Dhand in Hand with Gli3

Total Page:16

File Type:pdf, Size:1020Kb

Dhand in Hand with Gli3 HIGHLIGHTS GENE MAPPING mapping studies. This is why Singer the paternal meiotic contribution, and colleagues have embarked on a can be routinely generated in project to construct a meiotic map of zebrafish. Singer et al.generated 94 the male zebrafish (Danio rerio), using such embryos from a father who was Inequality of the sexes the genetic trickery that only these fish heterozygous for many polymorphic can offer. The result — that male markers. The haploid embryos were zebrafish recombine about three times genotyped at 185 of these markers, It’s no secret that there are differences less frequently than females — can be which were then placed on the male in how males and females behave, and put to good use in designing experi- meiotic map. The result was unam- it’s no less of a secret among geneticists ments. biguous: across the 25 chromosomes, that these differences often extend all The map that the authors have the male map is strikingly condensed the way to their chromosomes. When constructed is based on the recombi- (especially at the centromere), com- it comes to the rate at which homolo- nation frequency that occurs during pared with a previously generated gous chromosomes recombine during male meiosis. This is the equivalent of female meiotic map made with the meiosis, for instance, one sex can looking at how well genetic markers same markers; the sex-average map outdo the other severalfold. The rela- have been reshuffled on single sperm lies almost exactly in-between. tive recombination rates in the two derived from a parent that is het- So, what can we do now that we sexes aren’t always easy to quantify — erozygous at many loci. Although couldn’t do before? As zebrafish genetic maps are often averaged across such a direct experiment is beyond continues to raise its profile as an males and females — but such knowl- our current means, androgenetic experimental model for vertebrates, edge has useful implications for gene- haploid embryos, which contain only efficient gene mapping is becoming DEVELOPMENTAL BIOLOGY asymmetry, te Welscher and colleagues looked at a transcription factor, dHand, because it is required to establish Shh signalling and because its initially uniform dHand in hand with Gli3 expression becomes restricted to the posterior of the limb bud just before Shh activation — but how? The authors How vertebrate limbs are formed is reasoned that answering this question considered one of the better understood would provide information about the Limb bud processes in development. It is generally earliest events in limb bud patterning. accepted that the early patterning of a Shh is repressed in the anterior of the Anterior vertebrate limb requires a feedback loop limb bud by another transcription factor, between sonic hedgehog (Shh) and Gli3. The authors found that, unlike in fibroblast growth factor (Fgf) signals. But wild-type mice, dHand is expressed in the the limb bud is already patterned before anterior mesenchyme of Gli3-deficient Gli3 this feedback loop is established, and the limbs, which suggests that dHand is molecules responsible for this have until repressed by Gli3. In the posterior limb now remained unknown. New work by bud mesenchyme, Gli3 is in turn repressed Alx4 te Welscher and colleagues shows that the by dHand. earlier patterning results from a mutual How do these early events relate to the antagonism between two transcription Shh/Fgf-mediated patterning? As both factors — dHand and Gli3 — and that this Gremlin and the Fgfs are expressed before dHand interaction participates in positioning the Shh, the authors looked at their expression Shh/Fgf signalling feedback loop. in Gli3-deficient mice. It turns out that During limb development, Shh signalling Gli3 is required to repress Gremlin and from the posterior mesenchyme regulates Fgf4 in the anterior limb bud. The authors Shh Fgfs Fgf expression in the apical ectodermal argue that the anterior expansion of ridge, whereas the Fgfs maintain Shh Gremlin and Fgf4 in the absence of Gli3 Gremlin expression in the zone of polarizing could result from upregulating dHand in activity. But Gremlin, a molecule that the anterior. Their hypothesis was Posterior relays the Shh signal, and the Fgfs have confirmed by the anterior upregulation of asymmetric expression even before Shh Gremlin expression when dHand was comes on, suggesting that the limb bud is ectopically expressed. prepatterned. To investigate this Interestingly, the authors show that Alx4, 238 | APRIL 2002 | VOLUME 3 www.nature.com/reviews/genetics © 2002 Nature Publishing Group HIGHLIGHTS an imperative. The high rates of DEVELOPMENTAL BIOLOGY recombination of females can be exploited for fine-mapping muta- tions. Conversely, if a more approxi- Sharpening the mate map is desired, or if there is a need to preserve alleles in cis, then males, with their smaller map, focus on Crumbs would be preferred. Why there is such discrepancy in Thousands of people blinded by inherited retinal recombination between the sexes we dystrophies harbour mutations in CRB1 — don’t know, but this shouldn’t stop us which encodes a protein that is homologous to a from using it to our advantage. regulator of Drosophila epithelial polarity called Besides, where else can you get away Crumbs. It has therefore been proposed that with saying that males and females retinal epithelial cell disruption underlies the are suited for different tasks? pathology of certain human retinal disorders — Tanita Casci such as retinitis pigmentosa and Leber congenital References and links amaurosis — that are caused by CRB1 mutations. ORIGINAL RESEARCH PAPER Singer, A. et al. Sex-specific recombination rates in zebrafish. Now, Pellikka et al. and Izaddoost et al. report in Genetics 160, 649–657 (2002) Nature that Crumbs has two specific roles in In wild-type adult fly retinas, rhabdomeres extend into long rod-like WEB SITE elaborating the architecture of photoreceptor structures (left) but shorten by 50% of their normal length in the absence John Postlethwait’s lab: of Crumbs (right). Reproduced with permission from Pellikka, M. et al. http://www.neuro.uoregon.edu/postle/mydoc.html cells (PRCs) that, surprisingly, occur well after © (2002) Macmillan Magazines Ltd. early cell polarization. As these functions of Crumbs might be conserved in mammals, these findings shed new light on the cellular defects restricted to the stalk and inner segment, that underlie human blindness caused by CRB1 respectively. Both groups report a role for mutations. Crumbs in rhabdomere elongation, and Pellikka To overcome an early lethal phenotype and to et al. show that the extracellular domain of maintain its function in the earlier stages of Crumbs has a role in stalk formation as well. another transcription factor epithelial morphogenesis, both groups used First, they showed that loss of Crumbs shortened that is also expressed in anterior mosaic analysis to remove Crumbs specifically in the stalks in flies, whereas overexpressing its mesenchyme and participates in the developing retina of Drosophila. It was also extracellular domain during PRC development restricting Shh signalling, is not overexpressed in fly PRCs. Previous studies had extended them. They also show that required for regulating dHand shown that Crumbs organizes the zonula beta[[H]]spectrin physically associates with (or Gli3) expression. In fact, adherens (ZA) — a band of ‘glue’ that encircles Crumbs and contributes to stalk elongation, because Alx4 expression is each epithelial cell and attaches the cells together possibly by negatively regulating endocytosis. reduced in Gli3-deficient mice it in sheets. The studies reported here confirmed Together, the studies suggest that, in developing must lie genetically downstream that Crumbs maintains ZA integrity in PRCs PRCs, Crumbs binds through an intracellular of Gli3. during the rapid expansion of the rhabdomere, an domain to protein partners to position the ZA. This study provides important insight into the very early organelle that is packed with photosensitive Once the ZA is in place, it then interacts with patterning events in the membranes. During PRC differentiation, different protein partners on the inner and outer vertebrate limb, but before we rhabdomeres (called the outer segment in surfaces of the cells to recruit membranes into have the complete picture of vertebrates) elongate dramatically, and are the extending stalk. limb development, more factors supported by structures called stalks (or inner Although the eyes of flies and humans are will need to be incorporated segments in vertebrates). Both groups noticed strikingly different in their morphologies and into the already complex that loss of Crumbs in PRCs causes the abnormal phototransduction cascades, these studies network of interactions. positioning of the ZA and a striking shortening of highlight similarities in photoreceptor Magdalena Skipper rhabdomeres (see figure) but no significant loss of morphogenesis and provide new models and epithelial polarity. Izaddoost et al. showed that, approaches for uncovering the molecular when they overexpressed the intracellular interactions that might be involved in certain References and links ORIGINAL RESEARCH PAPER domains of both Crumbs and CRB1 in Drosophila forms of human blindness. te Welscher, P. et al. Mutual genetic PRCs, the ZA was strikingly mislocalized. This Natalie DeWitt, antagonism involving GLI3 and dHAND Senior Editor, Nature prepatterns the vertebrate limb bud suggested that Crumbs has a role in ZA formation mesenchyme
Recommended publications
  • 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.
    [Show full text]
  • 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).
    [Show full text]
  • 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).
    [Show full text]
  • 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)].
    [Show full text]
  • 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)].
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Chromosome 11
    Chromosome 11 Description Humans normally have 46 chromosomes in each cell, divided into 23 pairs. Two copies of chromosome 11, one copy inherited from each parent, form one of the pairs. Chromosome 11 spans about 135 million DNA building blocks (base pairs) and represents between 4 and 4.5 percent of the total DNA in cells. Identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to predict the number of genes on each chromosome, the estimated number of genes varies. Chromosome 11 likely contains 1, 300 to 1,400 genes that provide instructions for making proteins. These proteins perform a variety of different roles in the body. Health Conditions Related to Chromosomal Changes The following chromosomal conditions are associated with changes in the structure or number of copies of chromosome 11. Beckwith-Wiedemann syndrome Beckwith-Wiedemann syndrome results from the abnormal regulation of genes on part of the short (p) arm of chromosome 11. The genes are located close together in a region designated 11p15.5 near one end of the chromosome. People normally inherit one copy of chromosome 11 from each parent. For most genes on this chromosome, both copies of the gene are expressed, or "turned on," in cells. For some genes in the 11p15.5 region, however, only the copy inherited from a person's father (the paternally inherited copy) is expressed. For other genes, only the copy inherited from a person's mother (the maternally inherited copy) is expressed. These parent-specific differences in gene expression are caused by a phenomenon called genomic imprinting.
    [Show full text]
  • Phenotype Informatics
    Freie Universit¨atBerlin Department of Mathematics and Computer Science Phenotype informatics: Network approaches towards understanding the diseasome Sebastian Kohler¨ Submitted on: 12th September 2012 Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) am Fachbereich Mathematik und Informatik der Freien Universitat¨ Berlin ii 1. Gutachter Prof. Dr. Martin Vingron 2. Gutachter: Prof. Dr. Peter N. Robinson 3. Gutachter: Christopher J. Mungall, Ph.D. Tag der Disputation: 16.05.2013 Preface This thesis presents research work on novel computational approaches to investigate and characterise the association between genes and pheno- typic abnormalities. It demonstrates methods for organisation, integra- tion, and mining of phenotype data in the field of genetics, with special application to human genetics. Here I will describe the parts of this the- sis that have been published in peer-reviewed journals. Often in modern science different people from different institutions contribute to research projects. The same is true for this thesis, and thus I will itemise who was responsible for specific sub-projects. In chapter 2, a new method for associating genes to phenotypes by means of protein-protein-interaction networks is described. I present a strategy to organise disease data and show how this can be used to link diseases to the corresponding genes. I show that global network distance measure in interaction networks of proteins is well suited for investigat- ing genotype-phenotype associations. This work has been published in 2008 in the American Journal of Human Genetics. My contribution here was to plan the project, implement the software, and finally test and evaluate the method on human genetics data; the implementation part was done in close collaboration with Sebastian Bauer.
    [Show full text]
  • Investigating Contributions of Trisomy 21 in Down Syndrome to Alzheimer Disease Phenotypes in a Novel Mouse Cross
    Investigating contributions of trisomy 21 in Down syndrome to Alzheimer disease phenotypes in a novel mouse cross A thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy from University College London Xun Yu Choong Department of Neurodegenerative Disease Institute of Neurology University College London 2016 1 Declaration I, Xun Yu Choong, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 2 Acknowledgements The work done in this project was only possible with the support of numerous friends and colleagues, with whom I have grown an incredible amount. Foremost thanks go to Prof. Elizabeth Fisher and Dr. Frances Wiseman, who have been inexhaustibly dedicated supervisors and inspirational figures. Special mention also goes to two unofficial mentors who have looked out for me throughout the PhD, Dr. Karen Cleverley and Dr. Sarah Mizielinska. The Fisher and Isaacs groups have been a joy to work with and have always unhesitatingly offered time and help. Thank you to the Down syndrome group: Olivia Sheppard, Dr. Toby Collins, Dr. Suzanna Noy, Amy Nick, Laura Pulford, Justin Tosh, Matthew Rickman; other members of Lizzy’s group: Dr. Anny Devoy, Dr. Rosie Bunton-Stasyshyn, Dr. Rachele Saccon, Julian Pietrzyk, Dr. Beverley Burke, Heesoon Park, Julian Jaeger; the Isaacs group: Dr. Adrian Isaacs, Dr. Emma Clayton, Dr. Roberto Simone, Charlotte Ridler, Frances Norona. The PhD office has also been a second home in more ways than one, thanks to: Angelos Armen, Dr.
    [Show full text]
  • Probing the Gene Expression Database for Candidate Genes
    European Journal of Human Genetics (1999) 7, 910–919 t © 1999 Stockton Press All rights reserved 1018–4813/99 $15.00 http://www.stockton-press.co.uk/ejhg ARTICLE Probing the Gene eXpression Database for candidate genes Maurice AM van Steensel, J Celli, JH van Bokhoven and HG Brunner Department of Human Genetics, University Hospital Nijmegen, The Netherlands We report on a strategy for the identification of candidate genes for multiple malformation syndromes using expression data available in public databases. The basis for this pilot study was the assumption that, for a multiple malformation syndrome, the expression pattern of the causative gene should at least cover the organs or tissues affected by the syndrome. Twenty malformation syndromes were selected from the OMIM and defined by three to five main symptoms. These key symptoms were translated into anatomical terms that were used to query the Gene eXpression Database (GXD). The searches covered 65% of the database and yielded an average of 16 candidate genes per syndrome. Of these, 23% were ubiquitously expressed or housekeeping genes. Further database evaluation of these potential candidate genes was based on positional information and on information from mouse knockouts. In a first experiment, the correct gene was identified as a candidate in four of seven syndromes for which the causative gene is already known. In addition, this strategy identified new candidate genes for disorders for which the genetic basis is unknown. We identified candidate genes for the Walker-Warburg, DOOR, C, scalp–ear–nipple and oculocerebral hypopigmentation syndromes. Our results suggest that it may ultimately be feasible to identify disease genes by probing gene expression databases with simple syndrome descriptions.
    [Show full text]