22nd International Mammalian Genome Conference
2-5 November 2008
Prague, Czech Republic

Organiser:

Jiri Forejt, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic

Draft Report

Summary

The 22nd International Mammalian Genome Conference was held in the Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, in Prague. The meeting was organised by Jiri Forejt, with the aid of a local committee. The International Mammalian Genome Society Secretariat consists of Maja Bucan (President), Karen Steel (Vice-President), Monica Justice (Past President), Simon Foote, Xavier Montagutelli, Yoichi Gondo, Fuad Iraqi, Kent Hunter and David Threadgill. There were over 290 participants, with representatives from almost every continent. The 44 platform presentations, including the keynote Verne Chapman Memorial Lecture, were divided between eight sessions. Each session began with a plenary lecture and over the three days of the meeting there were also 123 poster presentations. Awards for oral and poster presentations are listed in Table 1. Many of the topics at this meeting were familiar from previous conferences, but there was a distinct emphasis on models of human disease. There were also several presentations that introduced the next-generation sequencing technologies that look set to revolutionise mammalian genomics. Prof. Philip Avner, from the Institute Pasteur, presented the Verne Chapman Memorial Lecture, covering the topic of X-chromosome inactivation as a paradigm for epigenetics.

Before the main conference, there was a very high quality satellite meeting, intended as a less challenging presenting environment for students and junior faculty. The main conference sessions comprised: Immunity/Infection/Epigenetics, Comparative Genomics/Computational Biology, Modeling Disease I, Development/Cancer Biology/Evolution/Aging, Other genomes and new approaches, Neuroscience/Behavior, Modeling Disease II and Mutagenesis.

Scientific Content

The main conference was preceded by a workshop on Bioinformatics tools divided into three sections, one on the Mouse Phenome Database (Molly Bogue from the JAX) , another on Creating and Accessing the Mouse Genome Assembly (Melissa Landrum from the NCBI) and the third, Introducing the Ensembl Genome Browser System (Xose Fernandez from the EBI).

The IMGS is keen to encourage students to give oral presentations at the satellite meeting preceding the main conference, and provides financial support to many attendees. The symposium was well attended, with a wide range of topics and some excellent presentations. Almost all the presentations addressed mouse genetics or genomics, in one form or another. Students giving the best presentations were selected for inclusion in the main conference and also considered for the prizes donated by the meeting sponsors. Several talks described phenotypic characterisation and identification of spontaneous or ENU-induced mutations, including mutations associated with embryonic lethality (Karen Mitchell, University of Manchester, UK – Nature Poster Prize), megakaryocyte differentiation (Nicole Anderson, University of Toronto, Canada), thrombosis (Randal Westrick, University of Michigan, USA), microphthalmia and hind-limb syndactyly (Joe Rainger, MRC Human Genetics Unit, Edinburgh, UK - Verne Chapman Award) and impaired glucose tolerance (Alison Hough, MRC Harwell, UK – genesis platform Prize). The field of complex / quantitative traits was also well represented including presentations devoted to ischemic stroke (Sehoon Keum, Duke University, NC, USA - Nature Genetics poster prize), cardiomyopathy, (Pei-Lun Chu, Duke University, USA) , obesity and fat depot-specific QTL (Zala Prevorsek, University of Ljubljana, Slovenia – GENETICS poster prize), anxiety-related behavior (Marijke Laarakker, Utrecht University & Rudolf Magnus Institute of Neuroscience, Netherlands), genetic susceptibility to low dose ionizing radiation (Rachel Lynch, Oak Ridge National Laboratory, USA - Genome Research poster prize) and susceptibility to pneumococcal infection (Laura Wisby, MRC Harwell, UK). Two presentations described detailed characterisation of the effects of mutant alleles for a single locus in the mouse; one on the obesity-associated gene, FTO (Christopher Church, MRC Mammalian Genetics Unit, UK) and another on the germ cell tumor susceptibility locus, Ter (Shirley Hammond, UT M.D. Anderson Cancer Center, USA). Finally, there were two talks that presented bioinformatics tools, one for genome-scale phenotypic analysis (Jeremy Jay, University of Tennessee, USA) and another linking gene expression changes to protein spatial location in muscle (Ashley Waardenberg, Griffith University, Australia). Some of the student presentations were selected for inclusion in the main conference - Alison Hough described how two independently-derived ENU alleles of Sox4, showed altered intra-peritoneal glucose tolerance and so represented models of type 2 diabetes. Furthermore, she presented evidence that Sox4 acts either directly upon, or downstream of, expression of a K+ATP channel. Karen Mitchell reported the identification and characterisation of two mouse mutants, with developmental defects, one with defective cardiovascular development causing embryonic lethality and the other exhibiting embryonic hydrocephalus, probably as a result of a mutation in the non muscle Myosin IIB gene.

Immunity/ Infection/Epigenetics
The first session began with a plenary lecture by Wolf Reik, who gave a highly illuminating presentation on epigenetic regulation of lineage commitment and pluripotency in the mammalian embryo. The main theme was a discussion of how gametes lose their DNA methylation imprint, and how new methylation patterns are produced in the embryo during development. A model was also proposed in which a specific gene, Elf5 , forms part of a positive feedback loop, acting as an epigenetic ‘switch' or gatekeeper.

The remainder of this session was eclectic, covering inflammatory disease (rheumatoid arthritis, Stefka Petkova), innate immunity (QTL regulating cytokine gene transcription, James Conner), infection susceptibility (Rift Valley fever virus, Jean-Jacques Panthier; H5N1 virus, Jacco Boon) and X-inactivation (epigenetic signatures of genes that escape inactivation, Christine Disteche).

Comparative Genomics & Computational Biology
The ability to perform large-scale genotyping, sequencing and expression profiling studies in multiple species is driving developments in comparative genomics & computational biology. The plenary lecture that kicked-off this session was a sobering affair, with the theme of how little we know about the workings of the genome. Nevertheless, Stylianos Antonarakis, presented a fascinating picture of the changing meaning of the word ‘gene' . This was based on work that formed part of the ENCODE project and included evidence that much more of the genome is transcribed than believed previously. Furthermore, high-throughput sequencing of products of circular chromatin conformation capture (“4C”), demonstrated that so-called conserved non-coding (CNC) sequences in the vicinity of two ENCODE genes interact in cis and with CNC on other chromosomes, in trans. Finally, the functional connectivity of micro-RNAs was discussed, including how a copy-number variant (CNV) appeared to control expression of 6 different miRNA. Three presentations followed in which the importance of genetic background was central. Firstly Petko Petkov reported on the evolutionary conservation of regional but not local rates of recombination. Using crosses between mouse sub-species, Toshihiko Shiroishi then described how whole genome resequencing of Japanese wild mouse-derived inbred strain MSM/Ms gives clues about the ancestry of the classical laboratory inbred strain, C57BL/6J. Finally, Harry Noyes talked about how differential gene expression observed between inbred strains is exquisitely dependent on genetic background.

Piero Carninci presented NanoCAGE, a method that produces cDNA sequence tags adjacent to transcriptional start sites from very small amounts of starting material, and described it's application to purified olfactory epithelia. David Aylor reported on the genotyping and phenotyping of a population of Pre-Collaborative Cross (Pre-CC) animals, indicating that despite not yet being fully inbred, these mice may have application in high-resolution QTL mapping. The description of the Pre-CC acted as a curtain-raiser to other talks, e.g. in the session on Modeling Disease, below. The session ended with a description from Michael Parsons of candidate miRNAs with potential roles in various behavioural traits.

The Verne Chapman Memorial Lecture, given by Philip Avner, explored X inactivation as an epigenetic paradigm. We heard a marvellous exposition of the mechanisms by which mammals achieve dosage compensation – coping with the difference in copy number of X-linked genes in males and females. Much of the talk focused on one particular locus, the Xist gene region, because this was well defined genetically. Dr Avner concluded that the process of X inactivation probably didn't arise at the same time as chromosomal sex determining mechanisms because the mechanisms are distinct in eutheria and metatheria.

Modeling Disease – part 1
A plenary presentation, by Timothy Aitman, opened the third session and highlighted the importance of the rat as a model for human disease. Several interesting mutants were discussed, including a model for type 2 diabetes associated with a mutation in Cd36, and a model for glomerular nephritis with copy number variation similar to that observed in humans with systemic lupus erythematosus. Dr Aitman proposed that rat genetics is now limited by only having access to the sequence of the Brown Norway strain and that the use of Next Generation Sequencing (NGS) to sequence more strains raises the prospect of genome-wide association studies to help identify more disease models.

A plethora of abstracts describing disease models clearly meant that the meeting organisers needed to arrange two sessions on this topic.

Morag Lewis described an ENU induced model for progressive hearing loss, diminuendo (Dmdo). The mutation occurs in the seed region of miRNA-96 and leads to hair cell abnormalities. As well as causing a loss of gene targets this may lead to a gain of novel targets too. This is the first report of a mutation in a microRNA associated with deafness. Birgit Rathkolb also highlighted the use of ENU by focusing on two lines with mutations in Slc12a1 and Umod. These exhibited kidney phenotypes that model aspects of human nephropathies.

Douglas Marchuk reported on phenotypic modifier loci of cardiac hypertrophy in a Calsequestrin (CSQ) transgenic mouse and presented evidence that the causative variant for one of these loci introduced a cryptic splice site in the Tnni3k (cardiac troponin I kinase) gene. Furthermore, there is an association between the severity of heart failure in some humans and SNPs in the TNNI3K gene. A hypomorphic mutant allele of the Ass1 gene was described by Fernando Benavides to cause a complex phenotype similar to that of people with a urea cycle disorder, citrullinemia type I. Two presentations reported on phenotyping the Pre-CC mice, indicating the breadth of phenotype assays (Fernando Pardo-Manuel de Villena) and also focusing on specific phenotypes, such as those that are related to asthma in humans (Samir Kelada).

Development/Cancer Biology/Evolution/Aging
Diethard Tautz opened this session with a plenary talk on the genetic basis of adaptations in wild mouse populations. He described that in a comparison of populations from France and Germany that diverged about 6000 years ago, there was evidence of 8 loci conferring a selective advantage. This was estimated to correspond to about 1-2 selective sweep events per 100 generations; higher than expected. Candidate genes that may be responsible for adaptive differences were uncovered by combining a search for loci that had lost heterozygosity with differences in expression profile. Yung-Hao Ching reported a novel ENU induced allele of the Zbtb16 gene (aka Plzf) called 7 toes (Zbtb167t). This was acting as a separation of function allele, by comparison with other mutant alleles, such as null, knockout alleles. An extensive study of the genetics of aging using 31 inbred mouse strains, described by Beverly Paigen, found that several lifespan QTLs co-localised with genes in the IGF1 pathway and that plasma IGF1 levels showed an inverse correlation with median lifespan. Beverly Mock reported that the Ifi207 gene is an excellent candidate for the Plasmacytoma Modifier of Resistance /Susceptibility (Pctmr) because it is partially deleted in DBA/2 mice. The Jeff mutant mouse has an ENU induced point mutation in the Fbxo11 gene and as well as having chronic otitis media, homozygote mutants display cleft palate, lung defects and are born with eyelids open (Hilda Tateossian).

Leonid Bystrykh described possible regulatory effects of known mouse miRNAs in hematopoietic development.

Other genomes and new approaches
This session encompassed mutagenesis and recombinant inbred strain resources in the rat and targeted high-throughput sequencing of the mouse genome. Tomoji Mashimo described the creation of Kyoto University Rat Mutant Archive (KURMA), an ENU-induced mutant archive and a method using Mu-transposition reactions that allows for fast screening of heterozygote mutants in G1 animals. Michal Pravenec, in a beautifully marshalled argument, used several lines of evidence about a blood pressure QTL found in crosses between SHR and BN inbred rat strains, to support the hypothesis that variation in the CD36 gene was responsible for the effects of this locus.

A combination of targeted enrichment of DNA fragments using a microarray for a 170 kb region around the Kit locus and next-generation sequencing was reported by Laura Reinholdt as a novel means of finding mutations. David Adams reported using flow-sorting of chromosomes as an alternative means of obtaining targeted sequence data and described the complete sequence of mouse chromosome 17 from two inbred mouse strains; A/J and CAST/Ei. At the end of this session Dr Adams also gave an unscheduled short presentation on the intention of the Wellcome Trust Sanger Institute to start a project to sequence the genomes of up to 17 inbred mouse strains. This provoked a lively discussion, especially concerning annotation of these genomes by comparison with the reference C57BL/6J sequence.

Neuroscience/Behaviour
Jonathan Flint opened this session with a plenary presentation discussing the neurotrophic theory of depression and the use of heterogeneous stock mice to map QTL for various traits that would be relevant to this condition, including neophobia, elevated plus maze, open field, home cage, startle, fear conditioning and blood measures,. More than 50 QTL were found, but one association was of particular note – a correlation between neurogenesis and blood CD4/CD8 levels, and furthermore, Dr Flint reported that blockade of CD4/CD8 with antibodies prevents neurogenesis. In summary, it seems that there is intriguing evidence for crosstalk between the immune system and neurogenesis.

Studies of the anorexia mouse model Anx, a mutant that exhibits decreased food intake and death by 3 to 5 weeks were discussed by Ida Nilsson and she proposed an association with microglia/macrophage activation. Christina Cota discussed the dark-like (dal) mutant, which displays a similar phenotype to that of the Attractin mutant (Atm); reproductive degeneration, a darkened coat and vacuolation of the seminiferous tubules. She suggested that finding the dal gene would help to provide insight into spongiform degeneration. Differences seen in obesity and voluntary exercise in the pre-Collaborative Cross strains were presented by Wendy Mathes. Jun Xu discussed a comparatively rare type of study on the effects of siRNA interference in vivo; specifically of Jarid1c, a X-linked gene coding for a histone demethylase enzyme. Jarid1c has been linked with mental retardation, epilepsy and aggression in humans. Jarid1c siRNA injected into the dorsal hippocampus was claimed to alter object recognition in female mice (only during pre-oestrous and oestrous, not meta-oestrous), social interaction, and also was associated with shorter dendrites on some neurons. A new physiological role for the Kcnn2 gene, based on studies of the frissonnant mouse, was proposed by Jean Jaubert. Tomio Ono described the behavioural characterisation of the Alivin1/Amigo2 knockout mouse. The characterization of Melody, an ENU-induced mutation that causes sensorineural hearing loss in mice was presented by Andrew Parker.

Modeling disease part 2
T he plenary lecture for this session was given by Barbara Wold on inferring the genome-wide architecture and evolution of gene networks from ChIP-Seq and RNA-Seq data. These methods depend on the new, ultra-high throughput sequencing platforms, such as the Illumina Genome Analyser or Applied Biosystems SOLID sequencer. Absolute or relative quantitation of transcripts and detection of novel transcripts e.g. splice isoforms can be achieved using RNA-seq, whereas chromatin immunoprecipitation sequencing (ChIPSeq) allows exquisitely sensitive detection of protein-DNA interactions. The main focus of the talk was on muscle gene networks, particularly studies of the regulatory targets of the MyoD gene.

The following three presentations all concerned the generation and analysis of large-scale mutant resources; genetraps on the C57BL/6N genetic background (Andrei Golovko), manual annotation of the mouse genome and the European Conditional Mutant Mouse project (Mark Thomas) and the Knockout-mouse Project Data Coordination Center (Martin Ringwald).

Mutagenesis
In the plenary talk opening the last session of the meeting, Lee Niswander gave a stunning presentation in which the old cliché – “a picture tells a thousand words” – was shown to need an afterword - “…a video tells you even more!” Dr Niswander's topic was the genetics of neural tube closure defects (NTD) & folic acid responsiveness. One of the highlights from this was the real-time imaging of mouse embryos in ex utero culture; with 1 frame captured every 3 minutes, it allowed us to watch neural tube closure. The hindbrain looked like a zipper, whereas the forebrain behaved differently; with multiple closure sites and what appeared to be filipodia dynamically forming ‘bridges' between folds. Abnormal closure was also shown in mutant mice that model Fraser syndrome in humans. Finally, Dr Niswander described testing the effects of supplementing the mouse diet with folic acid and how, paradoxically, this may both prevent and potentiate NTD, depending on circumstance.

All the presentations in the this session concerned ENU-induced mutations, associated with a wide range of phenotypes, including: arrest of spermatocytes before the first meiotic metaphase (Mary Ann Handel), eye defects and deafness (Sally Cross), altered differentiation of cytotoxic T cells (Ryo Kominami), behavior modeling aspects of attention-deficit hyperactivity disorder (Tamio Furuse), and abnormalities in cells of the neural crest lineage (Dawn Watkins-Chow).

The conference closed with a lovely meal in the ornate and beautiful surroundings of a restaurant in an Art Nouveau style building; a marvelous end to a productive and enjoyable meeting.

Table 1 Awards presented at the International Mammalian Genome Conference