Gene Regulatory Networks

Contributors
Preface
A gene regulatory network for cell fate specification in Ciona embryos
Introduction
Basic properties for the gene regulatory network in early ascidian embryos
Regulatory genes
Initial conditions for the gene regulatory network
Outputs of the gene regulatory network
Potentially unique properties of the gene regulatory network in early ascidian embryos
The gene regulatory network accounts for changes of gene expression in space and time
The initial set up in the 16-cell embryo by maternal factors
Specific gene expression in the 32-cell embryo
Specific gene expression at the 64-cell stage and thereafter
Specification of endodermal fate
Fate specification of mesenchymal cells
Fate specification of muscle cells and adult heart precursors
Fate specification of the notochord and the posterior neural plate
Epidermal cells
Cells for the lateral neural plate and its border
Cells for the anterior neural plate and its border
Perspectives
References
Early Xenopus gene regulatory programs, chromatin states, and the role of maternal transcription factors
Introduction
Roles of maternal TFs during germ layer specification
Localization of maternal gene products
Endodermally enriched TFs
Vegt
Otx1
Sox7
Ectodermally enriched TFs
Foxi2
Grhl1
Ubiquitously expressed TFs
Foxh1
Sox3
Pou5f3
Intracellular mediators of signaling pathways
Gdf1/Nodal/Smad2,3
Wnt/TCF/Ctnnb1 (β-catenin)
Other TFs
Enhancers, promoters and chromatin states
Genomic approaches to identifying enhancers
Chromatin states and ZGA
Repressive chromatin marking
Network structure analysis of the early Xenopus GRN
Summary and prospects
Acknowledgments
References
Dynamic and self-regulatory interactions among gene regulatory networks control vertebrate limb bud morpho ...
Introduction
Setting the stage: Molecular control of the limb field positions along the primary body axis
``Pre-patterning´´: Polarizing the limb bud axes upstream of morphogenetic SHH signaling
Establishment of AER-FGF signaling is linked dorso-ventral and proximo-distal axis patterning
The self-regulatory limb bud signaling system coordinately controls antero-posterior and proximo-distal axis patternin ...
Propagation and termination of the self-regulatory limb bud signaling system
A Turing-type mechanism controls the definitive periodic pattern of digit rays
Brief outlook
Acknowledgments
References
Gene regulatory networks during the development of the Drosophila visual system
Introduction
Design principles of the gene regulatory networks (GRNs) in the Drosophila visual system
The eye
The eye disc GRN
The GRN of the morphogenetic furrow
The GRN specifying photoreceptor fate
The GRN that determines photoreceptor terminal features: Ommatidial subtypes
The GRN that determines photoreceptor terminal features: Axon targeting
GRNs in the eye: A brief summary
The GRN that specifies lamina neurons in response to photoreceptor signals
Temporal and spatial GRNs specify medulla neurons
The GRNs leading to the formation of the lobula and lobula plate
Conclusion and perspectives
Acknowledgments
References
Cell fate decisions during the development of the peripheral nervous system in the vertebrate head
Introduction
The preplacodal region: A territory of sense organ and cranial ganglia progenitors
Subdivision of the embryonic ectoderm prior to gastrulation
The neural plate border
Signaling events at the neural plate border
Transcription factor interactions: From neural plate border to neural crest and placode precursors
Segregation of neural crest and sensory placode precursors
Subdividing the placode territory along the anterior-posterior axis
Otic and epibranchial placode formation: Signals and regulatory circuits
FGF signaling induces otic-epibranchial progenitors
Segregation of otic-epibranchial progenitors: Signals and regulatory circuits
Regulatory circuits at otic and epibranchial placode stages
Refining the OEP network: A cis-regulatory perspective
Conclusion
References
A Hox gene regulatory network for hindbrain segmentation
Introduction
A GRN controls segmental Hox expression in the hindbrain
Signaling determines early axial allocation
Wnt
RA
FGF
Spatial subdivision of the hindbrain territory by segmentation genes
Rhombomeric deployment of cell segregation factors
Establishment and maintenance of segmental Hox expression
Hox targets and cofactors
Hox regulatory networks and the neural crest GRN
Conclusions and key questions
Acknowledgments
References
Logical modeling of cell fate specification-Application to T cell commitment
Introduction
Overview of T cell development
Logical modeling of T cell specification
Delineation of the regulatory graph controlling T cell specification
Multilevel nodes
Logical rules
Computation of model stable states in the wild-type situation
Computation of model stable states upon environmental or genetic perturbations
Assessing the reachability of specific expression patterns from specific initial states
Stochastic simulations
Conclusions
Acknowledgments
References
Repressive interactions in gene regulatory networks: When you have no other choice
Introduction
The developing neural tube: A GRN in time and space
Concentration interpretation: More than Gli affinities
Gradient interpretation in time
Cis regulatory elements and the role of repression
From subcircuits to complex dynamics
What can the GRN do for you?
Molecular mechanisms for implementing the GRN cross-repressive interactions
CRE repression
Repression by protein-protein interactions
Repression at the RNA level
Conclusions
Acknowledgments
References
The function of architecture and logic in developmental gene regulatory networks
Introduction
The structure of developmental GRNs in theory and experiment
Logic processing in developmental GRNs
Architecture of circuit modules that are prevalent in developmental GRNs
The connection between circuit architecture and developmental function
Organization of circuit modules within developmental GRNs
Evolution of network architecture
Conclusion
Acknowledgments
References
The evolution of the gene regulatory networks patterning the Drosophila Blastoderm
Introduction
The Drosophila syncytial blastoderm
Axial patterning
Terminal patterning
Gap genes
Pair-rule genes
Segment polarity genes
Conclusions
References
The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to ve ...
The notochord, a synapomorphy of the chordate phylum and a sine qua non of chordate development
Evolutionary history of the notochord
Notochord development in Ciona
Morphogenetic milestones
The molecular blueprint for notochord formation in Ciona
Notochord induction and specification
Invagination and convergent extension
Formation of the notochordal sheath and elongation
Tubulogenesis and disappearance
Time is of the essence: Temporal cis-regulatory control of gene expression in a fast-developing chordate
The GRN underlying notochord formation in Ciona
The main regulatory nodes of the notochord GRN: Brachyury and Foxa2
Drawing edges, connecting nodes: Reconstructing the gene batteries controlled by notochord transcription factors
Reverse-engineering the notochord GRN: Lessons from notochord cis-regulatory modules
Ciona notochord CRMs can be synergistically activated by Foxa.a in cooperation with either Bra or other transcriptio ...
Additional notochord cis-regulatory mechanisms identified in Ciona
Comparative studies of notochord cis-regulatory regions across chordates
A comparative view of the notochord GRN in Ciona and other chordates
Concluding remarks and future perspectives
Acknowledgments
References
The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to ve ...
The notochord, a synapomorphy of the chordate phylum and a sine qua non of chordate development
Evolutionary history of the notochord
Notochord development in Ciona
Morphogenetic milestones
The molecular blueprint for notochord formation in Ciona
Notochord induction and specification
Invagination and convergent extension
Formation of the notochordal sheath and elongation
Tubulogenesis and disappearance
Time is of the essence: Temporal cis-regulatory control of gene expression in a fast-developing chordate
The GRN underlying notochord formation in Ciona
The main regulatory nodes of the notochord GRN: Brachyury and Foxa2
Drawing edges, connecting nodes: Reconstructing the gene batteries controlled by notochord transcription factors
Reverse-engineering the notochord GRN: Lessons from notochord cis-regulatory modules
Ciona notochord CRMs can be synergistically activated by Foxa.a in cooperation with either Bra or other transcriptio ...
Additional notochord cis-regulatory mechanisms identified in Ciona
Comparative studies of notochord cis-regulatory regions across chordates
A comparative view of the notochord GRN in Ciona and other chordates
Concluding remarks and future perspectives
Acknowledgments
References
On the specificity of gene regulatory networks: How does network co-option affect subsequent evolution?
How does one part become different from other parts?
Immediate outcomes of network co-option
Wholesale co-option
Partial network co-option and functionally-divergent network co-option
Co-option resulting in downstream regulatory expression only (aphenotypic co-option)
How do GRNs maintain or recover specificity after network co-option?
Changes in trans
Changes in cis
Regulatory input diversification
Specificity conferred by redundant CREs
The action of selection on co-opted networks over time
Initiating trans change with positive fitness effects
Initiating trans change with detrimental fitness effects
Initiating trans change with selectively neutral effects
Network co-option and the origin and diversification of traits
Concluding remarks
Acknowledgments
Glossary
References
Evolutionary dynamics of gene regulation
Conceptual approaches to understanding the evolution of gene regulation
The origin of metazoan regulatory novelties
The expansion and exploitation of combinatoric complexity
Evolutionary repatterning of gene regulatory networks
Micro- and macroevolutionary changes in gene regulatory networks
Do novel morphologies involve mechanistically distinct pathways?
Towards a general theory of GRN evolution
Concluding remarks
Acknowledgments
References
Further reading