Alx4 Relays Sequential FGF Signaling to Induce Lacrimal Gland Morphogenesis
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Leveraging Mouse Chromatin Data for Heritability Enrichment Informs Common Disease Architecture and Reveals Cortical Layer Contributions to Schizophrenia
Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Research Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia Paul W. Hook1 and Andrew S. McCallion1,2,3 1McKusick-Nathans Department of Genetic Medicine, 2Department of Comparative and Molecular Pathobiology, 3Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA Genome-wide association studies have implicated thousands of noncoding variants across common human phenotypes. However, they cannot directly inform the cellular context in which disease-associated variants act. Here, we use open chro- matin profiles from discrete mouse cell populations to address this challenge. We applied stratified linkage disequilibrium score regression and evaluated heritability enrichment in 64 genome-wide association studies, emphasizing schizophrenia. We provide evidence that mouse-derived human open chromatin profiles can serve as powerful proxies for difficult to ob- tain human cell populations, facilitating the illumination of common disease heritability enrichment across an array of hu- man phenotypes. We demonstrate that signatures from discrete subpopulations of cortical excitatory and inhibitory neurons are significantly enriched for schizophrenia heritability with maximal enrichment in cortical layer V excitatory neu- rons. We also show that differences between schizophrenia and bipolar disorder are concentrated in excitatory neurons in cortical layers II-III, IV, and V, as well as the dentate gyrus. Finally, we leverage these data to fine-map variants in 177 schiz- ophrenia loci nominating variants in 104/177. We integrate these data with transcription factor binding site, chromatin in- teraction, and validated enhancer data, placing variants in the cellular context where they may modulate risk. -
Original Articles the ALX4 Homeobox Gene Is Mutated in Patients With
916 J Med Genet 2000;37:916–920 J Med Genet: first published as 10.1136/jmg.37.12.916 on 1 December 2000. Downloaded from Original articles The ALX4 homeobox gene is mutated in patients with ossification defects of the skull (foramina parietalia permagna, OMIM 168500) Wim Wuyts, Erna Cleiren, Tessa Homfray, Alberto Rasore-Quartino, Filip Vanhoenacker, Wim Van Hul Abstract Foramina parietalia permagna (FPP) (OMIM 168500) is caused by ossification defects in the parietal bones. Recently, it was shown that loss of function mutations in the MSX2 homeobox gene on chromo- some 5 are responsible for the presence of these lesions in some FPP patients. How- ever, the absence of MSX2 mutations in some of the FPP patients analysed and the presence of FPP associated with chromo- some 11p deletions in DEFECT 11 (OMIM 601224) patients or associated with Saethre-Chotzen syndrome suggests ge- netic heterogeneity for this disorder. Starting from a BAC/P1/cosmid contig of the DEFECT 11 region on chromosome 11, we have now isolated the ALX4 gene, a previously unidentified member of the http://jmg.bmj.com/ ALX homeobox gene family in humans. Mutation analysis of the ALX4 gene in three unrelated FPP families without the Department of MSX2 mutation identified mutations in Medical Genetics, two families, indicating that mutations in University of Antwerp, Figure 1 Radiograph illustrating the presence of foramina ALX4 could be responsible for these skull parietalia permagna (white arrows) in a patient of family Universiteitsplein 1, 6 12 2610 Antwerp, Belgium defects and suggesting further genetic 3. X rays of patients of families 1 and 2 have previously been published. -
134 Mb (Almost the Same As the Size of Chromosome 10). It Is ~4–4.5% of the Total Human Genome
Chromosome 11 ©Chromosome Disorder Outreach Inc. (CDO) Technical genetic content provided by Dr. Iosif Lurie, M.D. Ph.D Medical Geneticist and CDO Medical Consultant/Advisor. Ideogram courtesy of the University of Washington Department of Pathology: ©1994 David Adler.hum_11.gif Introduction The genetic size of chromosome 11 is ~134 Mb (almost the same as the size of chromosome 10). It is ~4–4.5% of the total human genome. The length of its short arm is ~50 Mb; the length of its long arm in ~84 Mb. Chromosome 11 is a very gene–rich area. It contains ~1,500 genes. Mutations of ~200 of these genes are known to cause birth defects or some functional abnormalities. The short arm of chromosome 11 contains a region which is known to be imprinted. As a result duplications of this region will have different manifestations depending on the sex of the parent responsible for this defect. Phenotypes of persons with duplications of the maternal origin will be different from the phenotypes of the persons with a paternal duplication of the same area. There are ~1,400 patients with different structural abnormalities of chromosome 11 as the only abnormality or in association with abnormalities for other chromosomes. At least 800 of these patients had different deletions of chromosome 11. Deletions of the short arm have been reported in ~250 patients (including those with an additional imbalance); deletions of the long arm have been described in ~550 patients. There are two syndromes caused by deletions of the short arm (both of these syndromes have been known for several years) and one well–known syndrome caused by distal deletions of the long arm (Jacobsen syndrome). -
Aristaless-Like Homeobox Protein 1 (ALX1) Variant Associated with Craniofacial Structure and Frontonasal Dysplasia in Burmese Cats
Developmental Biology 409 (2016) 451–458 Contents lists available at ScienceDirect Developmental Biology journal homepage: www.elsevier.com/locate/developmentalbiology Aristaless-Like Homeobox protein 1 (ALX1) variant associated with craniofacial structure and frontonasal dysplasia in Burmese cats Leslie A. Lyons a,f,n, Carolyn A. Erdman b,f, Robert A. Grahn c,f, Michael J. Hamilton d,f, Michael J. Carter e,f, Christopher R. Helps g, Hasan Alhaddad h, Barbara Gandolfi a,f a Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, MO 65211, USA b Department of Psychiatry, University of California-San Francisco, San Francisco, CA 94143, USA c Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 96516, USA d Department of Cell Biology and Neuroscience, Institute for Integrative Genome Biology, Center for Disease Vector Research, University of California-Riv- erside, Riverside, CA 92521, USA e MDxHealth Inc, 15279 Alton Parkway, Suite #100, Irvine, CA 92618, USA f Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95776, USA g Langford Veterinary Services, University of Bristol, Bristol BS40 5DU, UK h College of Science, Kuwait University, Safat, Kuwait article info abstract Article history: Frontonasal dysplasia (FND) can have severe presentations that are medically and socially debilitating. Received 2 October 2015 Several genes are implicated in FND conditions, including Aristaless-Like Homeobox 1 (ALX1), which is Received in revised form associated with FND3. Breeds of cats are selected and bred for extremes in craniofacial morphologies. In 3 November 2015 particular, a lineage of Burmese cats with severe brachycephyla is extremely popular and is termed Accepted 20 November 2015 Contemporary Burmese. -
Genetic Interaction of Gli3 and Alx4 During Limb Development
Int. J. Dev. Biol. 49: 443-448 (2005) doi: 10.1387/ijdb.051984lp Short Communication Genetic interaction of Gli3 and Alx4 during limb development LIA PANMAN*,a, THIJS DRENTHb, PASCAL TEWELSCHERc, AIMÉE ZUNIGA1 and ROLF ZELLER1 Department of Developmental Biology, Utrecht University, Utrecht, The Netherlands and 1Developmental Genetics, DKBW Centre for Biomedicine, University of Basel Medical School, Basel, Switzerland. ABSTRACT The Gli3 and Alx4 transcriptional regulators are expressed in the anterior limb bud mesenchyme and their disruption in mice results in preaxial polydactyly. While the polydactylous phenotype of Alx4 deficient limb buds depends on SHH, the one of Gli3 deficient limb buds is completely independent of SHH signalling, suggesting that these genes act in parallel pathways. Analysis of limb buds lacking both Gli3 and Alx4 now shows that these two genes interact during limb skeletal morphogenesis. In addition to the defects in single mutants, the stylopod is severely malformed and the anterior element of the zeugopod is lost in double mutant limbs. However, limb bud patterning in Gli3-/- ; Alx4-/- double mutant embryos is not affected more than in single mutants as the expression domains of key regulators remain the same. Most interestingly, the loss of the severe preaxial polydactyly characteristic of Gli3 -/- limbs in double mutant embryos establishes that this type of polydactyly requires Alx4 function. KEY WORDS: Hox gene, limb development, preaxial polydactyly, radius, SHH, tibia The semi-dominant mouse mutations Extra-toes ( Xt ) and Strong’s forms in limbs lacking both Alx4 and Shh (for details see te Luxoid (Lst ), are loss-of-function mutations disrupting the zinc- Welscher et al., 2002b). -
Transcriptomic and Epigenomic Characterization of the Developing Bat Wing
ARTICLES OPEN Transcriptomic and epigenomic characterization of the developing bat wing Walter L Eckalbar1,2,9, Stephen A Schlebusch3,9, Mandy K Mason3, Zoe Gill3, Ash V Parker3, Betty M Booker1,2, Sierra Nishizaki1,2, Christiane Muswamba-Nday3, Elizabeth Terhune4,5, Kimberly A Nevonen4, Nadja Makki1,2, Tara Friedrich2,6, Julia E VanderMeer1,2, Katherine S Pollard2,6,7, Lucia Carbone4,8, Jeff D Wall2,7, Nicola Illing3 & Nadav Ahituv1,2 Bats are the only mammals capable of powered flight, but little is known about the genetic determinants that shape their wings. Here we generated a genome for Miniopterus natalensis and performed RNA-seq and ChIP-seq (H3K27ac and H3K27me3) analyses on its developing forelimb and hindlimb autopods at sequential embryonic stages to decipher the molecular events that underlie bat wing development. Over 7,000 genes and several long noncoding RNAs, including Tbx5-as1 and Hottip, were differentially expressed between forelimb and hindlimb, and across different stages. ChIP-seq analysis identified thousands of regions that are differentially modified in forelimb and hindlimb. Comparative genomics found 2,796 bat-accelerated regions within H3K27ac peaks, several of which cluster near limb-associated genes. Pathway analyses highlighted multiple ribosomal proteins and known limb patterning signaling pathways as differentially regulated and implicated increased forelimb mesenchymal condensation in differential growth. In combination, our work outlines multiple genetic components that likely contribute to bat wing formation, providing insights into this morphological innovation. The order Chiroptera, commonly known as bats, is the only group of To characterize the genetic differences that underlie divergence in mammals to have evolved the capability of flight. -
Genome-Wide Identification of Signaling Center Enhancers in the Developing Limb Julia E
© 2014. Published by The Company of Biologists Ltd | Development (2014) 141, 4194-4198 doi:10.1242/dev.110965 RESEARCH REPORT TECHNIQUES AND RESOURCES Genome-wide identification of signaling center enhancers in the developing limb Julia E. VanderMeer1,2, Robin P. Smith1,2, Stacy L. Jones1 and Nadav Ahituv1,2,* ABSTRACT signaling center required for the maintenance of the other [reviewed The limb is widely used as a model developmental system and changes by Zeller et al. (2009)]. to gene expression patterns in its signaling centers, notably the zone of Gene expression changes in signaling centers are known to affect polarizing activity (ZPA) and the apical ectodermal ridge (AER), are limb morphology. As the genes involved in the ZPA and AER are known to cause limb malformations and evolutionary differences in limb also expressed in other tissues, mutations in coding regions usually morphology. Although several genes that define these limb signaling cause additional phenotypes. Mutations in enhancers that are centers have been described, the identification of regulatory elements specific to these limb-signaling centers, however, only cause limb that are active within these centers has been limited. By dissecting phenotypes. For example, mutations in the ZPA regulatory mouse E11.5 limbs that fluorescently mark the ZPA or AER, followed by sequence (ZRS) enhancer that controls expression of Shh in the fluorescence-activated cell sorting and low-cell H3K27ac ChIP-seq, ZPA are known to cause isolated limb malformations in humans, we identified thousands of specific signaling-center enhancers. mice, cats and dogs, without any other phenotypes caused by coding Our ChIP-seq datasets show strong correlation with ZPA- and AER- disruptions to Shh [reviewed by VanderMeer and Ahituv (2011)]. -
Construction of a Natural Panel of 11P11.2 Deletions and Further Delineation of the Critical Region Involved in Potocki–Shaffer Syndrome
European Journal of Human Genetics (2005) 13, 528–540 & 2005 Nature Publishing Group All rights reserved 1018-4813/05 $30.00 www.nature.com/ejhg ARTICLE Construction of a natural panel of 11p11.2 deletions and further delineation of the critical region involved in Potocki–Shaffer syndrome Keiko Wakui1,12, Giuliana Gregato2,3,12, Blake C Ballif2, Caron D Glotzbach2,4, Kristen A Bailey2,4, Pao-Lin Kuo5, Whui-Chen Sue6, Leslie J Sheffield7, Mira Irons8, Enrique G Gomez9, Jacqueline T Hecht10, Lorraine Potocki1,11 and Lisa G Shaffer*,2,4 1Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA; 2Health Research and Education Center, Washington State University, Spokane, WA, USA; 3Dip. Patologia Umana ed Ereditaria, Sez. Biologia Generale e Genetica Medica, Universita` degli Studi di Pavia, Italy; 4Sacred Heart Medical Center, Spokane, WA, USA; 5Department of Obstetrics and Gynecology, National Cheng-Kung University Medical College, Taiwan; 6Department of Pediatrics, Taipei Municipal Women and Children’s Hospital, Taiwan; 7Genetic Health Services Victoria, Murdoch Children’s Research Institute, Department of Paediatrics, University of Melbourne, Victoria, Australia; 8Division of Genetics, Department of Medicine, Children’s Hospital, Harvard Medical School, Boston, MA, USA; 9Area de Gene´tica, Centro de Desarrollo Infantil y Departamento de Pediatrı´a Hospital Materno Infantil-Hospital Regional Universitario ‘Infanta Cristina’, Badajoz, Spain; 10Department of Pediatrics, University of Texas Medical School at Houston, TX, USA; 11Texas Children’s Hospital, Houston, TX, USA Potocki–Shaffer syndrome (PSS) is a contiguous gene deletion syndrome that results from haploinsufficiency of at least two genes within the short arm of chromosome 11[del(11)(p11.2p12)]. -
Identification of Shared and Unique Gene Families Associated with Oral
International Journal of Oral Science (2017) 9, 104–109 OPEN www.nature.com/ijos ORIGINAL ARTICLE Identification of shared and unique gene families associated with oral clefts Noriko Funato and Masataka Nakamura Oral clefts, the most frequent congenital birth defects in humans, are multifactorial disorders caused by genetic and environmental factors. Epidemiological studies point to different etiologies underlying the oral cleft phenotypes, cleft lip (CL), CL and/or palate (CL/P) and cleft palate (CP). More than 350 genes have syndromic and/or nonsyndromic oral cleft associations in humans. Although genes related to genetic disorders associated with oral cleft phenotypes are known, a gap between detecting these associations and interpretation of their biological importance has remained. Here, using a gene ontology analysis approach, we grouped these candidate genes on the basis of different functional categories to gain insight into the genetic etiology of oral clefts. We identified different genetic profiles and found correlations between the functions of gene products and oral cleft phenotypes. Our results indicate inherent differences in the genetic etiologies that underlie oral cleft phenotypes and support epidemiological evidence that genes associated with CL/P are both developmentally and genetically different from CP only, incomplete CP, and submucous CP. The epidemiological differences among cleft phenotypes may reflect differences in the underlying genetic causes. Understanding the different causative etiologies of oral clefts is -
Hedgehog Signaling Patterns the Oral- Aboral Axis of the Mandibular Arch
RESEARCH ARTICLE Hedgehog signaling patterns the oral- aboral axis of the mandibular arch Jingyue Xu1, Han Liu1, Yu Lan1,2,3,4, Mike Adam1, David E Clouthier5, Steven Potter1,3, Rulang Jiang1,2,3,4* 1Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, United States; 2Division of Plastic Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, United States; 3Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, United States; 4Shriners Hospitals for Children – Cincinnati, Cincinnati, United States; 5Department of Craniofacial Biology, School of Dental Medicine, Anschutz Medical Campus, University of Colorado, Aurora, United States Abstract Development of vertebrate jaws involves patterning neural crest-derived mesenchyme cells into distinct subpopulations along the proximal-distal and oral-aboral axes. Although the molecular mechanisms patterning the proximal-distal axis have been well studied, little is known regarding the mechanisms patterning the oral-aboral axis. Using unbiased single-cell RNA-seq analysis followed by in situ analysis of gene expression profiles, we show that Shh and Bmp4 signaling pathways are activated in a complementary pattern along the oral-aboral axis in mouse embryonic mandibular arch. Tissue-specific inactivation of hedgehog signaling in neural crest- derived mandibular mesenchyme led to expansion of BMP signaling activity to throughout the oral- aboral axis of the distal mandibular arch and subsequently duplication of dentary bone in the oral side of the mandible at the expense of tongue formation. Further studies indicate that hedgehog signaling acts through the Foxf1/2 transcription factors to specify the oral fate and pattern the oral-aboral axis of the mandibular mesenchyme. -
Cpg Island Hypermethylation in Human Astrocytomas
Published OnlineFirst March 16, 2010; DOI: 10.1158/0008-5472.CAN-09-3631 Molecular and Cellular Pathobiology Cancer Research CpG Island Hypermethylation in Human Astrocytomas Xiwei Wu2, Tibor A. Rauch3, Xueyan Zhong1, William P. Bennett1, Farida Latif4, Dietmar Krex5, and Gerd P. Pfeifer1 Abstract Astrocytomas are common and lethal human brain tumors. We have analyzed the methylation status of over 28,000 CpG islands and 18,000 promoters in normal human brain and in astrocytomas of various grades using the methylated CpG island recovery assay. We identified 6,000 to 7,000 methylated CpG islands in normal human brain. Approximately 5% of the promoter-associated CpG islands in the normal brain are methylated. Promoter CpG island methylation is inversely correlated whereas intragenic methylation is directly correlated with gene expression levels in brain tissue. In astrocytomas, several hundred CpG islands undergo specific hy- permethylation relative to normal brain with 428 methylation peaks common to more than 25% of the tumors. Genes involved in brain development and neuronal differentiation, such as BMP4, POU4F3, GDNF, OTX2, NEFM, CNTN4, OTP, SIM1, FYN, EN1, CHAT, GSX2, NKX6-1, PAX6, RAX, and DLX2, were strongly enriched among genes frequently methylated in tumors. There was an overrepresentation of homeobox genes and 31% of the most commonly methylated genes represent targets of the Polycomb complex. We identified several chromosomal loci in which many (sometimes more than 20) consecutive CpG islands were hypermethylated in tumors. Seven such loci were near homeobox genes, including the HOXC and HOXD clusters, and the BARHL2, DLX1,and PITX2 genes. Two other clusters of hypermethylated islands were at sequences of recent gene duplication events. -
Mutual Genetic Antagonism Involving GLI3 and Dhand Prepatterns the Vertebrate Limb Bud Mesenchyme Prior to SHH Signaling
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION Mutual genetic antagonism posterior AER are activated prior to SHH signaling (Zuniga et al. 1999), similarly to other posterior genes involving GLI3 and dHAND such as 5ЈHoxD genes (Kraus et al. 2001). These studies prepatterns the vertebrate indicate that the nascent limb bud mesenchyme is al- ready prepatterned (Chiang et al. 2001) and that the mes- limb bud mesenchyme prior enchymal responsiveness to polarizing region signals is established prior to SHH activation. However, little is to SHH signaling known about the mechanism acting upstream of SHH Pascal te Welscher,1 Marian Fernandez-Teran,2 signaling to polarize the limb field and early limb bud. 2 1,3 Several studies suggest a possible combinatorial involve- Marian A. Ros, and Rolf Zeller ment of Hox genes in positioning and polarizing the 1Department of Developmental Biology, Faculty of Biology, early limb field in response to retinoic acid (Lu et al. Utrecht University, 3584CH Utrecht, The Netherlands; 1997). In particular, anterior ectopic expression of Hoxb8 2Department of Anatomy and Cell Biology, Facultad de in forelimb buds of transgenic mouse embryos results in Medicina, Universidad de Cantabria, 39011 Santander, Spain establishment of an ectopic polarizing region and mirror image duplication of distal limb structures (Charité et al. The bHLH transcription factor dHAND is required for 1994). However, neither targeted inactivation of the establishment of SHH signaling by the limb bud orga- Hoxb8 gene (van den Akker et al. 1999) nor deletion of all Hox8 paralogs in the mouse alters limb morphogen- nizerin posteriormesenchyme,a step crucialto devel- esis (van den Akker et al.