Massively Parallel Sequencing Reveals the Complex Structure of an Irradiated Human Chromosome on a Mouse Background in the Tc1 Model of Down Syndrome

Down syndrome (DS) is caused by trisomy of chromosome 21 (Hsa21) and presents a complex phenotype that arises from abnormal dosage of genes on this chromosome. However, the individual dosage-sensitive genes underlying each phenotype remain largely unknown. To help dissect genotype – phenotype correlations in this complex syndrome, the first fully transchromosomic mouse model, the Tc1 mouse, which carries a copy of human chromosome 21 was produced in 2005. The Tc1 strain is trisomic for the majority of genes that cause phenotypes associated with DS, and this freely available mouse strain has become used widely to study DS, the effects of gene dosage abnormalities, and the effect on the basic biology of cells when a mouse carries a freely segregating human chromosome. Tc1 mice were created by a process that included irradiation microcell-mediated chromosome transfer of Hsa21 into recipient mouse embryonic stem cells. Here, the combination of next generation sequencing, array-CGH and fluorescence in situ hybridization technologies has enabled us to identify unsuspected rearrangements of Hsa21 in this mouse model; revealing one deletion, six duplications and more than 25 de novo structural rearrangements. Our study is not only essential for informing functional studies of the Tc1 mouse but also (1) presents for the first time a detailed sequence analysis of the effects of gamma radiation on an entire human chromosome, which gives some mechanistic insight into the effects of radiation damage on DNA, and (2) overcomes specific technical difficulties of assaying a human chromosome on a mouse background where highly conserved sequences may confound the analysis. Sequence data generated in this study is deposited in the ENA database, Study Accession number: ERP000439.

[1]  D. Nižetić,et al.  Tumour angiogenesis is reduced in the Tc1 mouse model of Down Syndrome , 2010, Nature.

[2]  N. Carter,et al.  Flow analysis and sorting of microchromosomes (<3 Mb) , 2007, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[3]  N. Nowak,et al.  Duplication of the entire 22.9 Mb human chromosome 21 syntenic region on mouse chromosome 16 causes cardiovascular and gastrointestinal abnormalities. , 2007, Human molecular genetics.

[4]  R. Redon,et al.  Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes , 2007, Nature Protocols.

[5]  Amy Slender,et al.  Altered regulation of tau phosphorylation in a mouse model of down syndrome aging , 2012, Neurobiology of Aging.

[6]  A. Andreadis,et al.  Heterogeneous nuclear ribonucleoprotein E3 modestly activates splicing of tau exon 10 via its proximal downstream intron, a hotspot for frontotemporal dementia mutations. , 2010, Gene.

[7]  Z. Ning,et al.  Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes , 2009, Nature Methods.

[8]  Suraiya Rasheed,et al.  Characterization of a newly derived human sarcoma cell line (HT‐1080) , 1974, Cancer.

[9]  P. Jeggo,et al.  Radiation-induced genomic rearrangements formed by nonhomologous end-joining of DNA double-strand breaks. , 2001, Cancer research.

[10]  L. Povirk.  Biochemical mechanisms of chromosomal translocations resulting from DNA double-strand breaks. , 2006, DNA repair.

[11]  N. Carter,et al.  Chromosome specific paints from a high resolution flow karyotype of the mouse , 1995, Nature Genetics.

[12]  V. Tybulewicz,et al.  New techniques to understand chromosome dosage: mouse models of aneuploidy. , 2006, Human molecular genetics.

[13]  Elizabeth M.C. Fisher,et al.  Impairments in motor coordination without major changes in cerebellar plasticity in the Tc1 mouse model of Down syndrome , 2009, Human molecular genetics.

[14]  Michael D. Wilson,et al.  Species-Specific Transcription in Mice Carrying Human Chromosome 21 , 2008, Science.

[15]  Amy Slender,et al.  Down's syndrome-like cardiac developmental defects in embryos of the transchromosomic Tc1 mouse , 2010, Cardiovascular research.

[16]  Y. Hérault,et al.  Inducing Segmental Aneuploid Mosaicism in the Mouse Through Targeted Asymmetric Sister Chromatid Event of Recombination , 2008, Genetics.

[17]  岩崎 民子.  SOURCES AND EFFECTS OF IONIZING RADIATION : United Nations Scientific Committee on the Effects of Atomic Radiation UNSCEAR 2000 Report to the General Assembly, with Scientific Annexes , 2002 .

[18]  S. Orkin,et al.  Perturbed hematopoiesis in the Tc1 mouse model of Down syndrome. , 2010, Blood.

[19]  Yueming Ding,et al.  Molecular characterization of the translocation breakpoints in the Down syndrome mouse model Ts65Dn , 2011, Mammalian Genome.

[20]  George Stoica,et al.  A mouse model of Down syndrome trisomic for all human chromosome 21 syntenic regions. , 2010, Human molecular genetics.

[21]  S. Minoshima,et al.  Initial characterization of an uromodulin-like 1 gene on human chromosome 21q22.3. , 2004, Biochemical and biophysical research communications.

[22]  K. Min,et al.  Upregulation of three Drosophila homologs of human chromosome 21 genes alters synaptic function: Implications for Down syndrome , 2009, Proceedings of the National Academy of Sciences.

[23]  J. M. Weitzner.  Alopecia areata. , 1990, American family physician.

[24]  Laura C. Andreae,et al.  Preservation of long-term memory and synaptic plasticity despite short-term impairments in the Tc1 mouse model of Down syndrome. , 2008, Learning & memory.

[25]  Kamaleldin E Elagib,et al.  RUNX1 and GATA-1 coexpression and cooperation in megakaryocytic differentiation. , 2003, Blood.

[26]  J. Lupski,et al.  A DNA Replication Mechanism for Generating Nonrecurrent Rearrangements Associated with Genomic Disorders , 2007, Cell.

[27]  P. Yarowsky,et al.  Astrocytosis and axonal proliferation in the hippocampus of S100b transgenic mice. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[28]  M. Löbrich,et al.  Repair of x-ray-induced DNA double-strand breaks in specific Not I restriction fragments in human fibroblasts: joining of correct and incorrect ends. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Lora J. H. Bean,et al.  Epidemiology of Down syndrome. , 2007, Mental retardation and developmental disabilities research reviews.

[30]  P Vincens,et al.  Computational method to predict mitochondrially imported proteins and their targeting sequences. , 1996, European journal of biochemistry.

[31]  J. Lupski,et al.  Complex human chromosomal and genomic rearrangements. , 2009, Trends in genetics : TIG.

[32]  Y. Hérault,et al.  Identification of the translocation breakpoints in the Ts65Dn and Ts1Cje mouse lines: relevance for modeling down syndrome , 2011, Mammalian Genome.

[33]  N. Carter,et al.  Factors affecting flow karyotype resolution , 2006, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[34]  Elizabeth M.C. Fisher,et al.  Down syndrome—recent progress and future prospects , 2009, Human molecular genetics.

[35]  Richard Durbin,et al.  A large genome center's improvements to the Illumina sequencing system , 2008, Nature Methods.

[36]  M. Delorenzi,et al.  Natural gene-expression variation in Down syndrome modulates the outcome of gene-dosage imbalance. , 2007, American journal of human genetics.

[37]  J M Delabar,et al.  Classification of human chromosome 21 gene-expression variations in Down syndrome: impact on disease phenotypes. , 2007, American journal of human genetics.

[38]  M. Pericak-Vance,et al.  Segregation of a missense mutation in the amyloid precursor protein gene with familial Alzheimer's disease , 1991, Nature.

[39]  Antony V. Cox,et al.  Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing , 2008, Nature Genetics.

[40]  Y. Hérault,et al.  Modeling the monosomy for the telomeric part of human chromosome 21 reveals haploinsufficient genes modulating the inflammatory and airway responses. , 2007, Human molecular genetics.

[41]  K. Gardiner.  Transcriptional Dysregulation in Down Syndrome: Predictions for Altered Protein Complex Stoichiometries and Post-translational Modifications, and Consequences for Learning/Behavior Genes ELK, CREB, and the Estrogen and Glucocorticoid Receptors , 2006, Behavior genetics.

[42]  H. Winter,et al.  Human hair keratin-associated proteins (KAPs). , 2006, International review of cytology.

[43]  Dean Nizetic,et al.  An Aneuploid Mouse Strain Carrying Human Chromosome 21 with Down Syndrome Phenotypes , 2005, Science.

[44]  Malcolm Crick,et al.  United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) activities and issues , 2011 .