A report on the 15th International Mouse Genome Conference, Edinburgh, UK, 21-24 October 2001

Beier, David Randolph

Herron, Bruce J

Genome Biology

Harvard University - DASH 

 2001: A Mouse Genome Odyssey  (Article begins on next page)The Harvard community has made this article openly available.Please share how this access benefits you. Your story matters.Citation Beier, David R., and Bruce J. Herron. 2002. 2001: a mousegenome odyssey. Genome Biology 3(2): reports4005.1-reports4005.4.Accessed February 19, 2015 8:09:40 AM ESTCitable Link http://nrs.harvard.edu/urn-3:HUL.InstRepos:4743731Terms of Use This article was downloaded from Harvard University's DASHrepository, and is made available under the terms and conditionsapplicable to Other Posted Material, as set forth athttp://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAAcommentreviewsreportsdeposited researchinteractionsinformationrefereed researchhttp://genomebiology.com/2002/3/2/reports/4005.1Meeting report2001: a mouse genome odyssey David R Beier and Bruce J HerronAddress: Genetics Division, Brigham and Women’s Hospital and Harvard Medical School, 20 Shattuck St, Boston, MA 02115, USA.Correspondence: David R Beier. E-mail: beier@rascal.med.harvard.eduPublished: 31 January 2002Genome Biology 2002, 3(2):reports4005.1–4005.4The electronic version of this article is the complete one and can befound online at http://genomebiology.com/2002/3/2/reports/4005© BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914)A report on the 15th International Mouse GenomeConference, Edinburgh, UK, 21-24 October 2001.The mouse genome sequenceIn  a  year  notable  for  the  completion  of  a  draft  humangenome sequence, it was appropriate that a major topicat the 15th International Mouse Genome Conference wasa  discussion  of  the  status  of  the  mouse  genome  project.Details of the public-domain effort were presented by JohnMcPherson (Washington University, St Louis, USA), KerstinLindblad-Toh  (Whitehead  Institute,  Cambridge,  USA),Shaying  Zhao  (The  Institute  for  Genomic  Research,Rockville,  USA),  Anne-Marie  Mallon  (Medical  ResearchCouncil  Mouse  Genome  Centre  and  Mammalian  GeneticsUnit  (MRC  MGU/MGC),  Harwell,  UK),  and  Jim  Thomas(National  Human  Genome  Research  Institute,  NationalInstitutes of Health (NIH), Bethesda, USA). The approachbeing taken combines sequencing of bacterial artificial chro-mosomes (BACs) - this was the main method for sequencingthe human genome - and whole-genome shotgun sequenc-ing, which is advocated by investigators at Celera Genomics.A  fingerprinted  physical  map  of  300,000  BAC  clones  hasbeen generated and aligned to the mouse radiation-hybridmap  using  sequence-tagged  sites  (STSs)  derived  frommicrosatellite  sequences  and  expressed  sequence  tags(ESTs). The precise position of the BACs on the map is beingrefined with the help of the sequences of the ends of many ofthe  BACs.  Nearly  threefold  (3x)  coverage  of  the  genomeusing shotgun sequence has been completed and depositedin public domain databases. One aim of the public mouse genome-sequencing effort is togenerate  shotgun-sequence  reads  from  different  mousestrains, in order to identify single-nucleotide polymorphisms(SNPs). (As plans for this component are in development, wepropose that the validation and characterization of SNPs in alarge number of commonly used inbred strains is as importantas SNP discovery itself, and urge that appropriate resources bedevoted to it). An important part of genomics is the informat-ics required for data management and analysis; programs fororganizing  and  annotating  mouse  genome  sequence  in  theEnsembl  project  [http://mouse.ensembl.org/]  and  at  theNational  Center  for  Biotechnology  Information  (NCBI[http://www.ncbi.nlm.nih.gov/genome/guide/M_musculus.html]) were  presented  by  Tim  Hubbard  (Sanger  Centre,Hinxton, UK) and Deanna Church (NCBI, NIH, Bethesda,USA), respectively. The  other  sequencing  effort  for  the  mouse  genome  is  theproprietary  sequence  completed  by  Celera  Genomics,described  by  Gene  Myers  (Celera  Genomics,  Rockville,USA).  Myers  and  colleagues  have  assembled  a  reasonablycomplete mouse sequence using only 5.3x shotgun sequencecoverage  together  with  a  bioinformatic  assembly  protocolthat combines analysis of sequence identity between shotgunsequence reads with ‘mate-pair’ information, that is, infor-mation from the pairing of reads derived from opposite endsof  each  clone.  Although  some  investigators  have  notederrors in the assembled sequence - and it is not clear what isbeing done to correct these - there can be little argumentthat Celera’s work provides an extremely valuable resourceto those who have access to it. It also validates the assertionmade by Craig Venter and colleagues (Celera) that assemblyof complex genome sequences using only shotgun sequencedata is feasible; the Celera human genome assembly was nota conclusive validation because it used public-domain BACsequences as well as shotgun sequence. An  emerging  theme  in  genomic  science  is  the  power  ofcomparative analysis for identification of genes and regu-latory regions. This was highlighted in a plenary presenta-tion  by  Jean  Weissenbach  (Genoscope,  Paris,  France)describing progress in sequencing the freshwater pufferfish2 Genome Biology Vol 3 No 2  Beier and HerronTetraodon  nigroviridis,  which  has  a  genome  about  aneighth the size of that of humans or mice. In addition to the3x  sequence  coverage  that  has  been  deposited  in  theGenBank genome sequence survey database, Weissenbachand  colleagues  have  developed  a  database  of  ‘Ecores’,sequences  that  are  conserved  between  pufferfish  andhumans and that are therefore likely to be coding regions([http://www.genoscope.cns.fr/proxy/cgi-bin/exofish.cgi]). With  the  rapidly  progressing  sequencing  of  the  mousegenome  comes  the  possibility  of  performing  true  genome-wide  investigation  using  techniques  that  permit  massivelyparallel analysis, such as expression profiling, similar to thekinds  of  studies  that  have  now  been  done  in  yeast  andCaenorhabditis  elegans.  For  example,  a  database  of  thetissue-specific expression levels of murine genes, containing2. 5x1 0 6 independent  measurements,  has  been  generatedusing hybridization to Affymetrix oligonucleotide arrays (TimWiltshire,  Genomics  Institute  of  the  Novartis  Foundation,San Diego, USA). Expression profiling has also been used toidentify genes that are expressed in sexually dimorphic pat-terns during development; these were validated using whole-mount  in  situ analysis  of  gonads  (Lee  Smith,  MRCMGC/MGU, Harwell). Among other approaches to genome-wide analysis that were also presented was a large set of full-length cDNAs generated by RIKEN, which is being furtherexplored  using  a  high-throughput  two-hybrid  screeningapproach to identify protein-protein interactions (HarukazuSuzuki,  RIKEN,  Yokohama,  Japan).  Over  500  interactionshave  been  identified  so  far.  Also,  Bill  Stanford  (SamuelLunenfeld  Research  Institute,  Toronto,  Canada)  describedone of several active large-scale programs for gene trapping,in which reporter constructs are randomly inserted into thegenome and are expressed only if they insert within a gene.As  well  as  being  a  resource  with  tremendous  potential  forannotation of gene function in its own right, the generationof  large  sets  of  STS-tagged  gene-trapped  embryonic  celllines by this project also provides a means to test candidateloci identified by phenotype-driven mutagenesis screens. MutagenesisThe mutagenesis session did not focus on large centers withbroad aims but instead highlighted innovative approaches toscreens focused on a particular region of the genome or on aspecific phenotype. Although new approaches to the genera-tion of mutations were briefly discussed, it is clear that ethyl-nitrosourea (ENU) remains the dominant method. MonicaJustice (Baylor College of Medicine, Houston, USA) openedthe session with an update on the Baylor ENU screen formutations on mouse Chromosome 11. This screen uses a bal-ancer-chromosome  strain  that  provides  a  way  to  readilyidentify  mice  homozygous  for  an  engineered  inversion  inrecessive  screens,  making  stock  maintenance  straightfor-ward. A wide variety of mutant phenotypes were described,many of which are embryonic-lethal.Specialized  phenotype  screens  were  a  major  focus  of  thesession.  Karen  Steel  (MRC  Institute  of  Hearing  Research,Nottingham) presented ongoing screens designed to identifyand  classify  mice  with  inner-ear  defects  arising  from  themutagenesis program at the MRC MGC/MGU. Using a com-bination  of  inner-ear  pathology  and  genetic  mapping,several  complementation  groups  were  defined;  several  ofthese  mapped  to  previously  known  vestibular  defects  inmice, but new loci were also uncovered. One example of anew  locus  is  Pardon,  mutants  in  which  have  malformedauditory ossicles; Pardon has been identified as a mutationin Emx2, a homeobox-containing gene.Discovery of new mutations from large mutagenesis centerswill rely heavily on methods for screening large numbers ofmice robustly and efficiently. Working in collaboration withthe Munich ENU center (GSF Research Center for Environ-ment and Health), Heinrich Flaswinkel (Technische Univer-sität, Munich, Germany) presented a method to identify micewith  immunological  defects  through  fluorescence-activatedcell  sorting  (FACS)  and  enzyme-linked  immunosorbentassay (ELISA) analysis. This approach was reported to identify54 heritable phenotypes from 8,857 lines screened. John Schi-menti (Jackson Laboratory, Bar Harbor, USA) introduced anovel  method  for  identifying  mice  with  defects  leading  togenome instability. Mice are irradiated and bone marrow isisolated for flow cytometry; those with defects in DNA repairpathways,  for  example,  will  have  a  higher  concentration  ofmicronuclei and can be readily identified. One benefit of point mutations, which are produced by ENU,is  that  they  often  produce  hypomorphic  alleles  and  couldthus complement the functional analysis of a gene for whicha null mutation has already been generated. Two talks pre-sented approaches directed at identification of more muta-tions in known genes from populations of mutagenized mice.Jay Vivian (University of North Carolina, Chapel Hill, USA)discussed  the  use  of  denaturing  high-performance  liquidchromatography  (DHPLC)  to  identify  differences  in  Smadgenes in mutagenized embryonic stem (ES) cells. Smads areintracellular  proteins  involved  in  signaling  through  thetransforming  growth  factor   (TGF)  family  of  receptors.This  approach  identified  approximately  one  coding-sequence mutation per 2 kilobases of the Smad2 gene, andwhen the mice were generated from the mutant ES cells, oneof the mutations resulted in a phenotype similar to that ofSmad2 knockout  mice.  Emma  Coghill  (MRC  MGC/MGU)presented  a  sequence-based  approach,  screening  archivedsperm  from  the  Harwell  ENU  mutagenesis  program.  Heranalysis provided a new allele of connexin 26 that had anembryonic-lethal phenotype.Gene discoveryAs the whole of the mouse genome sequence becomes avail-able, the positional cloning of many interesting mutations iscommentreviewsreportsdeposited researchinteractionsinformationrefereed researchhttp://genomebiology.com/2002/3/2/reports/4005.3being accelerated, as was evident in the array of topics dis-cussed in the Gene Discovery session of the meeting. Thesuccesses described below were not solely due to genome-sequencing  efforts,  however;  other  emerging  technologies,such as cross-species mapping and gene trapping, were alsoused to identify mutations.The  session  was  opened  by  Adrian  Bird  (Wellcome  TrustCenter  for  Cell  Biology,  Edinburgh,  UK)  who  presentedrecent data on a new mouse model for Rett syndrome, a pro-gressive  neurological  disorder  that  primarily  affects  girls.The mutated gene in this syndrome in humans encodes theDNA-binding protein MeCP2, which is known to selectivelybind CpG DNA motifs; the mechanism by which its absenceresults in the syndrome is unclear, however. Bird presenteddetails of the mouse null mutation that faithfully recapitu-lates several aspects of the human disorder in heterozygotes,including ataxia and breathing dysrhythmia. Mouse models of polycystic kidney disease have providedmuch  information  over  the  years  about  normal  kidneydevelopment.  We  (D.B.)  described  our  finding  that  therecessive polycystic kidney mutation jck is in a gene encod-ing  a  novel  Nek-family  kinase.  We  have  taken  a  newapproach to validate the function of the mammalian gene:using an antisense morpholino oligonucleotide in zebrafishto  reduce  expression  of  the  kinase,  the  cystic  phenotypewas recapitulated, confirming the importance of this genein  normal  kidney  development. A  gene  that  could  be  ofpotential therapeutic benefit was identified by analysis ofheterozygote  WldS/+ mice,  which  show  resistance  tomotor-neuron axon degeneration after transection (MichaelColeman, University of Cologne, Germany). A novel fusionbetween  the  ubiquitination  gene  E4B and  the  gene  fornicotinamide mononucleotide adenyltransferase was identi-fied in the WldS strain. Expression of a transgenic fusiongene in mice reproduced the phenotype, implying that mod-ulation  of  pyridine  nucleotide  metabolism  may  protectagainst axon degeneration.Rescue of mutants by BAC transgenes is another powerfultechnique that is becoming common practice in positional-cloning  projects.  This  approach  was  used  by  PhilomenaMburu (MRC MGC/MGU) in combination with a detailedphenotypic analysis of inner-ear hair cells to narrow downthe candidate genes to be tested for mutations in  whirlermice, which have inner-ear defects. A novel gene was pre-sented, encoding a PDZ-domain-containing protein, that isimplicated in the development of stereocilia.Genetic studies of coat-color defects in mice have providedmuch information on how the genes involved might interact.For example, the products of the dilute, ashen, and leadengenes are all thought to function in the same biochemicalpathway,  transporting  melanin  from  melanosome  to  pig-mented hair cells. Using a candidate gene approach, LydiaMatesic  (National  Cancer  Institute,  Frederick,  USA)  hasfound  a  novel  effector  protein  for  the  small  GTPase  Rab,called Mlph, that is mutated in leaden. Cross-species comparative analysis is an approach that wasused  by  several  speakers  to  identify  candidate  genes  formouse mutations. This approach has facilitated the cloningof  the  genes  defective  in  myodystrophy mutants  (PamGrewal, University of Nottingham, UK), in flavivirus suscep-tibility mutants  (Tomoji  Mashimo,  Institut  Pasteur,  Paris,France) and in a rat mutant queue courte (Kazuhiro Kitada,Kyoto  University,  Japan).  Along  with  other  strategies  pre-sented in this session, the success of this technique shows thata major bottleneck in positional cloning - gene identification -is quickly becoming resolved. Developmental geneticsDevelopmental  genetics  has  been  of  increasing  interest  atsuccessive  international  mouse  genome  meetings.  Thisyear’s session was opened by two talks that focused on epige-netic programming in cloned embryos. Ian Wilmut (RoslinInstitute,  Roslin,  UK)  presented  information  about  thesuccess of embryo cloning in several species. The current lowsuccess rates are attributed to inappropriate gene expressionthat may be due in part to a failure to maintain developmen-tally  appropriate  imprinting  in  transferred  somatic  cellnuclei.  This  hypothesis  was  supported  by  a  presentationfrom Kevin Eggan (Whitehead Insitute, Cambridge, USA),who  described  differences  in  imprinted  gene  expressionbetween cloned and normal mouse embryos. The imprinting theme was continued in a talk from JesseMager (University of North Carolina, Chapel Hill, USA), whodiscussed X-chromosome inactivation. The embryonic ecto-derm development gene was shown to be important for themaintenance of inactivation of the paternal X chromosomein female mice, as well as for development of trophoblastgiant cells in female embryos. This gene has been proposedto interact with a histone deacetylase in the extraembryonictissue, selectively deactivating the paternal X chromosome.Skin and hair defects are a group of phenotypes that havebeen well studied by mouse geneticists, and three talks inthis session were focused on a better understanding of thesephenotypes.  Karen  Fitch  (Stanford  University,  Palo  Alto,USA)  described  the  classification  of  mice  with  dark  skinphenotypes from the GSF mutagenesis program (Munich,Germany).  The  mutants  were  further  categorized  using  amelanocyte-specific reporter system, mapped, and assignedto  ten  linkage  groups.  Teresa  Gunn  (Cornell  University,Ithaca, USA) described recent work characterizing alleles ofmahogany, which was originally identified as a coat-colormutant but alleles of which have now been found to causebehavioral  abnormalities  caused  by  a  degenerative  neu-ropathy. Lastly, we (B.H.) described a mutation in a geneencoding a p53-binding-protein homolog in waved3 mice,which have abnormalities in skin and heart development.A major benefit of mouse models is their utility in providinga better understanding of disease in humans. The presenta-tion of Kenro Kusumi (University of Pennsylvania, Philadel-phia, USA), describing the role of mutations in the Dll3 gene,which  encodes  a  Delta-like  ligand  for  Notch  proteins,  inpudgy mice,  which  have  vertebral  and  rib  malformations,underscored the usefulness of this approach. Comparison ofthe mouse model to the human disorder spondylocostal dys-tosis  provides  some  insight  into  potential  neurologicaldefects in humans, as well as into the function of this gene innormal somitogenesis.Finally,  although  mapping  of  the  loci  contributing  to  acomplex trait is often readily done, identifying the causalgene(s)  remains  daunting,  even  in  a  well-defined  geneticsystem such as the mouse. Sarah Lloyd (Imperial College ofMedicine at St Mary’s, London, UK) reported the mappingof quantitative trait loci affecting incubation times of priondisease,  and  Ayo  Toye  (MRC  MGC/MGU)  reportedmapping  of  diabetes  intermediate  phenotypes.  AlainBalmain  (University  of  California,  San  Francisco,  USA)described progress in characterizing a locus that modifiessusceptibility to skin cancer and reported that haplotypeanalysis  of  susceptible  and  resistant  strains  facilitatedlocalization to a small genetic interval.Next  year’s  International  Mouse  Genome  Conferencewill be held in San Antonio, USA. With the imminent com-pletion of the public-domain mouse genome sequence, theproductivity of the diverse mutagenesis programs, and theincreasing sophistication of genome manipulation technolo-gies such as gene trapping and BAC transgenesis, we antici-pate that many exciting discoveries in mammalian biologywill be reported. 4 Genome Biology Vol 3 No 2  Beier and Herron

2001: A Mouse Genome Odyssey

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2001: A Mouse Genome Odyssey

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