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Proc Natl Acad Sci U S A
2022 Mar 15;11911:e2114802119. doi: 10.1073/pnas.2114802119.
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Gain of gene regulatory network interconnectivity at the origin of vertebrates.
Gil-Gálvez A
,
Jiménez-Gancedo S
,
Pérez-Posada A
,
Franke M
,
Acemel RD
,
Lin CY
,
Chou C
,
Su YH
,
Yu JK
,
Bertrand S
,
Schubert M
,
Escrivá H
,
Tena JJ
,
Gómez-Skarmeta JL
.
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SignificanceIn this manuscript, we address an essential question in developmental and evolutionary biology: How have changes in gene regulatory networks contributed to the invertebrate-to-vertebrate transition? To address this issue, we perturbed four signaling pathways critical for body plan formation in the cephalochordate amphioxus and in zebrafish and compared the effects of such perturbations on gene expression and gene regulation in both species. Our data reveal that many developmental genes have gained response to these signaling pathways in the vertebrate lineage. Moreover, we show that the interconnectivity between these pathways is much higher in zebrafish than in amphioxus. We conclude that this increased signaling pathway complexity likely contributed to vertebrate morphological novelties during evolution.
Aldea,
Genetic regulation of amphioxus somitogenesis informs the evolution of the vertebrate head mesoderm.
2019, Pubmed
Aldea,
Genetic regulation of amphioxus somitogenesis informs the evolution of the vertebrate head mesoderm.
2019,
Pubmed
Anders,
HTSeq--a Python framework to work with high-throughput sequencing data.
2015,
Pubmed
Azpeitia,
The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks.
2017,
Pubmed
Barabási,
Network biology: understanding the cell's functional organization.
2004,
Pubmed
Bertrand,
Developmental cell-cell communication pathways in the cephalochordate amphioxus: actors and functions.
2017,
Pubmed
Bian,
Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.
2017,
Pubmed
Böttcher,
Fibroblast growth factor signaling during early vertebrate development.
2005,
Pubmed
Bray,
Near-optimal probabilistic RNA-seq quantification.
2016,
Pubmed
Buenrostro,
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
2013,
Pubmed
Cadigan,
TCF/LEFs and Wnt signaling in the nucleus.
2012,
Pubmed
Casper,
The UCSC Genome Browser database: 2018 update.
2018,
Pubmed
Charney,
A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs.
2017,
Pubmed
,
Xenbase
Christoffels,
Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes.
2004,
Pubmed
Dehal,
Two rounds of whole genome duplication in the ancestral vertebrate.
2005,
Pubmed
Dobin,
STAR: ultrafast universal RNA-seq aligner.
2013,
Pubmed
Fan,
Reiterative use of FGF signaling in mesoderm development during embryogenesis and metamorphosis in the hemichordate Ptychodera flava.
2018,
Pubmed
Farnsworth,
A single-cell transcriptome atlas for zebrafish development.
2020,
Pubmed
Fortriede,
Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database.
2020,
Pubmed
,
Xenbase
Friedman,
The Foxa family of transcription factors in development and metabolism.
2006,
Pubmed
Fuentes,
Insights into spawning behavior and development of the European amphioxus (Branchiostoma lanceolatum).
2007,
Pubmed
Fuentes,
Preliminary observations on the spawning conditions of the European amphioxus (Branchiostoma lanceolatum) in captivity.
2004,
Pubmed
Ghyselinck,
Retinoic acid signaling pathways.
2019,
Pubmed
Gil-Gálvez,
Gain of gene regulatory network interconnectivity at the origin of vertebrates.
2022,
Pubmed
,
Xenbase
Heinz,
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
2010,
Pubmed
Hiller,
Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.
2013,
Pubmed
Hoodless,
FoxH1 (Fast) functions to specify the anterior primitive streak in the mouse.
2001,
Pubmed
Jia,
smad2 and smad3 are required for mesendoderm induction by transforming growth factor-beta/nodal signals in zebrafish.
2008,
Pubmed
Joshi,
CDX4 regulates the progression of neural maturation in the spinal cord.
2019,
Pubmed
Kiecker,
Molecular specification of germ layers in vertebrate embryos.
2016,
Pubmed
Kjolby,
Integration of Wnt and FGF signaling in the Xenopus gastrula at TCF and Ets binding sites shows the importance of short-range repression by TCF in patterning the marginal zone.
2019,
Pubmed
,
Xenbase
Kjolby,
Genome-wide identification of Wnt/β-catenin transcriptional targets during Xenopus gastrulation.
2017,
Pubmed
,
Xenbase
Lin,
Reproductive periodicity, spawning induction, and larval metamorphosis of the hemichordate acorn worm Ptychodera flava.
2016,
Pubmed
Love,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
2014,
Pubmed
Marlétaz,
Amphioxus functional genomics and the origins of vertebrate gene regulation.
2018,
Pubmed
McLean,
GREAT improves functional interpretation of cis-regulatory regions.
2010,
Pubmed
Onai,
Canonical Wnt/β-catenin and Notch signaling regulate animal/vegetal axial patterning in the cephalochordate amphioxus.
2019,
Pubmed
Pires-daSilva,
The evolution of signalling pathways in animal development.
2003,
Pubmed
Putnam,
The amphioxus genome and the evolution of the chordate karyotype.
2008,
Pubmed
Quinlan,
BEDTools: a flexible suite of utilities for comparing genomic features.
2010,
Pubmed
Ramírez,
deepTools2: a next generation web server for deep-sequencing data analysis.
2016,
Pubmed
Ravasz,
Hierarchical organization of modularity in metabolic networks.
2002,
Pubmed
Royo,
Transphyletic conservation of developmental regulatory state in animal evolution.
2011,
Pubmed
Shannon,
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
2003,
Pubmed
Simakov,
Hemichordate genomes and deuterostome origins.
2015,
Pubmed
Tian,
Nodal signals pattern vertebrate embryos.
2006,
Pubmed
,
Xenbase
Tuazon,
Temporally coordinated signals progressively pattern the anteroposterior and dorsoventral body axes.
2015,
Pubmed
,
Xenbase
Yasuoka,
Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus.
2019,
Pubmed
,
Xenbase
Ye,
seqMINER: an integrated ChIP-seq data interpretation platform.
2011,
Pubmed
Zhang,
Model-based analysis of ChIP-Seq (MACS).
2008,
Pubmed
