ECB-ART-48434
BMC Genomics
2018 Nov 03;191:795. doi: 10.1186/s12864-018-5186-8.
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Transcriptome analysis of Xenopus orofacial tissues deficient in retinoic acid receptor function.
Wahl SE
,
Wyatt BH
,
Turner SD
,
Dickinson AJG
.
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BACKGROUND: Development of the face and mouth is orchestrated by a large number of transcription factors, signaling pathways and epigenetic regulators. While we know many of these regulators, our understanding of how they interact with each other and implement changes in gene expression during orofacial development is still in its infancy. Therefore, this study focuses on uncovering potential cooperation between transcriptional regulators and one important signaling pathway, retinoic acid, during development of the midface. RESULTS: Transcriptome analyses was performed on facial tissues deficient for retinoic acid receptor function at two time points in development; early (35 hpf) just after the neural crest migrates and facial tissues are specified and later (60 hpf) when the mouth has formed and facial structures begin to differentiate. Functional and network analyses revealed that retinoic acid signaling could cooperate with novel epigenetic factors and calcium-NFAT signaling during early orofacial development. At the later stage, retinoic acid may work with WNT and BMP and regulate homeobox containing transcription factors. Finally, there is an overlap in genes dysregulated in Xenopus embryos with median clefts with human genes associated with similar orofacial defects. CONCLUSIONS: This study uncovers novel signaling pathways required for orofacial development as well as pathways that could interact with retinoic acid signaling during the formation of the face. We show that frog faces are an important tool for studying orofacial development and birth defects.
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F32 HD091977 NICHD NIH HHS , R01 DE023553 NIDCR NIH HHS, 1F32HD091977-01 Eunice Kennedy Shriver National Institute of Child Health and Human Development, 5R01DE023553-04 National Institute of Dental and Craniofacial Research
Genes referenced: LOC115925415 LOC590859 rarb
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References [+] :
Abe,
Retinoic acid affects craniofacial patterning by changing Fgf8 expression in the pharyngeal ectoderm.
2008, Pubmed
Abe, Retinoic acid affects craniofacial patterning by changing Fgf8 expression in the pharyngeal ectoderm. 2008, Pubmed
Ackermans, Vitamin A and clefting: putative biological mechanisms. 2011, Pubmed
Amann, Regulation of gene expression by retinoids. 2011, Pubmed
Anders, Differential expression analysis for sequence count data. 2010, Pubmed
Angrisano, Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells. 2011, Pubmed
Arima, Global analysis of RAR-responsive genes in the Xenopus neurula using cDNA microarrays. 2005, Pubmed
Ashburner, Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. 2000, Pubmed
Bajpai, CHD7 cooperates with PBAF to control multipotent neural crest formation. 2010, Pubmed
Balikova, FOXD1 Duplication Causes Branchial Defects and Interacts with the TFAP2A Gene Implicated in the Branchio-Oculo-Facial Syndrome in Causing Eye Effects in Zebrafish. 2010, Pubmed
Barrett, NCBI GEO: archive for functional genomics data sets--update. 2013, Pubmed
Bernier, Disruptive CHD8 mutations define a subtype of autism early in development. 2014, Pubmed
Beverdam, Severe nasal clefting and abnormal embryonic apoptosis in Alx3/Alx4 double mutant mice. 2001, Pubmed
Billington, Impact of retinoic acid exposure on midfacial shape variation and manifestation of holoprosencephaly in Twsg1 mutant mice. 2015, Pubmed
Brickell, Retinoic acid and retinoic acid receptors in craniofacial development. 1997, Pubmed
Brugmann, Wnt signaling mediates regional specification in the vertebrate face. 2007, Pubmed
Chen, Small molecule-mediated disruption of Wnt-dependent signaling in tissue regeneration and cancer. 2009, Pubmed
Chen, Mouth development. 2017, Pubmed
Chiquet, Variation in WNT genes is associated with non-syndromic cleft lip with or without cleft palate. 2008, Pubmed
Crabtree, NFAT signaling: choreographing the social lives of cells. 2002, Pubmed
Cunningham, Mechanisms of retinoic acid signalling and its roles in organ and limb development. 2015, Pubmed
Cunningham, Early molecular events during retinoic acid induced differentiation of neuromesodermal progenitors. 2016, Pubmed
Curtin, Zebrafish wnt9a is expressed in pharyngeal ectoderm and is required for palate and lower jaw development. 2011, Pubmed
Delacroix, Cell-specific interaction of retinoic acid receptors with target genes in mouse embryonic fibroblasts and embryonic stem cells. 2010, Pubmed
Dessau, [''R"--project for statistical computing]. 2008, Pubmed
Dickinson, Using frogs faces to dissect the mechanisms underlying human orofacial defects. 2016, Pubmed
Dickinson, The Wnt antagonists Frzb-1 and Crescent locally regulate basement membrane dissolution in the developing primary mouth. 2009, Pubmed
Dobin, STAR: ultrafast universal RNA-seq aligner. 2013, Pubmed
Dougherty, Distinct requirements for wnt9a and irf6 in extension and integration mechanisms during zebrafish palate morphogenesis. 2013, Pubmed
Dubey, Generating retinoic acid gradients by local degradation during craniofacial development: One cell's cue is another cell's poison. 2018, Pubmed
Duester, Retinoic acid synthesis and signaling during early organogenesis. 2008, Pubmed
Dupé, Retinoic acid receptors exhibit cell-autonomous functions in cranial neural crest cells. 2009, Pubmed
Eissenberg, Structural biology of the chromodomain: form and function. 2012, Pubmed
Fogelgren, Misexpression of Six2 is associated with heritable frontonasal dysplasia and renal hypoplasia in 3H1 Br mice. 2008, Pubmed
Francescatto, The activation of membrane targeted CaMK-II in the zebrafish Kupffer's vesicle is required for left-right asymmetry. 2010, Pubmed
Fukasawa, Mediator complex cooperatively regulates transcription of retinoic acid target genes with Polycomb Repressive Complex 2 during neuronal differentiation. 2015, Pubmed
Ge, [Role of Ezh2 in the all-trans retinoic acid induced P19 neural differentiation]. 2009, Pubmed
Gibbons, Alpha thalassaemia-mental retardation, X linked. 2006, Pubmed
Graef, NFAT signaling in vertebrate development. 2001, Pubmed
Guzman-Ayala, Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast. 2015, Pubmed
Helms, New insights into craniofacial morphogenesis. 2005, Pubmed
Henn, SIX2 gene haploinsufficiency leads to a recognizable phenotype with ptosis, frontonasal dysplasia, and conductive hearing loss. 2018, Pubmed
Ho, Chromatin remodelling during development. 2010, Pubmed
Hogan, Transcriptional regulation by calcium, calcineurin, and NFAT. 2003, Pubmed
Hu, Retinoic acid alters the proliferation and survival of the epithelium and mesenchyme and suppresses Wnt/β-catenin signaling in developing cleft palate. 2013, Pubmed
Huang, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. 2009, Pubmed
Huang, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. 2009, Pubmed
Huang, The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. 2007, Pubmed
Hufnagel, A new frontonasal dysplasia syndrome associated with deletion of the SIX2 gene. 2016, Pubmed
Ignatius, Distinct functional and temporal requirements for zebrafish Hdac1 during neural crest-derived craniofacial and peripheral neuron development. 2013, Pubmed
Inman, Interaction between Foxc1 and Fgf8 during mammalian jaw patterning and in the pathogenesis of syngnathia. 2013, Pubmed
Iwata, The mechanism of TGF-β signaling during palate development. 2011, Pubmed
Kanehisa, KEGG: kyoto encyclopedia of genes and genomes. 2000, Pubmed
Kao, Calcineurin/NFAT signaling is required for neuregulin-regulated Schwann cell differentiation. 2009, Pubmed
Karimi, Xenbase: a genomic, epigenomic and transcriptomic model organism database. 2018, Pubmed , Echinobase
Kashyap, Epigenomic reorganization of the clustered Hox genes in embryonic stem cells induced by retinoic acid. 2011, Pubmed
Kennedy, Quantification of orofacial phenotypes in Xenopus. 2014, Pubmed
Kennedy, Median facial clefts in Xenopus laevis: roles of retinoic acid signaling and homeobox genes. 2012, Pubmed
Kim, Selective induction of cyclin-dependent kinase inhibitors and their roles in cell cycle arrest caused by trichostatin A, an inhibitor of histone deacetylase. 1999, Pubmed
Klingenberg, MorphoJ: an integrated software package for geometric morphometrics. 2011, Pubmed
Kumar, Nuclear receptor corepressors Ncor1 and Ncor2 (Smrt) are required for retinoic acid-dependent repression of Fgf8 during somitogenesis. 2016, Pubmed
Laursen, Polycomb recruitment attenuates retinoic acid-induced transcription of the bivalent NR2F1 gene. 2013, Pubmed
Lee, Noggin and retinoic acid transform the identity of avian facial prominences. 2002, Pubmed
Liao, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. 2014, Pubmed
Liu, Distinct functions for Bmp signaling in lip and palate fusion in mice. 2005, Pubmed
Lohnes, Function of the retinoic acid receptors (RARs) during development (I). Craniofacial and skeletal abnormalities in RAR double mutants. 1994, Pubmed
Love, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. 2014, Pubmed
Lu, Variations in WNT3 gene are associated with incidence of non-syndromic cleft lip with or without cleft palate in a northeast Chinese population. 2015, Pubmed
Lu, Inactivation of NuRD component Mta2 causes abnormal T cell activation and lupus-like autoimmune disease in mice. 2008, Pubmed
MacDonnell, CaMKII negatively regulates calcineurin-NFAT signaling in cardiac myocytes. 2009, Pubmed
Mark, Retinoic acid signalling in the development of branchial arches. 2004, Pubmed
Medio, Wnt/β-catenin signaling and Msx1 promote outgrowth of the maxillary prominences. 2012, Pubmed
Menezes, Studies with Wnt genes and nonsyndromic cleft lip and palate. 2010, Pubmed
Myers, BMP-mediated specification of the erythroid lineage suppresses endothelial development in blood island precursors. 2013, Pubmed
Myers, Use of small molecule inhibitors of the Wnt and Notch signaling pathways during Xenopus development. 2014, Pubmed
Møller, Truncation of the Down syndrome candidate gene DYRK1A in two unrelated patients with microcephaly. 2008, Pubmed
Nie, BMP signalling in craniofacial development. 2006, Pubmed
Niederreither, Retinoic acid in development: towards an integrated view. 2008, Pubmed
Niemann, Homozygous WNT3 mutation causes tetra-amelia in a large consanguineous family. 2004, Pubmed
Pillai, Histone deacetylase 1 (HDAC-1) required for the normal formation of craniofacial cartilage and pectoral fins of the zebrafish. 2004, Pubmed
Rao, Signaling to gene expression: calcium, calcineurin and NFAT. 2009, Pubmed
Ronan, Familial 4.3 Mb duplication of 21q22 sheds new light on the Down syndrome critical region. 2007, Pubmed
Rothschild, Differential expression of CaMK-II genes during early zebrafish embryogenesis. 2007, Pubmed
Rothschild, Tbx5-mediated expression of Ca(2+)/calmodulin-dependent protein kinase II is necessary for zebrafish cardiac and pectoral fin morphogenesis. 2009, Pubmed
Rothschild, CaMK-II is a PKD2 target that promotes pronephric kidney development and stabilizes cilia. 2011, Pubmed
Samarut, Nuclear retinoic acid receptors: conductors of the retinoic acid symphony during development. 2012, Pubmed
Schneider, Local retinoid signaling coordinates forebrain and facial morphogenesis by maintaining FGF8 and SHH. 2001, Pubmed
Shitasako, Wnt and Shh signals regulate neural stem cell proliferation and differentiation in the optic tectum of adult zebrafish. 2017, Pubmed
Slusarski, Calcium signaling in vertebrate embryonic patterning and morphogenesis. 2007, Pubmed
Song, Lrp6-mediated canonical Wnt signaling is required for lip formation and fusion. 2009, Pubmed
Suzuki, Mutations in BMP4 are associated with subepithelial, microform, and overt cleft lip. 2009, Pubmed
Suzuki, Molecular mechanisms of midfacial developmental defects. 2016, Pubmed
Szabo-Rogers, New directions in craniofacial morphogenesis. 2010, Pubmed
Urvalek, Retinoic acid and histone deacetylases regulate epigenetic changes in embryonic stem cells. 2014, Pubmed
Usami, Wnt signaling in cartilage development and diseases: lessons from animal studies. 2016, Pubmed
Valetto, Molecular cytogenetic characterization of an interstitial deletion of chromosome 21 (21q22.13q22.3) in a patient with dysmorphic features, intellectual disability and severe generalized epilepsy. 2012, Pubmed
Wahl, The role of folate metabolism in orofacial development and clefting. 2015, Pubmed
Wang, The Proto-oncogene Transcription Factor Ets1 Regulates Neural Crest Development through Histone Deacetylase 1 to Mediate Output of Bone Morphogenetic Protein Signaling. 2015, Pubmed
Wedden, Pattern formation in the facial primordia. 1988, Pubmed
Wehner, Restoration of anatomical continuity after spinal cord transection depends on Wnt/β-catenin signaling in larval zebrafish. 2018, Pubmed
Yoshida, Calcineurin inhibitors block dorsal-side signaling that affect late-stage development of the heart, kidney, liver, gut and somitic tissue during Xenopus embryogenesis. 2004, Pubmed
Yu, BMP type I receptor inhibition reduces heterotopic [corrected] ossification. 2008, Pubmed
Yuan, The Key Role of Canonical Wnt/β-catenin Signaling in Cartilage Chondrocytes. 2016, Pubmed
Zentner, Molecular and phenotypic aspects of CHD7 mutation in CHARGE syndrome. 2010, Pubmed
Zhu, Comparison of phenotypic and global gene expression changes in Xenopus tropicalis embryos induced by agonists of RAR and RXR. 2017, Pubmed