338
Index
Cdt1 degradation, 18
Cell biology, proteomics (relationship), 200
Cell cycle
early development, relationship, 14
events, in vitro recapitulation, 13–15
oscillatory nature, impact, 17
pausing, 16
progression, cytoplasmic factors (impact), 15
protein degradation, impact, 15–16
regulation, 102
systems biology, 16–17
transitions, control, 16–17
Cell death, 294–295
Cell developmental biology, Xenopus (research
tool), 301–302
Cell division
control, study, 13
cycle, existence (demonstration), 13
Cell-fate reprogramming Xenopus NT
embryos, eff ciency, 332
Cell-free translation assays, usage, 26
Cell lineages, creation, 25
Cell nuclei, beta-catenin (β-catenin)
localization, 67
Cells, reprogramming, 325
Cellular activity, calcium-imaging, 282
Cellular proliferation, 295–296
Central left-right organizer (cLRO),
characterization, 227
Central nervous system (CNS)
accessibility, 282
circuitry, implementation, 284
manipulations, functional consequences,
281
morpho-physiological information, 277
visual feld representations, 278
Centrosomal biology, nucleoporins (presence),
237–238
Cerberus (secreted factor)
identif cation, 226
impact, 57
CerS, impact, 30
CG (CpG) dinucleotides, DNA methylation
(occurrence), 180
Channels (biophysics/pharmacological
properties), Xenopus oocytes (usage), 143
Charles, Enid, 7
Child, craniofacial skeleton, 247
ChIP-re-ChIP experiments, usage, 178
ChIP-seq analysis, 186
ChIP-seq data sets, training, 191
ChIP-sequencing experiments, 179
Chordamesoderm, formation, 188
Chordin/Tolloid/Twisted gastrulation/
Crossveinless-2/BMP ancestrally
conserved D-V patterning system, 47
Chromatin
accessibility, 176–178
accessibility, transcription factor binding
(relationship), 177–178
assembly, replication-coupled chromatin
assembly dynamics, 178
assembly, repressiveness, 177
assembly, usage, 177
chromatin-associated proteins, role, 173
heterochromatin marks, 180
immunoprecipitation, 174
remodeling, dynamics, 173
state, DNA packaging/regulatory substrate,
173–174
state maps, genome browser view, 175
Chromosomes
bouquet, formation, 34
comparison, 158
fusion sites, identif cation, 158
identif cation, 158–159
sex chromosomes, W-specif c/Z-specif c
regions, 161
Cilia-based fow reception, 229
Cilia biology, nucleoporins (presence),
237–238
Cilia cell fate determination, glycosylation, 237
Ciliary pore complex model, contradiction,
238
Cis-regulatory modules (CRMs)
binding, 188–189
regulatory effector interactions, display, 185
CLEAR consortium, 268
Cleavage-stage embryos
arrest, 16
Cleavage-stage Xenopus embryos
cleavage, occurrence (timing), 17
H3K4me3/H3K27me3, absence, 179
Cleft lip/palate, 250
Clinically relevant GEXMs, generation,
303–304
Clock hypothesis, postulation, 107, 111
Cluster-specifc gene expansions, 164
Clutch comparisons, making, 317–319
Clutch variability, 317
CMB:GFP neurula stage embryo, grafting, 210
CMV promoter, impact, 177
c-Myc promoter, usage, 177
Coherent feedforward loop, 189
Collateral projections, generation, 296
Collinearity, 163
Comparative genome analysis, 166
Complementary deoxyribonucleic acid (cDNA)
clones, synthesis, 144
data, usage, 157
functional expression library screening, 57
isolation, 143
libraries, preparation, 44
reverse transcription, 203
screen, gata4 identif cation, 235
sequencing, 316
transfection, 329
translating, 199
usage, 158
Congenital heart disease (CHD), 239–240
candidate CHD genes, identif cation,
235–236
cilia/centrosomal biology, nucleoporins
(presence), 237–238
clinical therapies, 234
developmental cell signaling, mysteries,
238–239
diagnosis/studying, diff culties, 234
disease mechanism analysis, left-right
patterning (usage), 236–237
genes, function (discovery), 233
historical/medical background, 233–234
patient cohorts, analysis, 235–236
roots, 233–234
shared molecular pathways, 239–240
study, future, 240
studying, approaches (Xenopus ), 236–237
studying, morphological/developmental
benef ts, 236
surgical interventions, 234
understanding, molecular genetic studies
(usage), 234–236
Congenital Malformations of the Heart
(Taussig), 234
Connexins, gap junction component, 146
Context-specifc Wnt signaling, 70
Copy-number variant (CNV)
analysis, 238
deletion, 237
identif cation, 235–236
Cortical rotation, 25–26
model, 26
molecular control, 31
Cranial neural crest (CNC)
cells, differentiation (requirements), 131
EAD reciprocal signaling, 248
population, impact, 246
Cranial placode development, notch pathway
role, 107
Craniofacial abnormalities (CFAs), 239–240
Craniofacial anomalies (CFAs), 245
causes, 249–250
cell-based approaches, 252
classes, 250–251
environmental causes, 249–250
factors, association, 249–250
genetic causes, 249
landscape, 249–251
list, 252
surgical approaches, 251
tissue engineering approaches, 251
treatment, 251–272
understanding, 252
vitamin defciency, impact, 250
Craniofacial ciliopathies, 251, 251
Craniofacial development
def ning, 245
Xenopus, contributions, 245
Xenopus model, 245–246
Craniofacial disorders, 245
Craniofacial microsomia, 250
Craniofacial organizer, function, 249
Craniofacial signaling center, extreme anterior
domain (comparison), 249
Craniofacial skeleton, 247
cells, presence, 246
Craniofacial structure, development, 250
Craniosynostosis, 250
Crew, Frank, 7
CRISPR
CRISPR-mediated genome editing, usage,
252, 303
knock-ins, presence, 203–204
screens, 268
systems, usage, 290
CRISPR-based genome editing, usage, 200
CRISPR-based mutations, isolation, 8
CRISPR/Cas9 genome editing, usage, 236
CRISPR/Cas9-mediated genome editing, 127
CRISPR/Cas9 Selection-mediated Identif cation
of Dependencies (CRISPR-SID)
development, 305
methodology, 306
Crosstalk, histone modifcations (usage), 181
C-terminal domain (CTD), 330
CUB domains, 47
Cuvier, Georges, 4
Cyclin/Cdk complex, impact, 19
Cyclin, identif cation, 14–15
Cys-loop family, oocyte expression, 147
Cytoplasm, canonical Wnt signaling, 66, 68
Cytoplasmic activation, 31–32
Cytoplasmic determinants, examples, 25–26
Index
Cdt1 degradation, 18
Cell biology, proteomics (relationship), 200
Cell cycle
early development, relationship, 14
events, in vitro recapitulation, 13–15
oscillatory nature, impact, 17
pausing, 16
progression, cytoplasmic factors (impact), 15
protein degradation, impact, 15–16
regulation, 102
systems biology, 16–17
transitions, control, 16–17
Cell death, 294–295
Cell developmental biology, Xenopus (research
tool), 301–302
Cell division
control, study, 13
cycle, existence (demonstration), 13
Cell-fate reprogramming Xenopus NT
embryos, eff ciency, 332
Cell-free translation assays, usage, 26
Cell lineages, creation, 25
Cell nuclei, beta-catenin (β-catenin)
localization, 67
Cells, reprogramming, 325
Cellular activity, calcium-imaging, 282
Cellular proliferation, 295–296
Central left-right organizer (cLRO),
characterization, 227
Central nervous system (CNS)
accessibility, 282
circuitry, implementation, 284
manipulations, functional consequences,
281
morpho-physiological information, 277
visual feld representations, 278
Centrosomal biology, nucleoporins (presence),
237–238
Cerberus (secreted factor)
identif cation, 226
impact, 57
CerS, impact, 30
CG (CpG) dinucleotides, DNA methylation
(occurrence), 180
Channels (biophysics/pharmacological
properties), Xenopus oocytes (usage), 143
Charles, Enid, 7
Child, craniofacial skeleton, 247
ChIP-re-ChIP experiments, usage, 178
ChIP-seq analysis, 186
ChIP-seq data sets, training, 191
ChIP-sequencing experiments, 179
Chordamesoderm, formation, 188
Chordin/Tolloid/Twisted gastrulation/
Crossveinless-2/BMP ancestrally
conserved D-V patterning system, 47
Chromatin
accessibility, 176–178
accessibility, transcription factor binding
(relationship), 177–178
assembly, replication-coupled chromatin
assembly dynamics, 178
assembly, repressiveness, 177
assembly, usage, 177
chromatin-associated proteins, role, 173
heterochromatin marks, 180
immunoprecipitation, 174
remodeling, dynamics, 173
state, DNA packaging/regulatory substrate,
173–174
state maps, genome browser view, 175
Chromosomes
bouquet, formation, 34
comparison, 158
fusion sites, identif cation, 158
identif cation, 158–159
sex chromosomes, W-specif c/Z-specif c
regions, 161
Cilia-based fow reception, 229
Cilia biology, nucleoporins (presence),
237–238
Cilia cell fate determination, glycosylation, 237
Ciliary pore complex model, contradiction,
238
Cis-regulatory modules (CRMs)
binding, 188–189
regulatory effector interactions, display, 185
CLEAR consortium, 268
Cleavage-stage embryos
arrest, 16
Cleavage-stage Xenopus embryos
cleavage, occurrence (timing), 17
H3K4me3/H3K27me3, absence, 179
Cleft lip/palate, 250
Clinically relevant GEXMs, generation,
303–304
Clock hypothesis, postulation, 107, 111
Cluster-specifc gene expansions, 164
Clutch comparisons, making, 317–319
Clutch variability, 317
CMB:GFP neurula stage embryo, grafting, 210
CMV promoter, impact, 177
c-Myc promoter, usage, 177
Coherent feedforward loop, 189
Collateral projections, generation, 296
Collinearity, 163
Comparative genome analysis, 166
Complementary deoxyribonucleic acid (cDNA)
clones, synthesis, 144
data, usage, 157
functional expression library screening, 57
isolation, 143
libraries, preparation, 44
reverse transcription, 203
screen, gata4 identif cation, 235
sequencing, 316
transfection, 329
translating, 199
usage, 158
Congenital heart disease (CHD), 239–240
candidate CHD genes, identif cation,
235–236
cilia/centrosomal biology, nucleoporins
(presence), 237–238
clinical therapies, 234
developmental cell signaling, mysteries,
238–239
diagnosis/studying, diff culties, 234
disease mechanism analysis, left-right
patterning (usage), 236–237
genes, function (discovery), 233
historical/medical background, 233–234
patient cohorts, analysis, 235–236
roots, 233–234
shared molecular pathways, 239–240
study, future, 240
studying, approaches (Xenopus ), 236–237
studying, morphological/developmental
benef ts, 236
surgical interventions, 234
understanding, molecular genetic studies
(usage), 234–236
Congenital Malformations of the Heart
(Taussig), 234
Connexins, gap junction component, 146
Context-specifc Wnt signaling, 70
Copy-number variant (CNV)
analysis, 238
deletion, 237
identif cation, 235–236
Cortical rotation, 25–26
model, 26
molecular control, 31
Cranial neural crest (CNC)
cells, differentiation (requirements), 131
EAD reciprocal signaling, 248
population, impact, 246
Cranial placode development, notch pathway
role, 107
Craniofacial abnormalities (CFAs), 239–240
Craniofacial anomalies (CFAs), 245
causes, 249–250
cell-based approaches, 252
classes, 250–251
environmental causes, 249–250
factors, association, 249–250
genetic causes, 249
landscape, 249–251
list, 252
surgical approaches, 251
tissue engineering approaches, 251
treatment, 251–272
understanding, 252
vitamin defciency, impact, 250
Craniofacial ciliopathies, 251, 251
Craniofacial development
def ning, 245
Xenopus, contributions, 245
Xenopus model, 245–246
Craniofacial disorders, 245
Craniofacial microsomia, 250
Craniofacial organizer, function, 249
Craniofacial signaling center, extreme anterior
domain (comparison), 249
Craniofacial skeleton, 247
cells, presence, 246
Craniofacial structure, development, 250
Craniosynostosis, 250
Crew, Frank, 7
CRISPR
CRISPR-mediated genome editing, usage,
252, 303
knock-ins, presence, 203–204
screens, 268
systems, usage, 290
CRISPR-based genome editing, usage, 200
CRISPR-based mutations, isolation, 8
CRISPR/Cas9 genome editing, usage, 236
CRISPR/Cas9-mediated genome editing, 127
CRISPR/Cas9 Selection-mediated Identif cation
of Dependencies (CRISPR-SID)
development, 305
methodology, 306
Crosstalk, histone modifcations (usage), 181
C-terminal domain (CTD), 330
CUB domains, 47
Cuvier, Georges, 4
Cyclin/Cdk complex, impact, 19
Cyclin, identif cation, 14–15
Cys-loop family, oocyte expression, 147
Cytoplasm, canonical Wnt signaling, 66, 68
Cytoplasmic activation, 31–32
Cytoplasmic determinants, examples, 25–26