Index A ATF1, 218, 238, 240 Abd-B, see Abdominal-B ATF2, 218–219 (Abd-B/Hox9-Hox13) family ATF4, 219 Abdominal-A (Abd-A), 101, 104, 106 ATPase nucleosome remodelling Abdominal-B (Abd-B/Hox9-Hox13) family, complexes, 225 101, 104–107 Autoimmunity (role of Nuclear Abf1, 30, 41, 232, 235, 238, 240 Receptors), 142 Ace1, 41, 237 Auxin response factors (ARFs), 33, 47, 50, 52 Acetylation (of histone tails), 136, 225–227, Azfh, 112 237, 264, 269–270, 288 Activating function (AF) domains, 265 B Affymetrix microarrays, 183 Bacillus subtilis, 11, 13 Afhx, 112 Bacterial one-hybrid (B1H), 89, 157, 160, 163, AFT, 30, 39, 232 165, 169 Alfin-like, 41 BAF45A/B, 230 All-trans retinoic acid, 126, 129, 133 BAF53A/B, 230 Alpha-globin, 285 BAF57, 270 Alx, 109 BAF60A/C, 230, 270 Amoeba, 48 BAF250, 270 Androgen receptor (AR), 128, 137, 183 BarH, 103 Androstane, 126, 133 Barx, 108 Anemonia sp, 125 Basic, 26, 29–33, 39, 44–45, 77, 89, 116, ANT-C complex, 103 193–195, 223, 244 Antennapedia (antp), 96–98, 100, 102–108 Basic helix-loop-helix (bHLH), 26–27, 29–30, AP-1, 265, 270 32, 46, 48–50, 52–54, 268 AP-2/Basic helix-span-helix (bHSH), type of Basic leucine zipper (bZIP), 27, 29–33, 46–47, DNA-binding domain, 32 49–54, 268 AP2/GBD/EREBP/ERF/GCC-box binding BBR/BPC, 41, 50, 52 protein, 39 Bbx, 46 Apicomplexa, 30–31, 39, 48–49, 53 BEAF, 241 Apo-receptor, 130, 133 BEL class, 115 APSES, 30, 35, 49–50 BES1/BZR1/LAT61, 32 Arabidopsis thaliana, 48, 52, 100, 117 Beta-globin, 177, 285 ArcA, 12 Beta-scaffold, 26, 29, 44–47, 231–232, 238, Archaebacteria, 5 270–271 Argfx, 109 Bicoid (bcd), 37, 106 ARID/BRIGHT, 30, 35, 51 Bilaterian, 50–52, 54, 95 Arnt, 32, 51 Bisphenol A (BPA), 142 Arx, 109 BMI1, 239 T.R. Hughes (ed.), A Handbook of Transcription Factors, Subcellular Biochemistry 52, 297 DOI 10.1007/978-90-481-9069-0, C Springer Science+Business Media B.V. 2011 298 Index Box-A (putative TF binding site), Cholesterol, 126, 135, 139–140, 143 213–214, 217 Chromatin 53BP1, 264 chromatin context, 194 Brahma (BRM), 230 conformation capture (3C, 4C, 5C), 281 Brahma related gene 1 (BRG1), 230, 270 immunoprecipitation (ChIP), 79–80, BRG1/BRM associated factors (BAFs), 230 160–163, 169, 178–179, 181–187, 224, Brinker, 30, 36 231, 236, 239, 241–242, 280, 282, Bromodomain, 227–228, 264, 269–270 288–289 Bsx, 108 loop, 241 BTB/POZ, 77, 83–84, 87–88, 271 modifier (CM), 224–225, 228, B3/VP1/IAA/Auxin response factor (ARF), 33 230–231, 243 BX-C complex, 103 remodelers, 195, 197–198, 265 structure, 84, 162, 187, 194–197, 199, 205, C 224–228, 230, 236, 238, 241, 243–244, C2H2 zinc finger, 2, 26, 28–29, 31, 42, 46, 49, 261, 270, 279 51–52, 75–90, 215, 230, 263 Chromodomain, 238, 264 C2H2 zinc finger/beta-beta-alpha zinc Chromosomal territory, 283, 285–287, 291 finger/Krüppel, 42 Chromosome, 7, 13, 76, 84, 86, 103, 105, 110, C2HC/CCHC zinc finger, 42 128, 182–183, 185, 188, 208, 242–243, Caenorhabditis elegans, 52, 96 280–283, 286, 288–289, 291 Calcium-responsive transactivator CHX10, 109 (CREST), 230 Circadian cycle, 139 Candida glabrata, 232 9-cis retinoic acid, 127, 129 Cap maturation of mRNA, 267 CLASS genes, 103, 108, 110–112 CARM1, 270 Clock, 51, 139–141, 143 Cascades, 11–12, 17 Clr3, 238, 240 CASTing, 160 Clr4, 238, 240 Catabolite repression, 14, 16 C-Myc, 267, 270 Caudal (cad/Cdx), 107 Cnidarians (corals/sea anemones/jellyfish), 50 CBF, 46, 215 Coactivator, 132–135, 264, 270 CBF/NF-Y, 30, 40, 46 Code, recognition, 5, 89 CCAAT (TF binding site), 213–215, 217 COE/EBF, 41 Cdk9, 267 Co-factor, 79, 88–89, 112, 129, 135, 197, 285 CDP (CCAAT displacement protein), 111 Cognate Site Identifier (CSI), 165 C/EBP, 27, 32, 219, 235 Cohesin, 287–288 CEBPA, 185–186, 188 Cold shock domain (CSD), 33, 45 C/EBPβ, 270 Combinatorial (regulation), 15, 17–18, 268 Ceh-7, 100–101, 114 COMPASS (CMP) class, 111–112 Ceh-20, 113 Competition, 3, 10, 13, 157, 167–169, 177, Ceh-36, 99 193–194, 198–199, 201, 212, 219, 224 Cell cycle, yeast, 179 Competition (among TFs), 212 CENPB, 30, 36, 51 Competition assay, 167–169 CG-1/CAMTA, 33, 52 Constitutive androstane receptor (CAR), CHA1 promoter, 237 126, 137 ChIA-PET, 281–282 Context-specificity, 79, 84, 194 Chicken ovalbumin upstream promoter- Cooperativity (among TFs), 198 transcription factor (COUP-TF), Copper fist, 30, 41, 49–50 125, 127 Copy number variation (CNV), 86 Chicken β-globin locus, 241 Coregulators, 224–229, 231, 235, 242 ChIP-chip, 80, 162, 178–179, 181, Corepressor, 4, 132–134, 224, 236, 265, 184–185, 289 270–271 ChIP-seq, 80–82, 157, 160, 162–163, 165, 169, Co-repressor nuclear-receptor [CoRNR] 184–187, 280, 288 box, 132 Index 299 CpG dinucleotide, 182, 206–208 Dof, 30, 42, 47–48, 50 CpG island microarrays, 182 Domain accretion, 2 CpG islands, 182, 206–207, 212, 226 Dosage compensation, 289, 291 CREB, 32, 218–219, 231, 269 DP (dimerization partner for E2F proteins), 27, CREB binding protein (CBP), 231, 269 30, 36–37, 268 CRE (TF binding site), 3, 54, 156, 180, 217, Dprx, 109 224, 226, 233–234, 236 Drgx, 109 Cross-hybridization (on microarrays), 184 Drosophila, 46, 75, 80, 84, 96, 103–114, 117, CRP, 12–18, 21, 112 125–127, 130, 137, 140, 205–220, Cryptosporidium parvum, 49 238–239, 241, 244 CSL/LAG1/Suppressor of hairless, 33 Duplication and divergence, 2, 29, 49, 54, 109 CTCF, 80, 82, 234, 240–241 Dux, 109 CTD (RNA polymerase C-terminal Domain), 267 E Ctenophores (comb jellies), 50 E12, 32, 179, 218 Cut (gene), 102, 110–112 E2F, 27, 30, 36–37, 45, 49–51, 182–183, 220, CUT/ONECUT/CDP, 36 265–266, 268–270 CUT superclass, 110–111 E2F1, 183, 265–266, 270 CUX class, 111 E2F4, 27, 182 CxC/CRC/CPP-like, 41 E2F6, 269 CxxC, 30, 41 E75, 125–126, 129, 133, 135, 139–140 CycT1, 267 E-box (TF binding site), 219 Ecdysozoans, 137 D Ecdysteroids, 130, 134–135 DAL82, 40 Ecocyc, 11 DamID, 224, 282, 288 E. coli, 8, 10–19, 170, 194, 201, 282 DAX1, 128 EcR (Ecdysone Receptor), 130, 135 DBD database, 11 Effector domains, 4, 77, 83–84, 228, 263–265, DBD (DNA-binding domain), 1 267–272 2DBD-NR, 128 Egl–5, 104, 106 DBP/DNC, 40 EIN3/EIN3-like (EIL), 40 Dbx, 108 Electrophoresis, 156, 158, 161, 178 DCTCF, 241 Electrophoretic mobility shift assay (EMSA), DDT class, 115–116 156–160, 268, 281–282 De Bruijn sequence, 165 ELKF, 270 Defective proventriculus (dve), 99 Elongation (of transcription), 3, 261–262 Deformed (Dfd/Hox4) family, 106 Ems, 101–103, 108 Demosponges, 50–52 Emx, 101, 108 Deutrostome, 52 ENCODE, 185–187, 208, 242 Dictyostelium discoideum, 47 project, 185–186 Dimerization, 2, 29, 44, 50, 54, 84, 88, 114, Endocrine (Nuclear Receptors), 137–138, 142 130–132, 268 Endocrinology, 135, 137–138, 140–142 Dinucleotide frequencies (in promoters), Engrailed (en), 96–97, 108 206–208 Enhancer, 130, 235, 240–241, 244, 262, DIP-chip, 160 285–286 Diversifying selection, 2 Enhancer blocking, 241 Dll, 101, 103, 108 Epigenetics, 3, 243 Dlx, 108 Epitope tagging, 181 Dmbx, 109 ErbA-related (EAR), 127 DM/Doublesex, 42 Estrogen receptor (ER), 127, 129, 183, 230, DNA affinity matrix, 159 284–285 DNA microarrays, 164, 179, 183–185 Estrogen-related receptor (ERR), 127, 142 DNAse I, 177, 224, 280, 282 Esx, 109 300 Index Ets, 27, 30, 36–37, 45, 50–51, 208–209, 211, Gli family, 285 213–215, 217, 220 GLP, 269 ETS (TF binding site), 217 Glucocorticoid receptor (GR), 127, 137, 140, Eumetazoa, 50–51 142, 237, 265 Evi1, 42, 81 Grainyhead/CP2/LSF, 34 Evolution, 3, 5, 8, 16–18, 31, 47, 49–54, GRAS/Scarecrow, 40 75–90, 103, 106, 109–111, 125–130, Gsc, 109 134, 137–138, 140, 160, 185–186, 197, Gsx, 107–108 201, 212, 230 GTF2I-like, 32 Evx, 101, 103, 107 Guggulsterone, 135 Extradenticle, 113 E(z) (Enhancer of zeste) (PRC2 H component), 239 Hairy, 51 Hbp, 46 F HB-PHD / ZF-HD, 37 FAR1/FRS, 42 H/C link, 76–77 Farnesoid X receptor (FXR), 126, 130, 135, HD-ZIP classes, 115 137, 142 Heat Shock Factor (HSF), 37, 45, 49 FAX/FAD-KZNFs, 88 Helix-turn-helix, 11, 26, 29, 44–45, 97, 110, Feed Forward Loop (FFL), 16–17 116–117 FIS/Fis, 12, 14–15 Heme, 129, 135–137, 139–140 FISH (fluorescence in situ hybridization), “H” enhancer (of olfactory receptors), 286 281–282, 290 Hepatocyte nuclear factor-4 (HNF4), 125, 127, FNR, 12, 97 129, 166 Footprinting, 156–158 Hesx, 109 Forkhead (FKH)/Forkhead box (Fox), 37 Heterochromatin exclusion zones, 290 Formaldehyde-assisted isolation ofregulatory Heterokonts/stramenopiles, 49 elements (FAIRE), 224 Hexapeptide motif, 100, 103 Formaldehyde crosslinking, 177 HGRα (human Glucocorticoid Receptor Fos, 31–32, 218 alpha), 265–266, 268 FOXA1/HNF3A, 234 Hhex, 108 FOXA2, 185 Hi-C, 281–283, 290 Fractal globule, 281 High Mobility Group (HMG) proteins, 195 FRAP (fluorescence recovery after Histone acetyl transferases (HATs), 225–226 photobleaching), 225 Histone arginine methytransferases, 134, 270 Fushi tarazu (ftz), 96, 106 Histone code, 225 Histone deacetylases (HDACs), 85, 134, G 235–238, 240, 264–265, 270–271, 288 G9a, 269 Histone H1, 195, 197, 234 GAGA factor (GAF), 239 Histone methyltransferases (HMTs), 269–270 Gal4, 48, 179, 228–229, 233, 235 Histone modifications, 4–5, 195, 201, 224–225, GAL genes, 231 227–228, 231, 242, 264, 269, 280, 288 GATA, 31, 49, 125 Histone modifiers, 198, 225, 227–228, 238 GATA1, 285 Histones, 183, 194, 199, 224, 227, 234, 236, GATA4, 230 239, 264, 269 GBF zinc finger (Dicty-ostelium), 42 H3K27me, 226, 239, 241, 243, 269, 287–289 G/C content, 197 H3K27me3, see H3K27 trimethylation GCM, 43, 47 (H3K27me3) Gcn5, 228, 265 H3K27 trimethylation (H3K27me3), 226, GCR1, 40 238–239, 241, 269, 288–289 Germ cell nuclear factor (GCNF), 125, 128 H3K4me, 226, 288 Giardia lamblia, 47, 49 H3K9me, see H3K9 methylation (H3K9me) Glaucophyta (simple glaucophyte algae), 46 H3K9 methylation