7B8 DB128_HUMAN chr8_sp Q8WTQ1 D104A_HUMAN chr11_sp Q8NET1 D108B_HUMAN chr8_sp P81534 D103A_HUMAN chr8_sp O15263 DFB4A_HUMAN chr8_sp P60022 DEFB1_HUMAN chr20_sp Q9H1M3 DB129_HUMAN chr8_sp Q8IZN7 D107A_HUMAN chr20_sp Q9BYW3 DB126_HUMAN chr8_sp Q4QY38 DB134_HUMAN chr20_sp Q8N690 DB119_HUMAN chr20_sp Q8N687 DB125_HUMAN chr6_sp Q30KQ6 DB114_HUMAN chr6_sp Q30KQ9 DB110_HUMAN chr6_sp Q30KQ8 DB112_HUMAN chr8_sp Q30KQ2 DB130_HUMAN chr20_sp Q30KQ4 DB116_HUMAN chr20_sp Q30KQ5 DB115_HUMAN chr8_sp Q30KP8 DB136_HUMAN chr6_sp Q30KQ7 DB113_HUMAN Figure S3 * * * * ------------MRVLFFVFGVLSLMFT---VPPAR-SFISNDE------------CPS-EY-YHCRL-KCNADEHAI----RYC--ADFSICCKL-------KIIEIDGQKKW-----------------------------------------------MKLLLLLLTVTLLLAQ---VTP-------VMK------------CWG-KS-GRCRT-TCKESEVYY----ILC--KTEAKCCVD-------PKYVPVKPKLTDTNTSLESTSAV-----------------------------------MKLLLLTLTVLLLLSQ---LTPG-----GTQR------------CWN-LY-GKCRY-RCSKKERVY----VYC--INNKMCCVK-------PKYQP-KERWWPF---------------------------------------------MKLLLLALPMLVLLPQ---VIPAY---SGEKK------------CWN-RS-GHCRK-QCKDGEAVK----DTC--KNLRACCIP-------SNEDHRRVPATSPTPLSDSTPGIIDDILTVRFTTDYFEVSSKKDMVE ------------MKFLLLVLAALGFLTQ---VIPAS---AGGSK------------CVS-NTPGYCRT-CCHWGETAL----FMC--NASRKCCIS-------YSFLP-KPDLPQLIGNHWQSRRRNTQRKDKKQQTTVTS--------------------MKIHVFLFVLFFFLVP---IATRVKCAVKDTY-----------SCFI-MR-GKCRH-ECHDFEKPI----GFCT-KLNANCYM--------------------------------------------------------------MALIRKTFYFLFAMFFILVQ---LPSGCQAGLDFSQPFPSGEFAVCESCKL-GR-GKCRK-ECLENEKPD----GNC--RLNFLCCRQ-------RI--------------------------------------------------------MRTFLFLFAVLFFLTP---AKN---AFF-DEK------------CNK-LK-GTCKN-NCGKNEELI----ALC--QKSLKCCRT-------IQPCGSIID-----------------------------------------------MATRSVLLALVVLNLLFY---VPPG------RSGP-NVYIQKIFASCWR--LQGTCRP-KCLKNEQYR----ILC--DTIHLCCVN-------PKYLPILTGK------------------------------------------------MTQLLLFLVALLVLGH---VPSG------RSE---------FKRCWK--GQGACQT-YCTRQETYM----HLC--PDASLCCLS-------YALKPPPVPKHEYE-----------------------------------------------MGLFMIIAILLFQ---KPTV------TEQ---------LKKCWNNYVQGHCRK-ICRVNEVPE----ALC--ENGRYCCLNIKELEACKKITKPPRPKPATLALTLQDYVTIIENFPSLKTQST-------------------------MKLFLVLIILLFE---VLTD------GAR---------LKKCFN-KVTGYCRK-KCKVGERYE----IGC--LSGKLCCANDEEEKKHVSFKKPHQHSGEKLS-VLQDYIIL----PTITIFTV----------------------MQRLVLLLAISLLLYQ---DLPVR----SEFEL--------DRICGY--GTARCRK-KCRSQEYRI----GRC--PNTYACCLR-------KWDESLLNRTKP----------------------------------------------MRIAVLLFAIFFFMSQ---VLPAR----GKFK----------EICER--PNGSCRD-FCLETEIHV----GRC--LNSQPCCLP-------LGHQPRIESTTPKKD-------------------------------------------MRIHYLLFALLFLFLV---PVPG----HGGIIN-----TLQKYYCRV--RGGRCAVLSCLPKEEQI----GKCS-TRGRKCCRRKK---------------------------------------------------------------MRVLYLLFSFLFIFLM---PLPGV---FGGIGD-----PVT---CLK--SGAICHPVFCPRRYKQI----GTCG-LPGTKCCKKP----------------------------------------------------------------MRTSYLLLFTLCLLLS---EMASGGNFLTGLGH-----RSDHYNCVS--SGGQCLYSACPIFTKIQ----GTCY-RGKAKCCK------------------------------------------------------------------MKLLFPIFASLMLQYQ---VNTEF---IGLRR------------CLM--GLGRCRD-HCNVDEKEI----QKC---KMKKCCVGPKVVKLIKNYLQYGTPNVLNEDVQEMLKPAKNSSAVIQRKHILSVLPQIKSTSF --------MPGAMKIFVFILAALILLAQ---IFQAR---TAIHR-----------ALISKRMEGHCEA-ECLTFEVKI----GGCRAELAPFCCKN-------RKKH------------------------------------------------------MKSLLFTLAVFMLLAQ---LVSGN---WYVKK------------CLN--DVGICKK-KCKPEEMHVKNGWAMC--GKQRDCCVPADRRANYPVFCVQTKTTRISTVTATTATTTLMMTTASMSSMAPTPVSPTG---------------MKPLLVVFVFLFLWDP---VLAGINSLSSEMHK----------KCYK---NGICRL-ECYESEMLV----AYC--MFQLECCVK-------GNPAP-----------------------------------------------------MKLLYLFLAILLAIEEP--VISGK---RHILR------------CMG--NSGICRA-SCKKNEQPY----LYC--RNCQSCCLQ-------SYMRISISGKEENTDWSYEKQWPRLP--------------------------------MNILMLTFIICGLLTR---VTKGS---FEPQK------------CWK-NNVGHCRR-RCLDTERYI----LLC--RNKLSCCISIISHEYTRRPAFPVIHLEDITLDYSDVDSFTGSPVSMLNDLITFDTTKFGETMT ------------MRIFYYLHFLCYVTFI----LPATCTLVNADR------------CTK--RYGRCKR-DCLESEKQI----DICS-LPRKICCTE-------KLYEEDDMF-------------------------------------------------MKIQLFFFILHFWVTIL--PAKKKYPEYGSLDLR--------RECRI--GNGQCKN-QCHENEIRI----AYCI-RPGTHCCLQQ-----------------------------------------------------MKLLTTICRLKLEKMYSKTNTSSTIFEK--ARHGTEKISTARSEGHHITFSRWKSCTA--IGGRCKN-QCDDSEFRI----SYCA-RPTTHCCVTECDPTDPNNWIPKDSVGTQEWYPKDSRH-------------------------------------MKLHSLISVLLLFVTL---IPKGKTGVIPGQKQ-----------CIA--LKGVCRDKLCSTLDDTI----GIC--NEGKKCCRR------WWILEPYPTPVPKGKSP---------------------------------------MSVMKPCLMTIAILMILAQK--TPGGLFRSHNGKSR------EPWNPCEL--YQGMCRN-ACREYEIQY----LTC--PNDQKCCLKLSVKITSSKNVKEDYDSNSNLSVTNSSSYSHI---------------------MLPDHFSPLSGDIKLSVLALVVLVVLAQT--APDG-----WIRR------------CYY--GTGRCRK-SCKEIERKK----EKC--GEKHICCVPKE-----KDKLSHIHDQKETSELYI----------------------------------------MNLCLSALLFFLVILLP--SGKGMFGNDGVKVR----------TCTS--QKAVCFF-GCPPGYRWI----AFC--HNILSCCKN------MTRFQPPQAKDPWVH--------------------------------------------MKILCIFLTFVFTVSCGPSVPQKKTREVAERKR----------ECQL--VRGACKP-ECNSWEYVY----YYC---NVNPCCAV-------WEYQKPIINKITSKLHQK----------------------------1...10...20...30...40...50...60...70...80...90...100...110...120...130...140...150 70 76 67 104 95 61 78 65 77 71 99 93 72 73 67 64 68 110 70 111 66 84 112 69 67 113 79 102 88 78 82
Figure S4 45 40 35 30 25 20 15 10 5 0 765 40 36 37 32 30 29 21 14 15 14 3 0 0 7 45 5 3 4 1 10 10 18 16 14 9 10 7 8 89 7 6 7 4 3 2 2 2 1 0 8 6 6 A->C A->G A->T C->A C->G C->T G->A G->C G->T T->A T->C T->G RNA RNC common Pro 2
Theoretical mass (M+H): 1378.7689 Experimental mass: 689.888 (2+) Theoretical mass (M+H): 2712.3032 Experimental mass: 923.779 (3+) Theoretical mass (M+H): 2073.0822 Experimental mass: 1037.044 (2+) Theoretical mass (M+H): 2317.0852 Experimental mass: 792.0400 (3+) Theoretical mass (M+H): 1783.9775 Experimental mass: 921.0031 (2+)
Theoretical mass (M+H): 982.4727 Experimental mass: 491.7400 (2+) Theoretical mass (M+H): 2170.0862 Experimental mass: 743.0407 (3+) Theoretical mass (M+H): 1850.9144 Experimental mass: 925.9608 (2+) Theoretical mass (M+H): 2343.0809 Experimental mass: 800.7056 (3+) Theoretical mass (M+H): 1801.8497 Experimental mass: 620.2953 (3+)
Theoretical mass(m+h):1399.6812 Experimental mass: 700.3442 (2+) Theoretical mass(m+h):1515.7285 Experimental mass: 758.3679 (2+) Theoretical mass(m+h): 897.5152 Experimental mass: 449.2613 (2+) Theoretical mass(m+h): 2023.1222 Experimental mass: 1012.0648 (2+) Theoretical mass(m+h): 1680.7235 Experimental mass: 840.8654 (2+)
Theoretical mass(m+h):1328.7056 Experimental mass: 664.8564 (2+) Theoretical mass(m+h):2382.1380 Experimental mass: 1220.0834 (2+) Theoretical mass(m+h): 3354.5670 Experimental mass: 867.9079 (4+) Theoretical mass(m+h): 1781.9432 Experimental mass: 891.4753 (2+) Theoretical mass(m+h): 1119.5945 Experimental mass: 560.3009 (2+)
Theoretical mass: 2390.2609 Experimental m/z: 868.466 (3+)
Figure S6 Hep3B MHCC97H HCCLM3 Hep3B MHCC97H HCCLM3 PYGB_LKQEYFVVASTLQDIIRR (Mut.) SEC23B_GAIQFVTHYQQSSTQR (Mut.) PYGB_LKQEYFVVAATLQDIIRR (WT) SEC23B_GAIQFVTHYQHSSTQR (WT) RRBP1_LTAEFEEAQTSACLLQEELEK (Mut.) RRBP1_LTAEFEEAQTSACR (WT) LAMA5_ALFSQISSAVSLR (F>S)