شبکه‌های تنظیم‌کننده ژن (جلد ۱۳۹) (موضوعات جاری در زیست‌شناسی توسعه، جلد ۱۳۹)

Gene Regulatory Networks, Volume 139 in the Current Topics in Developmental Biology series, highlights new advances in the field, with this new volume presenting interesting chapters written by an international board of authors. Topics in this release include Mouse hindbrain GRN, Xenopus endoderm GRN – organogenesis, Vertebrate limb GRN, The notochord gene regulatory network in chordate evolution: conservation and divergence from Ciona to vertebrates, Ciona early embryo GRNs, Boolean logic models, Modeling GRN response to morphogen gradient, GRN architecture, Theory of GRN evolution, Evolution of fly segmentation GRNs, GRN evolution in echinoderms, Evolution of network specificity, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Current Topics in Developmental Biology series Includes the latest information on 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

Gene Regulatory Networks, Volume 139 in the Current Topics in Developmental Biology series, highlights new advances in the field, with this new volume presenting interesting chapters written by an international board of authors. Topics in this release include Mouse hindbrain GRN, Xenopus endoderm GRN – organogenesis, Vertebrate limb GRN, The notochord gene regulatory network in chordate evolution: conservation and divergence from Ciona to vertebrates, Ciona early embryo GRNs, Boolean logic models, Modeling GRN response to morphogen gradient, GRN architecture, Theory of GRN evolution, Evolution of fly segmentation GRNs, GRN evolution in echinoderms, Evolution of network specificity, and more.

• Provides the authority and expertise of leading contributors from an international board of authors
• Presents the latest release in the Current Topics in Developmental Biology series
• Includes the latest information on gene regulatory networks

"Gene Regulatory Networks, Volume 139 in the Current Topics in Developmental Biology series, highlights new advances in the field, with this new volume presenting interesting chapters written by an international board of authors. Topics in this release include Mouse hindbrain GRN, Xenopus endoderm GRN - organogenesis, Vertebrate limb GRN, The notochord gene regulatory network in chordate evolution: conservation and divergence from Ciona to vertebrates, Ciona early embryo GRNs, Boolean logic models, Modeling GRN response to morphogen gradient, GRN architecture, Theory of GRN evolution, Evolution of fly segmentation GRNs, GRN evolution in echinoderms, Evolution of network specificity, and more."--publisher's web page, viewed May 25, 2020