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 (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 (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 , 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 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 , 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 , 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-, 267, 270 Caudal (cad/), 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 , 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 (COUP-TF), Copper fist, 30, 41, 49–50 125, 127 Copy number variation (CNV), 86 Chicken β-globin , 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 ), 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 , 183, 265–266, 270 CUX class, 111 , 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), (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 (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 (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, , 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 (FXR), 126, 130, 135, HD-ZIP classes, 115 137, 142 (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 (GCNF), 125, 128 H3K4me, 226, 288 Giardia lamblia, 47, 49 H3K9me, see H3K9 methylation (H3K9me) Glaucophyta (simple glaucophyte algae), 46 H3K9 methylation (H3K9me), 237–240 Index 301

H3K4 monomethylation, 231 Isx, 109 H4K16ac, 226, 288–290 IUPAC codes, 3, 44, 215 H4K20, 264, 270 Hlx, 103, 108 J HMG domains, 230 Jaspar (database), 82 HMG family, 285 Jun, 31 HMX, 107–108 HNF1A, 96, 99, 110, 185 K HNF4, 125, 129, 135, 137, 166, 185–186 KAP1, 85, 88–89, 238, 264, 271 HNF4A, 185–186 KilA-N, 49 HNF6, 185 Klf1, 287 HNF class, 110 , 81 H-NS, 10, 12–15 KLF (family of C2H2 zinc finger proteins), HOM-C complex, 103 80, 215 (Hox), 37, 95–96, 98–105, KNOX class, 115–116 107–117 Kozak sequence, 217 Homeodomain, 26, 29, 45–46, 48–53, 95–117, KRAB, 77, 80, 83, 85–90, 238, 264, 271 263–264 KRAB-A, 85 Homeotic, 96, 103 Krüppel (KRAB domain), 42, 85, 88, 238, 271 Homez, 112 Krüppel-type zinc fingers (KZNFs), 76–90 AT hook, 26–27, 30, 39, 50 Hopx, 109, 114 HOTAIR, 239 L Hox B gene cluster, 283 Labial (lab/Hox1) family, 105 HOX cluster, 100, 102–107, 114 LacI, 15 Hox D gene cluster, 283 Lac operon, 15 HOXD locus, 239 LBX, 108 HP1, 195, 237–240, 264, 271 LC-MS (liquid chromatography tandem mass HRE (hormone response element), 270 spectrometry), 159 HRT-like zinc finger, 43 LD class, 115 HTP sequencing, 184–185, 187 LEAFY/LFY/FLO, 38 HT-SELEX, 157, 160–162, 169–170 Leutx, 109 Hydra sp, 125 LFB1 (HNF1alpha), 99, 110 Hydrogen bonding, 175–177 Lhx families, 112 Ligand, 2, 89, 123–125, 129–143, 160–161, I 264, 268, 270 Iec1, 230 Ligand-binding domain (LBD), 2, 43, IFN-β enhanceosome, 229, 231 124–125, 129, 132–136 IHF, 12 LIM class (lin-11, Isl-1, mec-3), 112 Illegitimate recombination, 86–87 LIM domain, 112 Immunity (role of Nuclear Receptors), 135, Linker DNA, 195–196, 198 141–143 Liver receptor homolog 1 (LRH-1), 128 Initiation (of transcription), 8–9, 223–224, (LXR), 126, 130, 137, 143 228–229, 231–232, 234, 266–267 Lmx, 112 Inr binding domain (IBD), 37, 49 LOB/LBD/AS2, 43 INR element, 211 Localization factor (LF), 209–211, 215 Interferon-gamma, 286 LRP/Lrp, 12–14 Interferon regulatory factor (IRF), 37, 45 LxxLL motifs, 132, 270 IRX class, 114 Isl (Islet), 112, 183 M Isoflavones (phytoestrogens), 135 MADF, 38 Isw2, 236 MADS box / SRF, 34 ISWI (protein family), 227, 270 MafB, 239 302 Index

Major groove, 26, 45, 47, 77–78, 97, 99, 110, Myb/SANT, 38, 46, 48–49, 51, 53 130, 175–177, 217 Mycobacterium leprae, 11 Malignant brain tumor (MBT) domain, 264 MyoD, 31, 51, 218 Mass spectrometry (MS), 159 MATa1, 115 N MATalpha1, 38 NAC/NAM, 40 MATalpha2, 96–97, 115 Naegleria gruberi, 48 MBD, see MBD (methyl-CpG binding domain) NANOG, 108, 162, 186, 239 MBD1, 263–264 NCoR corepressor, 270–271 MBD2, 263–264 NCoR ( corepressor) MBD4, 263 complexes, 236 MBD (methyl-CpG binding domain), 34, Ndt80 / PhoG, 34 263–264 NDX class, 115 MBF (MCB-binding factor), 179, 181 Nerve Growth factor IB (NGFIB), 128 MeCP2, 263–264 Network: module, structure, hierarchical Mediator complex, 134, 270, 288 structure of, regulatory, 8, 16–18, 142, Megator, 289 181, 231 MEINOX domain, 116 Neuron-derived orphan receptor 1 MEIS class, 113–114 (NOR1), 128 Meisetz, 85 NFkappaB, 45, 265 Metabolic (Nuclear Receptors), 1, 12–13, NFX zinc finger / NF-X1, 43 31, 52, 123–144, 179, 181, 264, 267, NFY, 46 269–270 NiN/RWP-RK, 29, 53 Metabolites, 2, 15, 125, 137–139, 265 NK1, 103, 107–108 Metazoan, 2, 4, 26, 29–31, 45–47, 49–52, 75, NK3, 103, 107–108 79, 83–85, 89, 109, 125, 129, 137, NK4, 107–108 143, 205 Nk6, 108 Methylation (of DNA), 76, 195, 264, 280 NK cluster, 100, 103, 108 Methylation (of histone tails), 227 NKL class (of homeodomains), 103, 108 Methyltransferases (histone), 227, 269–270 Nkx2, 1, 108 Micrococcal nuclease (Mnase), 224 30-nm fiber, 195 Mineralocorticoid receptor (MR), 137 Nob-1, 104, 106 Minor groove, 26, 97, 99, 175–177 Nobox, 109, 114 MITOMI (Mechanically Induced Trapping of Noncoding RNA, 5, 180 Molecular Interactions), 157, 167 Nozzle/SPL, 29 Mix, 109 NRF1 (TF binding site), 213, 218 MKX class, 114 NR (nuclear receptor) subfamilies, 125 ModENCODE, 242 N-terminal tails (of histones), 225 MOF, 290 NuA4, 228–229 Mot1, 237 Nuclear compartments, 284 Motif, 3–4, 11, 13, 16–17, 25, 44–45, 51, Nuclear lamina, 241, 288 75–79, 84–85, 87–89, 96–97, 100, Nuclear periphery, 241, 283–284, 288, 291 102–103, 105, 108–110, 113–116, Nuclear pore complex, 53, 288–290 130–132, 165, 185, 193–194, 208, 211, Nuclear receptor, 26, 31, 43, 49, 52, 54, 215, 230–232, 237, 239, 263–264, 123–144, 235–236, 264, 267, 269–270 267–268, 270 Nuclear receptor/C4 zinc finger, 31, 43 Mox, 103, 107 Nuclear receptor classes, 131 Mox (Meox) family, 107 Nuclear receptor related 1 (NURR1), 128, Msh, 103, 107–108 136, 142 Msx, 108 Nuclear-speckle model, 284 MTERF, 43 Nucleoid, 4, 7, 9, 12, 19 Multiple sclerosis (role of Nuclear Nucleoid-associated protein (NAP), 4, 7, Receptors), 142 12–14 Index 303

Nucleoporin-associated regions (NARs), PFAM, 11, 29, 31, 83 289–290 PHD class, 37, 115–116, 264 Nucleoporins, 287, 289–291 Pho2, 101, 229 Nucleosome, 162, 177, 194–199, 201–202, , 199–201, 229 208, 212, 223–227, 230, 232–237, Pho5, 199, 200–201, 229 239–240, 270 PHO8, 229 Nucleosome breathing, 234 PHO (Pleiohomeotic), 239 Nucleosome-Depleted Region (NDR), 232 Phosphorylation (of histone tails), 13, 79, 136, Nucleosome positions, 195–197, 212, 232 225, 227, 264, 267 Nucleosome-remodelling and histone Photoreceptor cell-specific nuclear receptor deacytelase (NURD), 227, 236, 271 (PNR), 127 NUMAC (nucleosomal methylation activation) Phox, 109 complex, 230 Php-3, 104, 106 Nup153, 289–290 Ph (PRC1 component), 239, 241 NURD, see Nucleosome-remodelling and Phytophthora (water molds), 49 histone deacytelase (NURD) Phytoplankton, 48 Nurr1, 136, 142 PICh (proteomics of isolated chromatin segments), 242 O PINTOX class, 115–116 Oasis, 218 Pipsqueak (Psq), 30, 38, 239 OAZ, 79 Pitx, 109 Oct-1, 96, 110 Pknox, 113 OCT4, 45, 185, 239, 268–269 Plant homeodomain (PHD), 35, 37, 96, Odysseus (OdsH), 109 115–116, 264 Oestrogen receptor, 285, 287 PLATZ, 30, 43 Olfactory receptors, 286 PLINC class, 115–116 ONECUT class, 36, 111 Pollutants, 134 One-hybrid, 89–90, 157, 159–160, 163 Polyamides, 177 Operon, 12, 15–16, 18 Polycomb, 238–239, 241, 243–244, 269 Opisthokont, 50 Polycomb group (PcG), 238–239, 241, Orphan receptors, 126, 131, 133, 136, 138 244, 269 Otp, 109 Polycomb response elements (PREs), Otx, 99, 109 238–239, 241 Polydactyl C2H2 proteins, 83 P Poly(dA:dT) tracts, 232 , 28, 30, 34–35, 45, 234, 266–267, 287 Polyploidization, 53 P160/SRC, 265, 270 Polysome loading, 267 P300, 79, 229, 231, 265, 269–270 Positive selection, 85–87, 163 Paired box (Pax), 27, 30, 38, 50–51, 109 Post-translational modification, 136, 194 Paired (PRD) and PRD-like classes, 108–110 POU (Pit-1, Oct-1, Oct-2, and unc-86) class, Palindromic binding sequences, 29 27, 30, 36, 38, 45, 50–52, 101–102, Palindromic sequences, 176, 210, 213, 110, 114 218–219 POZ, 77, 83–84, 88, 271 ParaHox cluster, 102–103, 107–108 PRC1, 238–239, 241, 244 Paramecia/paramecium, 49, 53 PRC2, 238–239, 241, 264 Pax families, 109 PRD class, 27, 38, 50, 101–102, 108–110, 114 PBC (PBX) class, 113–114 Prdm9, 85 PBX1, 96, 101 (PXR), 126, Pcr1, 238, 240 136–137, 142 Pentapetide motif, 105 Preinitiation complex (PIC), 224, 244–245, PEPCK promoter, 235 261–262, 266–267, 272 Peroxisome proliferator-activated receptor PRE-kr, 239 (PPAR), 126, 268 PRE-NMR, 170 304 Index

PREP class, 113, 140 RNA polymerase, 3–5, 7–9, 18–19, 133, 163, PRMT1, 270 220, 229, 231, 244–245, 261, 265, 267, (pb/Hox2) family, 105 283–284, 286 (PR), 128, 137 Royal family domains, 264 Promoter RREB1, 81 architecture, 8, 206, 208, 211 RSC, 229–230, 233, 235, 237 clearance, 267 Rsc2, 237 microarrays, 179, 182, 185 Rsc3, 229–230 Prop, 109 Runt, 30, 35, 50–51 Prospero, 30, 38, 99, 102 RXR, see (RXR) Prospero/Pros/Prox, 38 PROS (prospero) class, 30, 38, 99, S 101–102, 113 Saccharomyces cerevisiae, 52, 100, 115, Protein binding microarray, 157, 160, 178–181 164–165, 169 SAGA (Spt-Ada-Gcn5 acetyltransferase), Protein microarrays, 159 228–229, 231, 265 Protists, 31, 47, 49–50, 54, 116 Salmonella, 15 Protostome, 50, 52, 100, 117, 129 SAND/KDWK, 40 Prrx, 109 Sanger sequencing, 184 Psc (PRC1 component), 239, 241 SANT domain, 27, 30, 38, 46, 48–51, 53, 227 P-TEFb (positive transcription elongation SART-1, 30–32 factor b), 267 SATB class, 111 PWMs (Position Weight Matrix), 3, SAWADEE class, 115–116 165–166, 168 SBF (SCB-binding factor), 179 SBP/SQUAMOSA, 43 SCAN, 77, 80, 83, 85, 87–88 R SCOP database, 11 Rap1, 30, 39, 50, 180, 236, 238, 240 Sebox, 109 RAR, see (RAR) Segmental duplication, 84–86 RAR-related orphan receptor (ROR), 126, 140 Selective GR agonists (SEGRAs), 142 Rax, 109 SELEX, 81–82, 89, 157, 160–162, 166, Reb1, 232, 235 169–170 Recognition code, 5, 89 SELEX-SAGE, 162 Regulatory Factor X (RFX), 27, 30, 39, 45, 165 SET, 85, 241, 271 Regulon, 10 SET 7/9 methyltransferase, 241 RegulonDB, 11–13 SETDB1, 264, 271 REIII element, 238 Shox, 109 RelA, 229, 266 SHP, 128 Rel Homology Region (RHR / RHD), 34, 45 S1FA, 30, 41 REST, 80–81 , 9–10 Retinoblastoma (Rb), 270 Sigma 70 (Plants), 39 Retinoic acid receptor (RAR), 28, 126, 129, SILAC, see Stable Isotope Labeling by Amino 133, 141–143, 235, 268, 270 acids on Cell culture (SILAC) Retinoid X Receptor (RXR), 28, 125, 127, SIR proteins, 238, 240 129–131, 137, 141, 235, 268 SIX/SO (SINE) class, 102, 112–113 Rev-erb, 135–136, 139–140 SLIDE domain, 227 Rev-erbalpha, 125–126, 140 Smad3, 28, 270 Rhodophyta (red algae), 30–31, 36 SMAD/MH1/DWA/NF-1, 43 Rhox, 109 SMRT corepressor, 270–271 Rickettsia prowazekii, 11 Sox, 26, 31, 41, 46, 50–51 RNAPII (RNA polymerase II), 133, 206, 220, SP1, 42, 82, 213–218, 266, 285 229, 231, 244–245, 262, 265, 267, 270, family, 215 283–284, 286 TF binding site, 80 Index 305

Spacer (with regard to C2H2 zinc fingers), Tpr, 289–290 76–77, 84 Tprx, 109 Stable Isotope Labeling by Amino acids on Transactivation domains (TADs), 228, Cell culture (SILAC), 159 265–267, 269, 287 STAT, 28, 30, 35, 40, 45, 54 Transcriptional repression domain (TRD), 264 Ste12, 179 Transcription Factor Binding Sites (TFBSs), (SF1), 128 197, 205–220, 262, 280, 285 Sth1, 237 Transcription factories, 194, 280, 283–285, Storekeeper (STK)/GeBP-like, 30, 33, 50, 52 287, 290 Subtelomeric antisilencing regions Trichomonas vaginalis, 49 (STARS), 240 Trihelix/GT, 33, 52 Su(Hw), 241 TrpR, 15 Sumoylation, 136, 227 Tshz, 112 of histone tails, 227 Tudor domain, 264 Supershift, 158–159 Tup1-Cyc8, 236 Surface plasmon resonance (SPR), 157, 167 Twist, 26, 40, 51 Swh3, 237 Two-component signalling, 12 Swi2/Snf2 chromatin remodelers, 228 Swi6, 238, 240 SWI/SNF, 227, 230, 234, 236–237, 265, 270 U Ubiquitination (of histone tails), 227, 238 Uncx, 109 T TAF1, 269 USF1, 241 TAFIIs, 265 USF2, 241 Tailless (TLX), 101–103, 107–108, 127 USP, 129, 135 TALE superclass, 113–114 Tamoxifen, 135, 141 V TATA-binding protein (TBP), 28, 30, 35, 217, Van der Waal interactions, 177 237, 262, 265–266 Vax, 101, 108 TATA element, 218 Ventx, 108 T-box, 28, 30, 35, 50, 52 VHR1, 30, 39 TBP-associated factors (TAFs), 266 Viridiplantae (green plants), 30–31, 46–47 TBP-associated proteins, 265 (VDR), 126, 135, 141–143, TBP, see TATA-binding protein (TBP) 230, 270 TBX5, 230 VOZ, 44, 50, 52 TCP, 30, 33 VP1, 33, 47, 287 TEA/ATTS/TEF, 39 VP16, 287 (TR), 127 Vsx, 109 Tether, 77, 84–85, 131 TFIIA, 244, 266 W TFIIB, 244, 266 WD40 repeat domain, 264 TFIID (TAFII 130), 244, 266 Whirly/PBF2, 35 TFIIH, 244, 266 WINAC complexes, 270 TGIF class, 114 Thalassiosira pseudonana, 48 WOX class, 115–116 THAP finger, 30, 43 WRKY, 26, 30, 42–44, 47–51, 53 Thyroid (TR), 126, 268, 270 Tiling microarrays, 182–183 X Tinman, 107–108 X chromosome inactivation, 208, 243, 291 TLX, see Tailless (TLX) Xenobiotics (Nuclear Receptors), 2, 26, 31, 52, TN motif, 102–103, 108 123–144, 264, 267, 269–270 Topoisomerase IIA, 47 Xist, 286, 291 Toxoplasma, 49 Xlox (Pdx), 101, 107 306 Index

Y Zeb, 112 Yamanaka factors, 45 Zerknüllt (zen/Hox3) family, 105–106 Yeast (Saccharomyces cerevisiae), 26, 31, 48, Zeste, 239 52, 76, 79, 96, 100, 114–115, 125, ZF class, 102, 112 165, 178–182, 195–197, 199, 201–202, Zfp423, 82 212, 215, 224, 226, 228–230, 232–233, Zfx, 82 235–238, 240, 285–286, 288–289, 291 Zhx, 112 YY1 (TF binding site), 79, 81, 214, 217, 239 Zinc cluster/C6 zinc finger, 26, 28, 30–31, 41, 44, 48, 50, 125 Z Zinc-coordinating, 26, 29, 31, 44, 47–48 ZAC, 79 Znf143, 82 ZAD, 77, 83–85, 88–89 ZNF263, 80 ZAP1, 44, 79 ZNF276, 84 ZBED6, 159 ZW5, 241