Supplementary Tables Table S1 Specificities and efficiency scores of sgRNAs targeting the reference gene and the CNS-specific promoters sgRNA Sequence 5‘to 3‘ PAMa Positionb MIT Guide CRISPspec Doench Potential Off -Targets Specificity Score Efficiency For Number of Mismatches Score Score (%) 0 1 2 3 RG1 GCGTTACTTC AGG -258 to -239 82 7.394 86 0 0 0 13 ACTGAAGCAG RG2 TAGAGCAGCA GGG -210 to -191 68 7.464 98 0 0 3 14 AGCTGCACAG RG3 ACTGGGGACT AGG -132 to -112 85 8.321 86 0 0 0 5 GTAGTAAGAC CNS1 AGATAATGAG TGG -69 to -82 89 8.362 63 0 0 0 4 CGAGCCGGGA CNS2 CGCAGAGCGA GGG -34 to -56 83 8.320 94 0 0 0 8 GAGACCGCAG CNS3 CGCACACACG AGG +5 to +24 83 8.030 56 0 0 1 7 CAGCCGGCAC *Protospacer Adjacent Motif; RG1-3, reference gene promoter-specific sgRNAs; CNS1-3, CNS-promoter specific sgRNAs. The MIT specificity and the Doench efficienty scores ranges from 0-100 and summarizes off-target effects into a single number; the higher the number the fewer off target effects are anticipated. The CRISPRspec score represents overall whole genome off-targeting; all scores were in the high range, indicating low off-target predictions (rth.dk/resources/crispr/crisproff); please see main text for additional references. Table S2a Effects of mismatches in sgRNAs targeting the CNS promoter on in silico off-targets sgRNA Potential Locus, Position CNS vs Scrambled* RG vs scrambled* Off-target number CNS 1 2 mismatches 0 3 mismatches 4 Intergenic MIR5095-CTCFL; chr 20:56017262(-) Not in file Not in file Intron ASAP1; chr6:131204007(+) 0.145-fold down, p=0.007 0.353-fold down, p =2.4E-11 Intergenic AK124832-CA10; chr 17:49479286(+) Not in file Not in file Intergenic AKAP7-ARG1; chr 6:131676375(+) n.s.; not in file n.s.; not in file CNS 2 2 mismatches 0 3 mismatches 8 Intergenic LYRM2-ANKRD6;chr 6:90300681(-) n.s.; n.s. n.s.; n.s. Intergenic TPCN2/BC064339.MYEOV;chr 11:68881239(-) n.s.; not in file n.s.; not in file Intron MAD1L1; chr 7:2122602(-) 0.476-fold up, p=3-19E-12 0.460-fold up, p =4.08E-11 Intergenic FBXO47-LRRC37A11P;chr17:37174551(+) Not in file; n.s. Not in file; n.s. Intron AACS;chr 12:125579071(+) n.s. n.s. Intergenic LOC100130700- Not in file Not in file RNA5SP411/FLJ26245;chr16:34778137(-) Intergenic NCOR2-SCARB1; chr 12:125090098(+) 0.387-fold up, p =1.95E- 0.419-fold up, p=1.69E-11; 10; 0.424-fold up, p=1.4E- 0.140-fold up, p =0.083 09 Intron UMODL1; chr 21:43516739(-) Not in file Not in file CNS 3 2 mismatches 1 Intergenic ZBTB18/AK310634-C1orf100; chr 1:244388184(+) n.s., not in file 0.132-fold-up, p =0.033, not in file 3 mismatches 7 Intron ACOT7;chr 1:6359884(+) 0.358-fold up, p =1.1E-09 0.246-fold up, p =8.90E-05 Intron AYA4;chr 6:133563395(-) n.s. n.s. Intergenic LANCL3-XK;chr X:37544905(+) Not in file Not in file Intron FGFR3;chr 4:1796528(+) 0.0423-fold down, p =0.01 n.s. Intergenic LOC100506207-OFCC1/MRDS1;chr 6:9399387(-) Not in file Not in file Intron BAIAP2;chr 17:79042391(+) n.s. n.s. Intron AJAP1;chr 1:4715528(-) Not in file Not in file *for intergenic regions, the first statement refers to the first gene mentioned and the second statement to the second gene mentioned; n.s., no significant change in expression. Table S2b Effects of mismatches in sgRNAs targeting the reference gene promoter on in silico off-targets sgRNA Potential Locus, Position RG vs scrambled* CNS vs scrambled* Off- target number RG 1 2 mismatches 0 3 mismatches 13 Intron MFSD10;chr 4:2933484 n.s. 0.248-fold up, p=0.0001 Intergenic PCP4-DSCAM;chr 21:41373320(+) Not in file Not in file Intergenic VPS37C-PGA3;chr 11: 609363324 n.s.; not in file n.s.; not in file Intergenic LINC00900-Mir_652;chr 11:115834494 Not in file Not in file Intergenic L37717-ZNF733P, CHR 7:62709008(-) Not in file Not in file Intergenic SEPT7P9;chr 10:38688991 Not in file Not in file Intergenic SEPT7P2;chr 7:45805745 Not in file Not in file Intergenic DL490813-ZNF479; chr. 7:57142701(-) Not in file Not in file Intergenic LOC100287834-MIR4283-1;chr 7:62955844(+) Not in file Not in file Intergenic DQ599872-AK124970;chr 1:224183241(+) Not in file Not in file Intron LOC645513;chr 4:120378771(+) Not in file Not in file Intergenic LOC100288069-LINC00115;chr 1:716961 Not in file Not in file Intergenic DQ599872-AK124970;chr 1224183241(+) Not in file Not in file Intron LOC645513;chr 4:120378771(+) Not in file Not in file Intergenic LOC100288069-LINC00115;chr 1:716961(+) Not in file Not in file Intergenic GABARAPL1-KLRD1;chr 12:10400702(-) n.s.; not in file 0.599-fold down, p= 4.6E-07; not in file RG 2 2 mismatches 3 Intergenic TNS4-CCR7;chr 17:38662563(-) Not in file Intergenic SMARCA4-LDLR;chr 19:11178504(+) n.s.; 0.219-fold up, 0.314-fold up, p =1.7E- p =0.014 09; 0.214-fold up p=0.01 Intron SCAI;chr 9:127874179(+) n.s. n.s. 3 mismatches 14 Intergenic ZCAH2-ZC3H12B;chr X:64689095(+) n.s.; n.s. n.s.; n.s. Intergenic U6atac-AK128059;chr 11:131260302(+) Not in file Not in file Intron WBSCR17;chr 7:70634123(-) Not in file Not in file Intergenic CALN-TYW1B;chr 771949606(-) Not in file; n.s. Not in file, n.s. Intron FAM185A;chr 7102447374(+) n.s. n.s. Intron TNRC6B;chr 22:40443758(-) n.s. 0.163-fold up, p=0.044 Intergenic FGFBP1-FGFBP2;chr 4:15953483(+) Not in file Not in file Intron OPCML;chr 11:132783443(+) Not in file Not in file Intergenic CYB561-ACE;chr 17:61528081 n.s.; n.s. 0.479-fold up, p =1.7E- 08; 0.3-fold up, p =0.0016 Intergenic LOC257396-FST;chr 5:52614293 Not in file Not in file Intergenic HAND1-MIR3141;chr 5:153961950(+) n.s.; not in file 0.434-fold up, p =6.6E- 10; not in file Intergenic TGFB2-LOC643723;chr 1:218917293(-) Not in file Not in file Intergenic PTPRD-JB1753000;chr 9:11502106(+) n.s.; not in file n.s.; not in file Intron LOC285501;chr 4:178904870(+) Not in file Not in file RG 3 2 mismatches 0 3 mismatches 5 Intergenic MFAP3L-BC031941;chr 4:170950596(-) n.s.; not in file n.s.; not in file Intron TNRC6B;chr 22:40529575(+) n.s. 0.163-fold up, p =0.044 Intron THSD7B;chr 2:137900825(-) Not in file Not in file Intergenic AF086294-FSTL4;chr 5:132460458(+) Not in file Not in file Intron SOX5;chr 12:23923679(+) n.s. n.s. *for intergenic regions, the first statement refers to the first gene mentioned and the second statement to the second gene mentioned; n.s., no significant change in expression. Table S3 Activation of CNS or reference PPARGC1A gene promoters and differential expression of genes encoded by mitochondria Gene Mitochondrial CNS PPARGC1A Reference PPARGC1A complex Log2-fold Change p-adj Log2-fold Change p-adj MT-ND1 I 0.330 4.14E-06 0.123 1.02E-01 MT-ND2 I 0.318 1.02E-05 -0.063 4.95E-01 MT-ND3 I 0.206 1.86E-03 -0.114 1.31E-01 MT-ND4 I 0.293 2.44E-04 0.080 4.20E-01 MT-ND4L I 0.599 3.33E-18 0.486 8.20E-12 MT-ND5 I 0.504 7.38E-10 0.230 1.11E-02 MT-ND6 I 1.192 9.89E-58 0.411 2.94E-07 MT-CYB III 0.320 3.82E-06 0.112 1.68E-01 MT-CO1 IV 0.263 1.83E-05 0.104 1.42E-01 MT-CO2 IV 0.286 7.43E-04 0.104 3.06E-01 MT-CO3 IV 0.322 5.02E-06 0.031 7.58E-01 MT-ATP6 V 0.082 2.73E-01 -0.218 2.47E-03 MT-ATP8 V -0.151 1.90E-02 -0.559 1.36E-19 Data show the differences in comparison between CNS or RG promoter activations with transfections of scrambled sgRNA. Table S4 Predicted physical protein-protein interactions and physical Local Network Clusters (STRING) Table S4a Predicted physical protein-protein interactions of proteins encoded by various genes sets Gene set1 Number of Genes Protein-Protein Interactions Average Local Clustering Coefficient (STRING) Predicted Expected P2 RGP all up 872 517 449 0.0010 0.237 CNSP all up 1792 1834 1591 1.5E-09 0.218 RGP selective up 452 138 125 0.1300 0.173 CNSP selective up 1374 963 811 1.1e-07 0.203 RGP up CNSP down 29 18 8 0.0018 0.363 RGP down CNSP up 27 11 6 0.0392 0.262 RGP up CNSP up 391 120 94 0.0064 0.199 1For gene sets refer to Figure 4a; RGP, RG promoter; CNSP, CNS promoter; selectively upregulated genes without down- or upregulation by the activation of the other promoter; RGP up CNSP up refers to genes upregulated by both RG and CNS promoters. 2 The smaller the value, the higher the probability that the proteins encoded by the respective gene set show more interactions among themselves than would be expected for a random set of proteins of similar size, drawn from the genome.