Subject Index

α-Actinin, 32–33Actinomycin D (Act D), 94Action potential-generated signals,

to nucleus, 102gene transcription, effects on, 104–105transcription factors (TFs), effects on,

103–104Activating transcription factor 4 (ATF4), 177Activator protein-1 (AP-1) family, 19, 188

as prototypical transcription factor, byneuronal activity, 277–279

TIMP-1 and MMP-9 as, 279–288Activity-dependent gene transcription

functional outcome of, 302–307input-output function of neuron and, 307singing behavior, gene regulation by, 14–15song auditory stimulation, gene regulation

by, 6–9auditory activation and gene expression

uncoupling, 14context dependence, 11experience dependence, 12–13stimulus dependence, 9–11

see also SongbirdsActivity dependent survival and death, MEF2

and, 236–240Activity-regulated cytoskeletal-associated

protein (Arc)cellular functions of, 404–405cloning and early characterization of,

399–400dendritic targeting of, 400–402expression, 405–408IEG mRNAs in neurons, FISH method and,

408–410MEK 1/2 and, 16neural plasticity and memory consolidation,

402–404transcription activation in hippocampal

neurons, 410–412

Adenylyl cyclases (AC), 131Adrenocorticotrophin hormone (ACTH), 359Age-associated memory impairment

(AAMI), 143AIDA-1, nucleolus and, 38–40Albumin D-site-binding protein (DBP), 318Alternative splicing, synapse-to-nucleus

signaling and, 35–36Alzheimer’s disease, 144, 262, 3445-Aminolevulinate synthase, 218amnesiac (amn), pituitary adenylyl cyclase

activating peptide (PACAP) mutant, 255Amnesia resistant memory (ARM), 255–256AMPA receptors, 278, 404–405AMP-dependent protein kinase, 240Amyloid precursor protein (APP), 34, 262Anatomical mapping, of learning and memory

centers, 255Anterior forebrain pathway, of song control

system, 4ApCREB-1 in, Aplysia sensory neurons,

136–137Aplysia, 140, 298

CRE-driven genes, 134–135LTP in, 96sensory neurons

ApCREB-1 in, 136–137, 179long-term facilitation (LTF) in, 135, 381

ApoER, reelin receptor, 36appl gene, 267Arc/Arg3.1, 93, 399arc gene, 7–9, 15, 18, 102–105Armadillo repeat protein deleted in

velo-cardio-facial syndrome (ARVCF),30, 32

Ataxia-telangiectasia-mutated (ATM) proteinkinase, 378

ATF/CREB family, of transcription factors,127–128

atf-1 gene, 128

417

418 Subject Index

Auditory activation and gene expressionuncoupling, 14

Auditory neurons, song-induced geneexpression regulation in, 15–17

Auditory pathway, in songbirds, 4–5Axin/GSK3b/APC degradation pathway, 30

Basic helix-loop-helix (bHLH)-PAStranscription factors, 314

Basic region/leucine zipper (bZIP) family,127–128, 178, 188, 256, 378

Basolateral complex of amygdala (BLA), 403Bdnf gene, 20, 155, 165

activity-dependent histone modifications at,165–166

functional organization of, 156alternative promoters, 157–158transcription start sites, 158–161transcript splicing and polyad-

enylation, 161IV/VI, 163–164

BDNF-GFP fluorescence spots, 339Bdnf mRNA, neuronal activity-dependent

expression, 156BDNF val66met polymorphism, 343Birdsong, activity-dependent transcription

singing behavior, gene regulation by, 14–15song auditory stimulation, gene regulation

by, 6–9auditory activation and gene expression

uncoupling, 14context dependence, 11experience dependence, 12–13stimulus dependence, 9–11

see also SongbirdsBlood oxygenation level-dependent functional

magnetic resonance imaging (BOLDfMRI), 342

BMP signaling, Drosophila, 260Brain, connection of gut with, 354–356Brain, CREB and

learning and memory, 141–143neurodegenerative diseases, 144–145synaptic plasticity pathologies, 143–144

Brain derived neurotrophic factor (BDNF),81, 131, 140, 191, 194–196, 337, 402

genetically driven variation in, learning andmemory and, 343

synaptic plasticity, gut feelings and,347–349

connection of gut with brain and, 354–356energy expenditure, metabolism, and,

353–354energy metabolism, 350–352

from hypothalamus to hippocampus,352–353

transcription, activity-dependent regulationof, 155

Bdnf gene, functional organization of,156–161

Bdnf mRNA, neuronal activity-dependentexpression of, 156

chromatin regulation of, 164–166molecular mechanisms, 161–164RNA stability and translation, 167see also Neurotrophins

Brain, NFATc discovery in, 189–190BTB/POZ repressor kaiso, 30

Ca2+CREB activation and, 82and CREB phosphorylation, 83–85CREB regulation and, 82–83internal, release in neurons

distinguishing features of, 77–79mechanism, 74–75during neuronal maturation, 79–81waves propagation, 75–77

sources of, 74Ca2+-dependent gene transcription, 81Cadherin-based junctions, 30Cajal bodies (CBs), 38–40Cajal-Retzius neurons, 59Calcineurin, 133Calcium/calmodulin-dependent kinases

(CaMKs), 130, 177, 232, 236Calcium/calmodulin-dependent serine protein

kinase (CASK), 30, 51CaMK and L27 domains, 54–55domain structure and protein-protein

interactions of, 51guanylate kinase (GK) domain, 54, 61interacting proteins, 55PDZ domain, 52–53protein 4.1 binding motif, 56Src homolog 3 (SH3) domain, 54subcellular distribution in brain, 56–57Tbr-1 transcriptional activity enhancement

by, 61–62Calcium/calmodulin kinase II (CAMKII), 327,

344–346, 404–407activity, in Drosophila, 259–260

Calcium-calmodulin kinase IV (CaMKIV),115, 412

Calcium response element (CRE), 112, 137,161, 163

availability and competition for bindingsites, 134–135

TATA box, 139

Subject Index 419

CaliforniaVerbal Learning Memory Test(CVLT), 342

Calories per meal (CR), 355–356Calpain I, Ca2+-dependent protease, 34CaMK and L27 domains, 54–55CaMKIIα expression, 181CaMKIIα mRNA, LTP and, 35CaMKK, 113, 115cAMP/CREB pathway, 141cAMP response element-binding protein

(CREB), 16, 27, 81–82, 278,298–299, 344

activation regulation, by synapticactivity, 129

as Bdnf promoter I, 162and brain function, 141–143and brain malfunction, 143–145Ca2+ dependent regulation of, 82–83CREB family of transcription factors,

127–129dependent transcription, 114–116, 127, 133internal Ca2+ release, phosphorylation and,

83–85KID domain of, 130, 132–134L-type channels and c-fos, 112–114and memory formation, 381–382

acute versus chronic, 385–386conflicting data, 383–385correlation, 383Drosophila dCREB2, 391–393mammalian acute intervention

experiments, 386–388, 388–391in mammals, 382–383

molecular organization of, 377–381phosphorylation, at Ser133, 130–132SUMOylation of, 133synaptic activity, activation regulation by,

129–135synaptic function regulation by, 135–141transcriptome identification, 137–139

cAMP response element binding protein -2(CREB2), 176, 178–179

cAMP-responsive-element (CRE), 127Canary (Serinus canaria), 9–10CA1 pyramidal neurons, 79, 83–85, 102CaRE-binding transcription factors, 164Casein kinase 1 (CK1), 189Casein kinase I epsilon (CKIε) gene, 319CASK interacting nucleosome assembly

protein (CINAP)synaptic stimulation and, 63–64Tbr-1 target gene expression and, 62–63

α/γ Catenin, 28β-catenin, cotranscriptional activator, 30Catenin p0071, 30

Caudomedial mesopallium (CMM), 4, 6, 11zenk expression in, 12

Caudomedial nidopallium (NCM), 4, 6, 18Arc expression in, 8zenk-expressing cells in, 11–12

CaV1.2 and CCAT, 117–120CCAAT-box, 164C2C12 cells, NRF-1 and NRF-2 gene

expression in, 223Cdk5/p35 complex, 239C. elegans, 52, 55, 230Cellular adhesion molecules (CAMs), 28–30Central nervous system (CNS), 314, 348Cerebral cortex development, Tbr-1 for, 57–60c-fos gene, 7, 9, 15, 178, 278, 324, 407

L-type channels and CREB, 112–114MEK 1/2 and, 16

ChIP-on chip assays, 298Chromatin immunoprecipitation (ChIP)

techniques, 19, 138, 164, 215, 280Chromatin remodeling, 359CINAP-CASK-Tbr-1 transcriptional complex,

in neurons, 63–66Class IIa HDACs, neuronal transcription

factors and, 176, 236–237, 240CREB2, 178–179MEF2 family, 177–178physiological roles, in nervous system,

182–183post-translational modifications, 181signal-dependent intracellular trafficking,

179–181SRF, 178

CLOCK/BMAL1- dependent transcription,317–318

Coffin-Lowry syndrome, 143Collapsin response-mediating protein

(CRMP), 29Complex neuronal structure, 73–74Corticotropin-releasing factor (CRF), 359–360COS-7 cells, 213COX6A1, COX subunit genes, 216–217, 222COX 4i1 promoter, 216–217cpg-15, candidate plasticity gene, 298CREB α� B6/129 F1 hybrids, 384CREB-binding protein (CBP), 82, 113, 129,

132–133, 361–362, 378, 383KIX domain of, 134

CREB-CBP complex, 379CREB/CREM/ATF-1 genes, 389CREB1 gene, 382CREB genes, 134, 377–378, 380CRE-loxP system, 316Cyclooxygenase-2 (COX-2), 200Cyclosporin A (CsA), 189

420 Subject Index

Cytochrome c oxidase, 209–212genes, bigenomic coordinators of

nuclear respiratory factor 1 (NRF-1),217–221

nuclear respiratory factor 2 (NRF-2),214–217

mitochondrial transcription factors A and B,213–214

Cytochrome c oxidase-II, 349

dCREB2 C28 transgene, 392dCREB2 gene, 256, 380–381, 388DGluR-IIA, glutamate receptor, 257DHP-insensitive channels, 115Diacylglycerol (DAG), 75, 1925,6-dichloro-1-β-D-ribofuranosyl benzimida-

zole (DRB), 94Dihydropyridines (DHPs), 1121, 25-dihydroxyvitamin D3 (D3), 349, 354D1-like receptors, activation, 17DLX2 and DLX5, homeodomain proteins, 32Dnmt1, methyltransferase for Bdnf promoter

IV, 166Dopamine-β-hydroxylase (DBH),

noradrenaline-synthesizing enzyme, 170Dorsal root ganglia (DRG) sensory neurons,

144, 196Dorsolateral thalamic nucleus (DLM), 4Downstream regulatory element antagonistic

modulator (DREAM), 27repressor protein, 82

Drosophila, 300activity induction of transcription, 267–269BMP signaling, 260CaMKII signaling, 259–260cellular adhesion, 261–263cytoskeletal regulation, 263–264dCREB2 gene, 391–393disc large tumor suppressor (Dlg), 52ERK/MAPK pathway, 258–259intercellular signaling, 265–266neuronal transcription regulation in,

253–258PKA signaling, 258post-translational machinery, 264–265temperature-sensitive (TS) seizure mutants

in, 267transcriptional control of synaptic translation

during LTM, 269–270Drosophila melanogaster, 379Drosophila radish (rad) mutants, 256–257dunce (dnc), cAMP phosphodiesterase mutant,

255–256, 261Dystrophy type 2 (DM2), 34

E-box-containing genes, 314E-cadherin/α-catenin/APC complexes, 31Electroconvulsive shock (ECS), 407Electrophoresis mobility shift assay (EMSA),

60, 103, 215, 323Elk-1, member of ETS oncogene family, 16Enteric nervous system (ENS), 347Epigenetics

mechanisms, 357–358and memory, 361–363role, in brain, 359–360

ErbB2 receptor, 31, 32ERK/MAPK pathway, Drosophila, 258–259ether-a-go-go (eag), hyperexcitability mutant,

257, 261N-Ethyl-N-nitrosourea (ENU)

mutagenesis, 315E26 transformation-specific (Ets), 214Every-other-day-fasting (EODF), 355–356Evoked junctional potentials (EJPs), 254Extracellular signal-regulated kinases 1 and 2

(ERK1/2), 16, 99, 180Extracellular signalregulated protein kinase

(ERK), 131cell-wide player in plasticity, 99–102

Ezrin, cytoskeletal linker protein, 33–34

Fasciclin II (FasII), 261–263FasII-APPL signaling pathway, 262fasII gene, 261–262, 264Fat Facets (faf), deubiquitin protease, 264FK506, calcineurin inhibitors, 189Fluorescence in situ hybridization (FISH)

method, for IEG mRNAs co-regulationin neurons, 408–410

FMRFa, neurotransmitter, 179Fragile X related (dFxr) protein, 263Fragile X Tremor Ataxia Syndrome

(FXTAS), 34Futsch protein, Drosophila, 263–264

GABA receptor, 15, 101–102GA-binding protein (GABP), 214GAD65/67+ cells, 406Gene regulation, songbirds and

by singing behavior, 14–15by song auditory stimulation, 6–9

auditory activation and gene expressionuncoupling, 14

context dependence, 11experience dependence, 12–13stimulus dependence, 9–11

Gene transcription,Ca2+-dependent, 81glass bottom boat (gbb), Wit ligand, 264GluR2, AMPA receptor, 32

Subject Index 421

Glutamate induced cell death, 65Glycogen synthase kinase-3β (GSK3β),

189, 319G protein-coupled receptors (GPCRs), 74,

131, 196Grb2–SOS complex, 192GRIP1, AMPA receptor scaffolding protein,

31–32Growth hormone secretagogue (GHS)

receptor, 354Guanine nucleotide exchange factor

(GEF), 327Guanylate kinase (GK) domain, of CASK

protien, 54, 61

Hairy/Enhancer of Split (HES) bHLHtranscriptional repressors, 317

HDAC7, histone deacetylase, 33HDAC1/PP1 complex, 133HDAC9 protein, 182hda1, yeast protein, 236Hepatic leukemia factor (HLF), 318Heterogeneous nuclear RNA binding

proteins (hnRNPs), 34–36Hidden Markov model (HMM), 138High mobility group (HMG) proteins, 213Highwire (hiw), ubiquitin ligase, 264–265Hippocampal pyramidal neurons, 39, 63

Ca2+ release in, 74–75see also Ca2+

Hippocampal synaptic plasticity, 194–195Histone acetyltransferases (HATs), 229Histone deacetylase (HDAC), 145, 175,

229, 360Histone deacetylase 1 (HDAC1), 133Histones (H3 and H4), 357Homo sapiens, 379Hook motif see Protein 4.1 binding motifHuntington disease (HD), CREB and,

144–145, 163Hyperkinetic (Hk), hyperexcitability

mutant, 257Hypothalamic-pituitary-adrenal (HPA),

359–360

Immediate early genes (IEGs), 135–136, 162,256, 258, 296–297, 399

Inducible cAMP early repressor (ICER), 129Inducible transcription factors (ITFs), 6–9Inositol 1,4,5 triphosphate receptors

(InsP3-R), 412Inositol-1,4,5-trisphosphate (IP3), 74, 192Insulin, BDNF and, 352–353Integrin-based nuclear signaling, 31Intense intranuclear foci (INF), 408

Internal Ca2+ release, mechanism, 74–75Internal granule layer (IGL), 241IP3 receptors (IP3Rs), 74–75, 79

JAB-1 signaling complex, 31Janus kinases (JAK), 31c-Jun N-terminal kinase (JNK), 189

Kaiso-p120(ctn) complex, 30Kinase-inducible domain (KID), 128

L-Afadin, 29Late-LTP-inducing stimulation, 99Lateral magnocellular nucleus of anterior

nidopallium (LMAN), 4L1-CAM, 29LEF-1/TCR transcription factors, cMyc

expression and, 30Leucine-rich repeat (LRR), 268Long-term depression (LTD), 28, 100,

103, 286Long-term facilitation (LTF), in Aplysia,

254, 381Long-term memory (LTM), 345, 362, 382Long-term potentiation (LTP), 28, 60, 91,

100–102, 135, 194, 355, 402in Aplysia, 96Arc protein and, 34blocking, by transcriptional inhibitors, 92CaMKIIα mRNA, 35CREB-regulated transcription in, 255de novo gene expression and, 141getting to nucleus, 93

direct test, 98–99stoichiometric constraints, 97–98timing, 94–97

in mammalian hippocampus, 254LTP-inducing stimulation, 103L-type calcium channels (LTCs), 111, 181

CaV1.2 and CCAT, 117–120CREB and c-fos, 112–114mechanisms, 114–116

Luciferase reporter assay, 59

MADS box family, 178MADS/MEF2 domains, 234, 237Mammalian circadian clock, transcriptional

mechanisms, 313communicating with SCN, neurotransmitter

system, 319–322CREB and SCN clock, 322–324kinase signaling, from cell surface to

nucleus, 324–329molecular clock, 314–319

Manic depression, 352

422 Subject Index

MAPK/ERK kinase (MEK), 258MAP kinase activation, 83Mass spectrometry based proteomic

studies, 29Matrix metalloproteinases (MMPs), 182, 280Maximal electroconvulsive seizure (MECS),

399–401, 408MeCP2, 166Medium-term memory (MTM), 256, 258MEF2A, RNAi-induced dendritic claw

phenotype, 241MEF2A-Ser453, 238MEF2 proteins, 177–178, 229

and activity dependent survival and death,236–240

differential splicing of, 231–232function regulation, at protein-DNA

interface, 234–235gene expression, transcriptional control of,

230–231layers of complexity, 235–236multiple signaling pathways and,

232–233and synaptic dendritic morphogenesis,

240–244MEF2 response element (MRE), 234Melanocortin-4 receptor (MC4R), 354Membrane associated guanylate kinase

(MAGUK) proteins, 51, 53“Metabolic syndrome,” 353Metabotropic glutamate receptors

(mGluRs), 75Methyl-CpG-binding protein (MeCP2), 362Microtubule affinity-regulating kinase

(MARK)/Par-1 family, 180Mint1-CASK-Veli protein complex, 55Mitochondrial RNA processing (MRP)

RNA, 218Mitochondrial Transcription Factors A and B,

213–214Mitogen-activated extracellular-signal-

regulated protein kinase kinases 1 and 2(MEK 1/2), 16

Mitogen-activated protein kinase (MAPK),99, 113–114, 263, 324, 344–346

Mitogen and stress-activated kinase (MSK),131, 325–326

MMP-9 and TIMP-1as AP-1 target genes in brain, 279–280neural plasticity-lessons from experimental

models and, 281–288Modulatory calcineurin interacting protein

(MCIP1.4), 199–200Morris water maze (MWM) task, 340,

382, 384

mRNAsactivity-dependent induction of, 296–297activity-induced, 297–298

mtTFA /TFAM and mtTFB1-2/TFB1-2M seeMitochondrial Transcription FactorsA and B

Muscarinic acetylcholine receptors(mAChRs), 75

Mutations altering neuronal activity, inDrosophila, 257

Myocyte enhancer factor-2 (MEF2) family, 175Myogenic bHLH proteins, 230

N-cadherin, 29, 30Nerve growth factor inducible protein A

(NGFI-A), 360Nerve growth factor (NGF), 131, 191, 195, 337Nervous system

genes regulated by NFAT in, 198–200neurotrophins in (see Neurotrophins)NFATc expression characterization,

190–191physiological roles in, 182–183

Neuregulin/ErbB receptor stimulation, 31Neurexin, 29, 53Neuromuscular junctions (NMJs), 254,

256–257Neuronal cell adhesion molecules (NCAMs),

29, 261, 263, 268Neuronal excitation, 27Neuronal transcription factors, interaction of

class IIa HDACs with, 176CREB2, 178–179MEF2, 177–178SRF, 178

Neurotrophin-3 (NT-3), 191, 337Neurotrophins, 191–192

BDNF function, genetically driven variationin, 343

BDNF-mediated synaptic plasticity, gutfeelings and, 347–349

connection of gut with brain and, 354–356energy expenditure, metabolism, and,

353–354energy metabolism, 350–352from hypothalamus to hippocampus,

352–353exercise, synaptic plasticity, and learning

and memory, 343–347experience-dependent modulation of, 337

BDNF genotype in human cognitivefunction, 341–342

from LTP to learning and memory,339–341

Subject Index 423

signaling, NFAT-dependent trans-cription and

embryonic axonal outgrowth, 193–194hippocampal synaptic plasticity, 194–195inflammation-induced persistent pain,

195–196NFATc2 homodimer complexes, 188NFATc/NFATn protein complexes, 188, 193,

197, 199NFATc transcription factor, 187–189

discovery, in brain, 189–190genes in nervous system regulated by,

198–200in nervous system, expression characteriza-

tion, 190–191neurotrophin signaling and

embryonic axonal outgrowth, 193–194hippocampal synaptic plasticity, 194–195inflammation-induced persistent pain,

195–196NF-κB, transcription factor, 27, 96, 98NGFI-A binding protein (Nab-1), 300–301NMDA receptor subunit 2b (NR2b) gene, 60,

64, 66protein expression, regulation, by

CINAP-CASK-Tbr-1 protein complex,64–65

NMDAR-mediated channels, 77, 81NMDA-type ionotropic glutamate receptors

(NMDARs), 94, 98, 100–101, 103N-methyl-D-aspartate (NMDA) receptor, 28,

39, 55, 60, 112, 344, 410TLS/FUS associated with, 37

Novel nucleocytoplasmic shuttling proteins, inPSD, 32–34

Novel splicing factors, at PSD, 36–37Novel transcriptional regulators, at PSD, 30–31NPAS2, CLOCK homolog, 316N-terminal c-Jun kinase 2 (JNK2), 31Nuclear factor of activated T-cells (NFATc),

179, 187Nuclear localization sequences (NLSs), on

proteins, 28, 32, 37Nuclear receptor corepressor (N-CoR), 175Nuclear respiratory factor 1/2 (NRF-1/2),

214–220Nuclear signaling, scaffolding/cytoskeletal

proteins and, 31with potential nuclear functions at PSD,

32–34Nucleocytoplasmic shuttling, 34

novel RNA binding proteins, at PSD, 35novel splicing factors, at PSD, 36–37synapse-to-nucleus signaling, alternative

splicing and, 35–36

Nucleolus, AIDA-1 and, 38–40Nucleosome assembly protein (NAP)

domain, 62nur77, orphan nuclear receptor, 242

O-GlcNAc glycosylation, 133Oligodeoxynucleotides (ODNs), 19, 323,

402–403

paralytic (paraTS1), TS activity mutant, 257Paraventricular nucleus (PVN), 63–64PC12 cells, REB and, 138pCREB, phosphorylated form of CREB, 129,

132–133, 346p120(ctn), armadillo-related proteins, 30PDZ domain

of CASK protein, 52–53, 57ligand interactions, 31

PDZ-motif peptides, 115Pentylenetetrazole (PTZ), 280PER-CRY complexes, 314Peroxisome proliferator-activated receptor

gamma (PPARγ) coactivator-1α(PGC-1αp, 221–223

Per1/Per2 double mutants, 317Phosphatidylinositide 4,5-bisphosphate

(PIP2), 75Phospholipase C (PLC), 75Phosphotidylinositol-4,5-bisphosphate, 192Phosphotidylinositol-3 kinase (PI3K), 192PKA-dependent CREB gene, 377PKA signaling, Drosophila, 258Plakoglobin (γ-catenin), 30–31Plasticity transcriptome dynamics, 300

activity-dependent gene transcription and,302–307

sensory experience and transcription factoroverexpression, 301

p42/44 MAPK pathways, 134Polypyrimidine-tractbinding-protein

(PTB)-associated splicing factor (PSF),36–37

POU family transcription factors, 36PP-2B see CalcineurinProline and acidic amino acid-rich basic

leucine zipper (PAR bZIP) family, 318Protein 4.1 binding motif, CASK and, 56Protein-DNA interface, MEF2 function at,

234–235Protein kinase A/C/D (PKA/C/D), 130, 137,

179, 378PSD-95, 29, 32, 36, 39, 52PSD95/synapsin coclusters, 241pumilio (pum), translational repressor, 269

424 Subject Index

Purified postsynaptic density (PSD), 27, 64CAMs and nucleocytoplasmic regulation,

29–30dynamic nature of, 28novel RNA binding proteins, 35novel scaffolding/cytoskeletal proteins,

32–34novel splicing factors at, 36–37novel transcriptional regulators, 30–31

Purkinje cells, 58, 63PYK2, calcium regulated tyrosine

kinase/scaffolding protein, 116

Quantitative real time PCR analysis,cytochrome c oxidase and, 211–212

Raf, 99, 325Rapsyn, 30Ras/MAPK signaling, 116, 131Real-time PCR analysis, arc gene and, 104Receptor tyrosine kinases (RTK), 131Reduced potassium dependency 3 (Rpd3), 175Reelin gene, 59–60Regulatory transcription factors (RTFs), 16Rel homology regions (RHR), 188Rel/NFκB family, 187REST-dependent repression, Bdnf promoter II,

162–163Retinal ganglion cells (RGCs), 314Retinohypothalamic tract (RHT), 314Retinoic acidrelated nuclear orphan receptors

(ROR), 317Rett syndrome, 166REV-ERBα, 317–318Ribonucleoproteins (RNPs), 34, 38–39Ribosomal S6 kinases (RSKs), 131, 326RING-H2 E3 ubiquitin-protein ligase, 264RNA interference (RISC) pathway, 259RNA polymerase II complex, 129RNase protection assay, 189Rubinstein-Taybi syndrome (RTS), 143rut mutant, 256Ryanodine receptors (RyRs), 74–75

SAP97, GluR1 scaffolding protein, 32SAS motif, 243Scaffolding/cytoskeletal proteins, nuclear

signaling and, 31with potential nuclear functions at PSD,

32–34Sea snail see AplysiaSEEDTOP, BLAST program, 37seizure (seiTS1), TS activity mutant, 257Ser133, CREB phosphorylation and, 130–132

Serial analysis of gene expression (SAGE),138, 266–267

Serinearginine rich SR proteins, 36Ser408 phosphorylation, MEF2 and, 243Serum response element (SRE), 112Shaker (Sh), hyperexcitability mutant, 257, 261SH-2 containing protein (SHC), 192SHC/Ras/ERK pathway, 192, 193Short-hairpin RNA interference (shRNA), 216Short-term memory (STM), 256Signal-responsive intracellular trafficking, of

HDAC5, 179–181Signal transducer and activator of transcription

(STAT1), 31Silencing mediator for retinoic and thyroid

receptors (SMRT), 175Silent information regulator 2 (Sir2), 175Small ubiquitin-related modifier (SUMO),

178, 243Song auditory stimulation, gene regulation

by, 6–9auditory activation and gene expression

uncoupling, 14context dependence, 11experience dependence, 12–13stimulus dependence, 9–11

Songbirdsbirdsong, activity-dependent trans-

cription andsinging behavior, gene regulation by,

14–15song auditory stimulation, gene regulation

by, 6–14neurobiology of vocal communication

in, 3–6song-induced gene expression

functions, in auditory and song controlareas, 17–20

regulation, in auditory neurons, 15–17song-induced transcriptional response in, 8

Song control system, 4–6see also Songbirds

Song-induced gene expressionfunctions, in auditory and song control

areas, 17–20regulation, in auditory neurons, 15–17

Spinal cerebellar ataxias type 8/10/12, 34Src homolog domain 2 (SH2)-containing

proteins, 192Src Homolog 3 (SH3) domain, of CASK, 54Stable isotope labeled amino acids in cell

culture (SILAC), 40–41Starling (Sturnus vulgaris), 9Staufen, Drosophila RNA binding protein, 35STREX exon, STREX exon, 36

Subject Index 425

Sumoylation-acetylation switch (SAS)motif, 232

Suprachiasmatic nuclei (SCN), 313CREB and entrainment of, 322–324neurotransmitter systems, 319–322Per1 and Per2 rhythms in, 315–316

Synapses, 302Synapse-to-nucleus signaling, 34

alternative splicing and, 35–36uncovering novel, with proteomics and

bioinformatics, 37–40Synapsin I, 344–345Synaptic cell adhesion molecule (SynCAM),

29, 53Synaptic dendritic morphogenesis, MEF2 and,

240–244Synaptic plasticity, transcription and

translation in, 296Synaptic stimulation, CINAP and, 63–64Synaptotagmin 4, 265–266Syndecan-3, 30, 57

Tbet/Tbx21, in T lymphoytes, 58T-box transcription factor 1 (Tbr-1), 30, 51

CASK, transcriptional activity enhancementby, 61–62

for cerebral cortex development, 57–60target gene expression, CINAP and, 62–63

Tbr-1-CASK complex, in neuraldevelopment, 61

Tbr-2/Eomes, in neuronal progenitor cells, 58Temporal lobe epilepsy (TLE), 284Tensin homologue deleted on chromosome 10

phosphatase (PTEN), 133Tetrodotoxin (TTX), 210, 216Theta burst pattern of stimulation (TBS),

95, 100Thyrotroph embryonic factor (TEF), 318TIMP-1 and MMP-9

as AP-1 target genes in brain, 279–280neural plasticity-lessons from experimental

models and, 281–288timp-1 mRNA expression, 280TonEBP (NFAT5), transcription factor, 188Transcriptional start sites (TSSs), Bdnf

promoters and, 158–161Transcription factor-DNA interactions,

298–300Transcription factors (TFs), 103

CREB family of, 127–129see also specific types

Transducers of Regulated CREB activity(TORCs), 113

Transporter of outer mitochondrialmembrane20 (TOM20), 217

Triton X-100, 29Two-dimensional differential in-gel

electrophoresis (2DE-DIGE), 41Tyrosinase-related protein-1 (TRP-1) gene, 60Tyrosine kinase receptor (TrkA/B), 192, 344,

347, 350, 354Tyrosine phosphatase 1B (PTP1B), 133

U2AF splice factor, 36UAS-Gal4 system, 254Ubiquitin proteasome pathway, 30Uncoupling protein 1/2 (UCP-1/2), 349, 354U1 snRNP splice factor, 36

Val66Met BDNF gene polymorphism, 352Veli/MALS/mLIN-7 protein, in mammalian

brain, 54–55Visual-paired comparison task (VPC), 361Vocal communication neurobiology, in

songbirds, 3–6see also Songbirds

Vocal-motor pathway, direct, 4–5Voltage-dependent anion channel

(VDAC1), 217Voltage-gated Ca2+ channels (VGCCs), 74,

77, 79, 81–82, 111–112, 114see also L-type calcium channels (LTCs)

Voltage-sensitive calcium channels(VSCC), 131

Wechsler Memory Scale, revised version(WMS-R), 342

Wnt receptor, 31

Y-box transcriptional factor ZONAB, 30, 32

ZENK-expressing cells, 12ZENK protein expression, 11

DNA-binding motif of, 18zenk, song-induced gene, 7, 9–10, 14–16,

18–19MEK 1/2 and, 16

zif-268, egr-1, NGFI-A and krox-24 see zenk,song-induced gene

zif-268 genes, 93, 102, 301, 407Zona Occludens-1/2 (ZO-1/2), scaffolding

protein, 30, 32, 52