1 Supplementary Figure 1 2 3 Promoter analysis for the putative BRCA1 target genes. (A) A graph for luciferase reporter assay of 4 the CKS1B and MEIS2 promoter plasmids, in combination with wild type BRCA1 (wtBRCA1) or non- 5 functional mutant (C61G). (B) ChIP results for CKS1B and MEIS2 promoter with two different BRCA1 6 antibodies and HDAC2. IgG and Input was used as a negative or positive control, respectively. 7 8 9 Supplementary Table 1. The BRCA1 ChIP signal from ENCODE database and BRCA1 dependent expression change from two GEO datasets GSE22259 GSE30822 Gene Name ENCODE data (BRCA1 CHIP seq) Expression Expression data data ANPEP unnamed (-79179) #N/A 0.140046483 CENPE unnamed (-76) 0.463340941 0.155474015 ID1 unnamed (-32379), unnamed (+7707) 1.020982905 0.214958903 PNN unnamed (+161) 0.772059373 0.215856379 SUSD2 unnamed (-24295) #N/A 0.230809307 LEMD1 unnamed (-63610) #N/A 0.254516474 DLGAP5 unnamed (-79580) 0.914187251 0.281355563 DARS2 unnamed (-11) 0.9045215 0.289088038 SMC3 unnamed (-361) 1.021103204 0.309860113 TNNI3 unnamed (-3119) #N/A 0.318065991 FUT8 unnamed (+1870) 0.992421144 0.322867733 MOB1B unnamed (-154) #N/A 0.328830217 HMGCS1 unnamed (-283) 1.677479154 0.338263784 CTH unnamed (-163) 1.30602241 0.341207388 SEPT10 unnamed (+15) 1.04077455 0.345515568 SLC45A3 unnamed (-68696), unnamed (+49304) #N/A 0.346195509 TAF1B unnamed (-73) 0.797296768 0.348470135 OXCT1 unnamed (-33516) 0.996978985 0.353844424 KIF15 unnamed (+76) 0.678047851 0.356200772 FBP1 unnamed (-87049) #N/A 0.36391027 C4orf21 unnamed (-234) #N/A 0.367754534 HMGB2 unnamed (-1054) 1.137292779 0.368187682 PTGR2 unnamed (+147) #N/A 0.375853006 IDI1 unnamed (-58) 0.760898277 0.376427911 NSRP1 unnamed (-20) #N/A 0.378117286 FER unnamed (+1060) 0.8294352 0.37987163 KIF18A unnamed (-2078) 0.858023151 0.381624982 PHF3 unnamed (-73235) 0.589242724 0.385235959 CORO6 unnamed (-140127) #N/A 0.394731959 TTC18 unnamed (-3) #N/A 0.397570018 STAG1 unnamed (-149) 0.820095844 0.400692437 CUL4B unnamed (+14495) 0.826892 0.401545178 SFR1 unnamed (+109822) #N/A 0.404459958 CWC27 unnamed (+80) 0.91259454 0.405328964 FYTTD1 unnamed (-8) 0.566419036 0.410533966 FADS1 unnamed (+84) 1.113099392 0.410780339 CELSR3 unnamed (+8998) #N/A 0.413508261 MRPS18B unnamed (-1491) 0.859723503 0.415137504 AHSA2 unnamed (-352) 0.326957844 0.418477842 CREBZF unnamed (-28) 0.793315308 0.421151257 AGBL2 unnamed (-51902) #N/A 0.423998893 PCM1 unnamed (-54) 0.693233394 0.427891438 IER2 unnamed (+4941) 1.32968529 0.429742875 LGALS3 unnamed (-77469) 1.073609087 0.431220222 GJC1 unnamed (+55821) 0.765822073 0.431282472 PJA2 unnamed (+661092) 1.004277127 0.433109387 SMARCAD1 unnamed (+96) 0.830872651 0.433959047 STX16 unnamed (-124) 0.783611628 0.437318659 EIF5B unnamed (-959) 0.546961619 0.44208339 SPOCD1 unnamed (+26565) #N/A 0.44294245 ZBTB25 unnamed (-1052), unnamed (-23) 0.963847438 0.445669273 TMF1 unnamed (+2) 1.403000802 0.449739795 DARS unnamed (-101) 0.996569457 0.451375361 MYSM1 unnamed (+137) 1.338821339 0.455914991 TUBA1B unnamed (+1070) 1.035181245 0.456099714 EFHA1 unnamed (+123) 1.014915078 0.457187082 GNE unnamed (+18507) 1.178785378 0.460751632 MRPS9 unnamed (+295) 0.957214321 0.46081088 YIPF3 unnamed (-39) 0.974015333 0.462831691 CFL2 unnamed (-158742) 1.071882131 0.465198096 TBC1D5 unnamed (-102) 0.63021023 0.465575013 WNT7A unnamed (+229497) #N/A 0.467512187 RANBP2 unnamed (-49), unnamed (+67189) 0.985749145 0.468284624 NEMF unnamed (-10152) #N/A 0.470033855 SMARCAL1 unnamed (-243) 1.258806314 0.470929141 DNTTIP2 unnamed (-30) 0.950002933 0.474349306 RBBP8 unnamed (+62) 1.258783826 0.474576323 TTC32 unnamed (+153) 0.83599461 0.4756728 MTHFD1 unnamed (-108) 0.992885456 0.478477648 DALRD3 unnamed (-3517), unnamed (-2835) 0.780682291 0.479377527 MYL12A unnamed (+96) 0.715193136 0.482497558 DDX27 unnamed (+66) 1.066801662 0.482638644 WRN unnamed (+453) #N/A 0.482865316 FZD2 unnamed (+132439) 1.463979329 0.483434728 PIBF1 unnamed (-206) 0.837491244 0.483440865 MYL12B unnamed (-82) 1.158012413 0.485099694 RPL26 unnamed (+199) 0.942067041 0.488757831 C8orf45 unnamed (+54811) #N/A 0.489973284 ABHD15 unnamed (-1837) 1.35646249 0.490135984 PTCD2 unnamed (-103) 0.784423362 0.491987581 PIK3C2A unnamed (-38084) 0.866073062 0.492322837 IFT74 unnamed (+22) 0.980687007 0.493561426 ZNF33B unnamed (-125) 0.504812323 0.493840564 FKBP3 unnamed (+279) 0.928847661 0.494618435 USO1 unnamed (-431) 1.10033935 0.49992946 SREK1 unnamed (+180) 0.814338842 0.499997287 WDR6 unnamed (+136) 1.030953641 0.50139691 DZIP3 unnamed (+252) #N/A 0.501446168 TRMT61B unnamed (-17) 1.202193217 0.502075521 SIRT1 unnamed (-35136), unnamed (-182) 1.345268044 0.502874307 NCOR2 unnamed (-199732) 1.452910334 0.502914155 DHX29 unnamed (-336) 0.88383919 0.504268385 XPO1 unnamed (-108) 0.876640976 0.504425492 RPS6 unnamed (-13) 0.836769321 0.506523013 FANCM unnamed (-1406) #N/A 0.507235835 SKIV2L2 unnamed (+281) 0.82493928 0.507854399 MATR3 unnamed (-4) 0.648285837 0.50811514 MTIF2 unnamed (+151) 1.088390892 0.508573501 CCP110 unnamed (-1795) #N/A 0.508672443 FAM174B unnamed (-153470) #N/A 0.508703969 FYCO1 unnamed (-89) #N/A 0.508784893 ARL6IP6 unnamed (-370), unnamed (+611) 0.982441245 0.509097408 KIAA0196 unnamed (+10) 0.862717371 0.509895147 TMEM41B unnamed (-137) 1.126248035 0.510039241 CCDC99 unnamed (+231) 1.116666597 0.51345111 METTL4 unnamed (+108) 1.099489708 0.513785132 RPGRIP1L unnamed (-230) 0.829525311 0.516450805 MKRN2 unnamed (-125) 0.800701455 0.516583401 GCC2 unnamed (+17) 1.019550709 0.517152323 RAB42 unnamed (-10554) 1.34291915 0.518066868 CTR9 unnamed (-104) 0.954013154 0.518450282 DDIT4 unnamed (+61) 0.673959548 0.519209825 IPO11 unnamed (-6228) 0.823808048 0.519552137 TLE2 unnamed (-6539) 0.667176356 0.52176234 DBN1 unnamed (+19014) 0.939822984 0.522444304 NUF2 unnamed (-383) 0.772921169 0.523014843 TLCD2 unnamed (-6054) 0.657502608 0.523092656 ZDHHC3 unnamed (-68) 0.809660159 0.523816835 ARHGEF40 unnamed (+22309) #N/A 0.524061266 CALM2 unnamed (-118) 0.992701546 0.524316755 COPS2 unnamed (-105) 0.593330326 0.524386166 SENP7 unnamed (-236) #N/A 0.524436259 EIF1B unnamed (-150) 0.805460345 0.524645688 KNTC1 unnamed (-477) 0.776829935 0.527817073 TAF1D unnamed (+432) 0.897045176 0.528445346 COASY unnamed (-12) 0.865192992 0.529293947 CDNF unnamed (-204) #N/A 0.529850135 ZZZ3 unnamed (-834), unnamed (+85) 0.852681176 0.530594634 CBR4 unnamed (+302) 0.884638731 0.532001901 RAB5A unnamed (-287) 0.98126523 0.533440677 LIG4 unnamed (-2933) 0.997700723 0.533897573 DFNB59 unnamed (+194) #N/A 0.534070662 CETN3 unnamed (+63) 0.977189771 0.534319884 ZBTB11 unnamed (-200) 0.870179964 0.534561207 GIN1 unnamed (+89) 0.711356152 0.534617816 ATG16L2 unnamed (+189) #N/A 0.534757444 TGDS unnamed (+151), unnamed (+46416) 1.225683706 0.534941987 MRPS31 unnamed (-47) 1.083926731 0.535181668 PRPF40A unnamed (-1043), unnamed (-62) 0.957916058 0.537013979 PPIG unnamed (+40) 0.966641871 0.537016537 RBBP7 unnamed (-960) 1.088827692 0.537933296 USP8 unnamed (-31) 0.419457672 0.539868384 DUSP13 unnamed (-2151) #N/A 0.54056628 KIF18B unnamed (-202) 1.259865988 0.541004972 C15orf23 unnamed (+161) 0.777861394 0.542959881 NCAPG unnamed (+1) 0.787987203 0.543743932 PIM1 unnamed (-445) 1.359836913 0.544021585 THAP9 unnamed (+45) 1.535761887 0.545715611 RPL14 unnamed (-4366), unnamed (-57) 0.617296484 0.546698833 THUMPD3 unnamed (+113), unnamed (+33517) 0.976501203 0.546705312 TMEM55A unnamed (-29186) #N/A 0.547022319 SRSF2 unnamed (-145) 0.76059065 0.547461291 EIF3A unnamed (+708) 0.85585189 0.550391746 APPL1 unnamed (-149) 0.727878269 0.550765559 KBTBD6 unnamed (-144) 1.010497121 0.552237117 CCNH unnamed (+295) 0.853542732 0.552630847 NKRF unnamed (-578) 0.861622649 0.552718387 HEXIM1 unnamed (+987) 1.043847281 0.553962082 OXNAD1 unnamed (-218) 1.323607751 0.554477506 ENOPH1 unnamed (-979), unnamed (-97) 0.903774006 0.555059749 HELLS unnamed (-327) 0.572755837 0.556497987 PLCD3 unnamed (-663) #N/A 0.55655551 ZMYM1 unnamed (+75) 0.839394238 0.558220882 DDX5 unnamed (-498) 0.976638597 0.559204873 ZNF518A unnamed (+228) 1.324832806 0.559989713 RRAGA unnamed (-103) 1.094485198 0.560586474 MRPS25 unnamed (-24) 0.634050069 0.561591513 C1D unnamed (-1) 0.792077747 0.561828919 TTC7B unnamed (+57801) #N/A 0.563396662 ZC3H15 unnamed (-216) 1.03897568 0.563441268 GPBP1 unnamed (-39982) 0.738343719 0.56373824 MAK16 unnamed (-21) 0.903259655 0.565240025 C3orf23 unnamed (+137) 0.828773823 0.566276787 MNS1 unnamed (+99762) #N/A 0.566494584 FAM110A unnamed (+61) #N/A 0.570633266 CCNJ unnamed (-13) 1.230814738 0.570978648 CNOT7 unnamed (+1) 0.797735205 0.57499947 OAZ1 unnamed (+4281) 1.29717828 0.575054782 DLG1 unnamed (-211723) 0.670474221 0.575687737 RPL23A unnamed (+124) 0.973659717 0.577102396 NKAP unnamed (+43) 0.526640578 0.577392153 CCDC88A unnamed (-43) 0.433928126 0.57853153 COX15 unnamed (+501) 1.448195544 0.57918922 GTPBP2 unnamed (-604) 1.312319649 0.580047729 RPL36AL unnamed (-95) 0.983460761 0.581601462 DHX36 unnamed (+75) 0.805997171 0.581972825 PNPLA2 unnamed (+783) #N/A 0.582135848 KDM1A unnamed (-124) 0.988486644 0.582883237 H2AFX unnamed (-101) 1.009357569 0.583110866 DNAAF2 unnamed (+789), unnamed (+1617) #N/A 0.583373584 DNAJC28 unnamed (+11275) #N/A 0.586136243 CD2AP unnamed (-56) 0.955885708 0.586969339 NDUFAF3 unnamed (-222), unnamed (+460) 0.582777657 0.587688474 PARP2 unnamed (-34) 0.663952077 0.589039911 FANCD2 unnamed (-24) 0.705909016 0.589303745 SMC1B unnamed (+40) #N/A 0.589367358 CCNE1 unnamed (+33391) 0.829094241 0.590069121 BAZ1A unnamed (+2082) 1.096976654 0.590344082 TSC22D2 unnamed (-909) 0.928908126