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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