Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle
Arthrogryposis syndrome; PIGH gene; Splice site mutation; Glycophosphatidyl inositol deficiency; Belgian blue cattle breed
Research Center/Unit :
Giga-Genetics - ULiège
Disciplines :
Genetics & genetic processes Veterinary medicine & animal health
Author, co-author :
Sartelet, Arnaud ✱; Université de Liège > Département des Animaux de Production > GIGA-R : Génomique animale
Li, Wanbo ✱; Université de Liège - ULiège > Département des Animaux de Production > GIGA-R : Génomique animale
Pailhoux, Eric; Institut Scientifique de Recherche Agronomique - INRA > UMR1198 > Biologie du Développement et Reproduction
Richard, Christophe; Institut Scientifique de Recherche Agronomique - INRA > UMR1198 > Biologie du Développement et Reproduction
Tamma, Nico ; Université de Liège > Département de productions animales > GIGA-R : Génomique animale
Karim, Latifa ; Université de Liège > Département des sciences de la vie > GIGA-R : Biologie et génétique moléculaire
Fasquelle, Corinne ; Université de Liège > Département des sciences biomédicales et précliniques > GIGA-R : Génétique humaine
Druet, Tom ; Université de Liège > Département de productions animales > GIGA-R : Génomique animale
Coppieters, Wouter ; Université de Liège > Département de productions animales > GIGA-R : Génomique animale
Georges, Michel ; Université de Liège > Département de productions animales > GIGA-R : Génomique animale
Charlier, Carole ; Université de Liège > Département de productions animales > GIGA-R : Génomique animale
✱ These authors have contributed equally to this work.
Language :
English
Title :
Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle
Publication date :
2015
Journal title :
BMC Genomics
eISSN :
1471-2164
Publisher :
BioMed Central
Volume :
16
Issue :
316
Peer reviewed :
Peer Reviewed verified by ORBi
Name of the research project :
Rilouke
Funders :
DGA - Région wallonne. Direction générale de l'Agriculture
Charlier C, Coppieters W, Rollin F, Desmecht D, Agerholm JS, Cambisano N, et al. Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat Genet. 2008;40:449-54.
Zhang Z, Guillaume F, Sartelet A, Charlier C, Georges M, Farnir F, et al. Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification. Bioinformatics. 2012;28:2467-73.
Sartelet A, Stauber T, Coppieters W, Ludwig CF, Fasquelle C, Druet T, et al. A missense mutation accelerating the gating of the lysosomal Cl-/H + -exchanger ClC-7/Ostm1 causes osteopetrosis with gingival hamartomas in cattle. Dis Mode Mech. 2014;7:119-28.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60.
Li, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-9.
Trapnell C, Roberts A, GoffL, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562-78.
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24-6.
Burset M, Seledtsov IA, Solovyev VV. SpliceDB: database of canonical and non-canonical mammalian splice sites. Nucleic Acids Res. 2001;29:255-9.
Almeida A, Layton M, Karadimitris A. Inherited glycosylphosphatidyl inositol deficiency: a treatable CDG. Biochim Biophys Acta. 2009;1792:874-80.
Mayor S, Riezman H. Sorting GPI-anchored proteins. Nat Rev Mol Cell Biol. 2004;5:110-20.
Freeze HH. Understanding human glycosylation disorders: biochemistry leads the charge. J Biol Chem. 2013;288:6936-45.
Watanabe R, Kinoshita T, Masaki R, Yamamoto A, Takeda J, Inoue N. PIG-A and PIG-H, which participate in glycosylphosphatidylinositol anchor biosynthesis, form a protein complex in the endoplasmic reticulum. J Biol Chem. 1996;271:26868-75.
Kamitani T, Chang HM, Rollins C, Waneck GL, Yeh ET. Correction of the class H defect in glycosylphosphatidylinositol anchor biosynthesis in Ltk- cells by a human cDNA clone. J Biol Chem. 1993;268:20733-6.
Nicholas FW, Hobbs M. Mutation discovery for Mendelian traits in non-laboratory animals: a review of achievements up to 2012. Anim Genet. 2014;45:157-70.
Sonnhammer ELL, von Heijne G, and Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 175-182, Menlo Park, CA, 1998. AAAI Press. (http://www.cbs.dtu.dk/services/TMHMM/).
