Genetic basis for divergence in developmental gene expression in two closely related sea urchins

[1]  G. Wray,et al.  A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins , 2019, Evolution & development.

[2]  Hunter B. Fraser,et al.  Improving Estimates of Compensatory cis-trans Regulatory Divergence. , 2019, Trends in genetics : TIG.

[3]  Hunter B. Fraser,et al.  Improving Estimates of Compensatory cis-trans Regulatory Divergence. , 2019, Trends in genetics : TIG.

[4]  Isabelle S. Peter,et al.  Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids , 2018, Development.

[5]  C. Ettensohn,et al.  From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms , 2018, Genesis.

[6]  S. Nuzhdin,et al.  The Evolution of Gene Expression in cis and trans. , 2018, Trends in genetics : TIG.

[7]  Daniel E. Runcie,et al.  Uneven Distribution of Mutational Variance Across the Transcriptome of Drosophila serrata Revealed by High-Dimensional Analysis of Gene Expression , 2018, Genetics.

[8]  Nicola J. Rinaldi,et al.  Genetic effects on gene expression across human tissues , 2017, Nature.

[9]  M. Byrne,et al.  Australian Echinoderms: Biology, Ecology and Evolution , 2017 .

[10]  R. Raff,et al.  Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris , 2016, PLoS biology.

[11]  P. Wittkopp,et al.  Contrasting Frequencies and Effects of cis- and trans-Regulatory Mutations Affecting Gene Expression. , 2016, Molecular biology and evolution.

[12]  Jia L. Song,et al.  microRNA-31 modulates skeletal patterning in the sea urchin embryo , 2015, Development.

[13]  C. Balakrishnan,et al.  Gene Regulatory Evolution During Speciation in a Songbird , 2015, G3: Genes, Genomes, Genetics.

[14]  Matti Pirinen,et al.  Assessing allele-specific expression across multiple tissues from RNA-seq read data , 2015, Bioinform..

[15]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[16]  David L. Aylor,et al.  Analyses of Allele-Specific Gene Expression in Highly Divergent Mouse Crosses Identifies Pervasive Allelic Imbalance , 2015, Nature Genetics.

[17]  Wandrille Duchemin,et al.  HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species , 2015, BMC Bioinformatics.

[18]  Scott L. Allen,et al.  Pleiotropic Mutations Are Subject to Strong Stabilizing Selection , 2014, Genetics.

[19]  P. Wittkopp,et al.  Tempo and mode of regulatory evolution in Drosophila , 2014, Genome research.

[20]  D. McClay,et al.  Sub-circuits of a gene regulatory network control a developmental epithelial-mesenchymal transition , 2014, Development.

[21]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[22]  C. J. McManus,et al.  Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins , 2014, Development.

[23]  E. Davidson,et al.  New regulatory circuit controlling spatial and temporal gene expression in the sea urchin embryo oral ectoderm GRN. , 2013, Developmental biology.

[24]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[25]  D. McClay,et al.  Frizzled1/2/7 signaling directs β-catenin nuclearisation and initiates endoderm specification in macromeres during sea urchin embryogenesis , 2012, Development.

[26]  C. Ettensohn,et al.  The genomic regulatory control of skeletal morphogenesis in the sea urchin , 2012, Development.

[27]  Thomas M. Keane,et al.  Mouse genomic variation and its effect on phenotypes and gene regulation , 2011, Nature.

[28]  T. Lepage,et al.  Maternal Oct1/2 is required for Nodal and Vg1/Univin expression during dorsal-ventral axis specification in the sea urchin embryo. , 2011, Developmental biology.

[29]  Martin Goodson,et al.  Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. , 2011, Genome research.

[30]  T. Lepage,et al.  Ancestral Regulatory Circuits Governing Ectoderm Patterning Downstream of Nodal and BMP2/4 Revealed by Gene Regulatory Network Analysis in an Echinoderm , 2010, PLoS genetics.

[31]  C Joel McManus,et al.  Regulatory divergence in Drosophila revealed by mRNA-seq. , 2010, Genome research.

[32]  E. Davidson,et al.  Information processing at the foxa node of the sea urchin endomesoderm specification network , 2010, Proceedings of the National Academy of Sciences.

[33]  M. Kirkpatrick Patterns of quantitative genetic variation in multiple dimensions , 2009, Genetica.

[34]  Eric H Davidson,et al.  A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. , 2009, Developmental biology.

[35]  R. Raff,et al.  Nodal expression and heterochrony in the evolution of dorsal-ventral and left-right axes formation in the direct-developing sea urchin Heliocidaris erythrogramma. , 2008, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[36]  E. Davidson,et al.  Global regulatory logic for specification of an embryonic cell lineage , 2008, Proceedings of the National Academy of Sciences.

[37]  Andrew G Clark,et al.  Independent Effects of cis- and trans-regulatory Variation on Gene Expression in Drosophila melanogaster , 2008, Genetics.

[38]  F. Zito,et al.  Skeletogenesis by transfated secondary mesenchyme cells is dependent on extracellular matrix–ectoderm interactions in Paracentrotus lividus sea urchin embryos , 2007, Development, growth & differentiation.

[39]  Andrew R. Jackson,et al.  The Genome of the Sea Urchin Strongylocentrotus purpuratus , 2006, Science.

[40]  L. Kruglyak,et al.  Genetics of global gene expression , 2006, Nature Reviews Genetics.

[41]  R. Raff,et al.  Major regulatory factors in the evolution of development: the roles of goosecoid and Msx in the evolution of the direct‐developing sea urchin Heliocidaris erythrogramma , 2005, Evolution & development.

[42]  R. Raff,et al.  Dissociation of expression patterns of homeodomain transcription factors in the evolution of developmental mode in the sea urchins Heliocidaris tuberculata and H. erythrogramma , 2005, Evolution & development.

[43]  Eric H Davidson,et al.  SpHnf6, a transcription factor that executes multiple functions in sea urchin embryogenesis. , 2004, Developmental biology.

[44]  T. Lepage,et al.  Nodal and BMP2/4 signaling organizes the oral-aboral axis of the sea urchin embryo. , 2004, Developmental cell.

[45]  R. Raff,et al.  Evolution of OTP-independent larval skeleton patterning in the direct-developing sea urchin, Heliocidaris erythrogramma. , 2003, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[46]  Eric H Davidson,et al.  A regulatory gene network that directs micromere specification in the sea urchin embryo. , 2002, Developmental biology.

[47]  L. Hood,et al.  A Genomic Regulatory Network for Development , 2002, Science.

[48]  R. Angerer,et al.  Sea urchin goosecoid function links fate specification along the animal-vegetal and oral-aboral embryonic axes. , 2001, Development.

[49]  R. Raff,et al.  Novel gene expression patterns in hybrid embryos between species with different modes of development , 2000, Evolution & development.

[50]  R. Raff,et al.  A novel ontogenetic pathway in hybrid embryos between species with different modes of development. , 1999, Development.

[51]  R. Raff,et al.  Maternal factors and the evolution of developmental mode: Evolution of oogenesis in Heliocidaris erythrogramma , 1999, Development Genes and Evolution.

[52]  G. Wray Parallel Evolution of Nonfeeding Larvae in Echinoids , 1996 .

[53]  R. Emlet Larval spicules, cilia, and symmetry as remnants of indirect development in the direct developing sea urchin Heliocidaris erythrogramma. , 1995, Developmental biology.

[54]  R. Raff,et al.  Direct‐developing sea urchins and the evolutionary reorganization of early development , 1992, BioEssays : news and reviews in molecular, cellular and developmental biology.

[55]  R. Raff,et al.  The dorsoventral axis is specified prior to first cleavage in the direct developing sea urchin Heliocidaris erythrogramma. , 1990, Development.

[56]  R. Raff,et al.  Novel origins of lineage founder cells in the direct-developing sea urchin Heliocidaris erythrogramma. , 1990, Developmental biology.

[57]  R. Raff,et al.  Single-copy DNA distance between two congeneric sea urchin species exhibiting radically different modes of development. , 1990, Molecular biology and evolution.

[58]  R. Raff,et al.  Evolutionary modification of cell lineage in the direct-developing sea urchin Heliocidaris erythrogramma. , 1989, Developmental biology.

[59]  R. Raff,et al.  Molecular analysis of heterochronic changes in the evolution of direct developing sea urchins , 1988 .

[60]  R. Raff,et al.  Localization and expression of msp130, a primary mesenchyme lineage-specific cell surface protein in the sea urchin embryo. , 1987, Development.

[61]  R. Britten,et al.  Limited complexity of the RNA in micromeres of sixteen-cell sea urchin embryos. , 1980, Developmental biology.

[62]  R. Britten,et al.  RNA complexity in developing sea urchin oocytes. , 1979, Developmental biology.

[63]  B. Wold,et al.  Appearance and persistence of maternal RNA sequences in sea urchin development. , 1977, Developmental biology.

[64]  R. Raff Constraint, flexibility, and phylogenetic history in the evolution of direct development in sea urchins. , 1987, Developmental biology.

[65]  D. Anderson,et al.  The Reproductive System, Embryonic Development, Larval Development and Metamorphosis of the Sea Urchin Heliocidaris erythrogramma (Val.) (Echinoidea : Echinometridae) , 1975 .