A large fraction of genome variation between individuals is comprised of submicroscopic copy number variation of genomic DNA segments. We assessed the relative contribution of structural changes and gene dosage alterations on phenotypic outcomes with mouse models of Smith-Magenis and Potocki-Lupski syndromes. We phenotyped mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+), and balanced 2n compound heterozygous (Deletion/Duplication) copies of the same region. Parallel to the observations made in humans, such variation in gene copy number was sufficient to generate phenotypic consequences: in a number of cases diametrically opposing phenotypes were associated with gain versus loss of gene content. Surprisingly, some neurobehavioral traits were not rescued by restoration of the normal gene copy number. Transcriptome profiling showed that a highly significant propensity of transcriptional changes map to the engineered interval in the five assessed tissues. A statistically significant overrepresentation of the genes mapping to the entire length of the engineered chromosome was also found in the top-ranked differentially expressed genes in the mice containing rearranged chromosomes, regardless of the nature of the rearrangement, an observation robust across different cell lineages of the central nervous system. Our data indicate that a structural change at a given position of the human genome may affect not only locus and adjacent gene expression but also “genome regulation.” Furthermore, structural change can cause the same perturbation in particular pathways regardless of gene dosage. Thus, the presence of a genomic structural change, as well as gene dosage imbalance, contributes to the ultimate phenotype.
References
[1]
Iafrate A. J, Feuk L, Rivera M. N, Listewnik M. L, Donahoe P. K, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949–951.
[2]
Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525–528.
[3]
Redon R, Ishikawa S, Fitch K. R, Feuk L, Perry G. H, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444–454.
[4]
Conrad D. F, Pinto D, Redon R, Feuk L, Gokcumen O, et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature 464: 704–712.
[5]
Reymond A, Henrichsen C. N, Harewood L, Merla G (2007) Side effects of genome structural changes. Curr Opin Genet Dev 17: 381–386.
[6]
Hurles M. E, Dermitzakis E. T, Tyler-Smith C (2008) The functional impact of structural variation in humans. Trends Genet 24: 238–245.
[7]
Henrichsen C. N, Chaignat E, Reymond A (2009) Copy number variants, diseases and gene expression. Hum Mol Genet 18: R1–R8.
[8]
Carvalho C. M, Zhang F, Lupski J. R (2010) Evolution in health and medicine Sackler colloquium: genomic disorders: a window into human gene and genome evolution. Proc Natl Acad Sci U S A 107: Suppl 11765–1771.
[9]
Merla G, Howald C, Henrichsen C. N, Lyle R, Wyss C, et al. (2006) Submicroscopic deletion in patients with Williams-Beuren syndrome influences expression levels of the nonhemizygous flanking genes. Am J Hum Genet 79: 332–341.
[10]
Stranger B. E, Forrest M. S, Dunning M, Ingle C. E, Beazley C, et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848–853.
[11]
Molina J, Carmona-Mora P, Chrast J, Krall P. M, Canales C. P, et al. (2008) Abnormal social behaviors and altered gene expression rates in a mouse model for Potocki-Lupski syndrome. Hum Mol Genet 17: 2486–2495.
[12]
Henrichsen C. N, Vinckenbosch N, Zollner S, Chaignat E, Pradervand S, et al. (2009) Segmental copy number variation shapes tissue transcriptomes. Nat Genet 41: 424–429.
[13]
Cahan P, Li Y, Izumi M, Graubert T. A (2009) The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nat Genet 41: 430–437.
[14]
Perry G. H, Dominy N. J, Claw K. G, Lee A. S, Fiegler H, et al. (2007) Diet and the evolution of human amylase gene copy number variation. Nat Genet 39: 1256–1260.
[15]
Lupski J. R (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 14: 417–422.
[16]
Stankiewicz P, Lupski J. R (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet 18: 74–82.
[17]
Lupski J. R (2009) Genomic disorders ten years on. Genome Med 1: 42.
[18]
Ionita-Laza I, Rogers A. J, Lange C, Raby B. A, Lee C (2009) Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis. Genomics 93: 22–26.
[19]
Zhang F, Gu W, Hurles M. E, Lupski J. R (2009) Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 10: 451–481.
[20]
Fanciulli M, Petretto E, Aitman T. J (2010) Gene copy number variation and common human disease. Clin Genet 77: 201–213.
[21]
Stankiewicz P, Lupski J. R (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61: 437–455.
[22]
Chen K. S, Manian P, Koeuth T, Potocki L, Zhao Q, et al. (1997) Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome. Nat Genet 17: 154–163.
[23]
Bi W, Yan J, Stankiewicz P, Park S. S, Walz K, et al. (2002) Genes in a refined Smith-Magenis syndrome critical deletion interval on chromosome 17p11.2 and the syntenic region of the mouse. Genome Res 12: 713–728.
[24]
Potocki L, Chen K. S, Park S. S, Osterholm D. E, Withers M. A, et al. (2000) Molecular mechanism for duplication 17p11.2- the homologous recombination reciprocal of the Smith-Magenis microdeletion. Nat Genet 24: 84–87.
[25]
Slager R. E, Newton T. L, Vlangos C. N, Finucane B, Elsea S. H (2003) Mutations in RAI1 associated with Smith-Magenis syndrome. Nat Genet 33: 466–468.
[26]
Bi W, Saifi G. M, Girirajan S, Shi X, Szomju B, et al. (2006) RAI1 point mutations, CAG repeat variation, and SNP analysis in non-deletion Smith-Magenis syndrome. Am J Med Genet A 140: 2454–2463.
[27]
Walz K, Paylor R, Yan J, Bi W, Lupski J. R (2006) Rai1 duplication causes physical and behavioral phenotypes in a mouse model of dup(17)(p11.2p11.2). J Clin Invest 116: 3035–3041.
[28]
Zhang F, Potocki L, Sampson J. B, Liu P, Sanchez-Valle A, et al. (2010) Identification of uncommon recurrent Potocki-Lupski syndrome-associated duplications and the distribution of rearrangement types and mechanisms in PTLS. Am J Hum Genet 86: 462–470.
[29]
Potocki L, Shaw C. J, Stankiewicz P, Lupski J. R (2003) Variability in clinical phenotype despite common chromosomal deletion in Smith-Magenis syndrome [del(17)(p11.2p11.2)]. Genet Med 5: 430–434.
[30]
Yan J, Bi W, Lupski J. R (2007) Penetrance of craniofacial anomalies in mouse models of Smith-Magenis syndrome is modified by genomic sequence surrounding Rai1: not all null alleles are alike. Am J Hum Genet 80: 518–525.
[31]
Edelman E. A, Girirajan S, Finucane B, Patel P. I, Lupski J. R, Smith A. C, Elsea S. H (2007) Gender, genotype and phenotype differences in Smith-Magenis syndrome: a meta-analysis of 105 cases. Clin Genet 71: 540–550.
[32]
Yang Y, Chung E. K, Wu Y. L, Savelli S. L, Nagaraja H. N, et al. (2007) Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am J Hum Genet 80: 1037–1054.
[33]
Elsea S. H, Girirajan S (2008) Smith-Magenis syndrome. Eur J Hum Genet 16: 412–421.
[34]
Walz K, Caratini-Rivera S, Bi W, Fonseca P, Mansouri D. L, et al. (2003) Modeling del(17)(p11.2p11.2) and dup(17)(p11.2p11.2) contiguous gene syndromes by chromosome engineering in mice: phenotypic consequences of gene dosage imbalance. Mol Cell Biol 23: 3646–3655.
[35]
Walz K, Spencer C, Kaasik K, Lee C. C, Lupski J. R, et al. (2004) Behavioral characterization of mouse models for Smith-Magenis syndrome and dup(17)(p11.2p11.2). Hum Mol Genet 13: 367–378.
[36]
Nadler J. J, Moy S. S, Dold G, Trang D, Simmons N, et al. (2004) Automated apparatus for quantitation of social approach behaviors in mice. Genes Brain Behav 3: 303–314.
[37]
Le Hellard S, Muhleisen T. W, Djurovic S, Ferno J, Ouriaghi Z, et al. (2010) Polymorphisms in SREBF1 and SREBF2, two antipsychotic-activated transcription factors controlling cellular lipogenesis, are associated with schizophrenia in German and Scandinavian samples. Mol Psychiatry 15: 463–472.
[38]
Joober R, Benkelfat C, Toulouse A, Lafreniere R. G, Lal S, et al. (1999) Analysis of 14 CAG repeat-containing genes in schizophrenia. Am J Med Genet 88: 694–699.
[39]
Toulouse A, Rochefort D, Roussel J, Joober R, Rouleau G. A (2003) Molecular cloning and characterization of human RAI1, a gene associated with schizophrenia. Genomics 82: 162–171.
[40]
Treadwell-Deering D. E, Powell M. P, Potocki L (2010) Cognitive and behavioral characterization of the Potocki-Lupski syndrome (duplication 17p11.2). J Dev Behav Pediatr 31: 137–143.
[41]
Potocki L, Bi W, Treadwell-Deering D, Carvalho C. M, Eifert A, et al. (2007) Characterization of Potocki-Lupski syndrome (dup(17)(p11.2p11.2)) and delineation of a dosage-sensitive critical interval that can convey an autism phenotype. Am J Hum Genet 80: 633–649.
[42]
Carelle-Calmels N, Saugier-Veber P, Girard-Lemaire F, Rudolf G, Doray B, et al. (2009) Genetic compensation in a human genomic disorder. N Engl J Med 360: 1211–1216.
[43]
Wolfer D. P, Crusio W. E, Lipp H. P (2002) Knockout mice: simple solutions to the problems of genetic background and flanking genes. Trends Neurosci 25: 336–340.
[44]
Valor L. M, Grant S. G (2007) Clustered gene expression changes flank targeted gene loci in knockout mice. PLoS One 2: e1303. doi:10.1371/journal.pone.0001303.
[45]
Gerlai R (1996) Gene-targeting studies of mammalian behavior: is it the mutation or the background genotype? Trends Neurosci 19: 177–181.
[46]
Alberts R, Terpstra P, Li Y, Breitling R, Nap J. P, et al. (2007) Sequence polymorphisms cause many false cis eQTLs. PLoS One 2: e622. doi:10.1371/journal.pone.0000622.
[47]
Benovoy D, Kwan T, Majewski J (2008) Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments. Nucleic Acids Res 36: 4417–4423.
[48]
Walter N. A, McWeeney S. K, Peters S. T, Belknap J. K, Hitzemann R, et al. (2007) SNPs matter: impact on detection of differential expression. Nat Methods 4: 679–680.
[49]
Fiering S, Epner E, Robinson K, Zhuang Y, Telling A, et al. (1995) Targeted deletion of 5′HS2 of the murine beta-globin LCR reveals that it is not essential for proper regulation of the beta-globin locus. Genes Dev 9: 2203–2213.
[50]
Pham C. T, MacIvor D. M, Hug B. A, Heusel J. W, Ley T. J (1996) Long-range disruption of gene expression by a selectable marker cassette. Proc Natl Acad Sci U S A 93: 13090–13095.
[51]
Scarff K. L, Ung K. S, Sun J, Bird P. I (2003) A retained selection cassette increases reporter gene expression without affecting tissue distribution in SPI3 knockout/GFP knock-in mice. Genesis 36: 149–157.
[52]
Muller U (1999) Ten years of gene targeting: targeted mouse mutants, from vector design to phenotype analysis. Mech Dev 82: 3–21.
[53]
Kleinjan D. A, van Heyningen V (2005) Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet 76: 8–32.
[54]
Dermitzakis E. T, Reymond A, Scamuffa N, Ucla C, Kirkness E, et al. (2003) Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science 302: 1033–1035.
[55]
Reymond A, Marigo V, Yaylaoglu M. B, Leoni A, Ucla C, et al. (2002) Human chromosome 21 gene expression atlas in the mouse. Nature 420: 582–586.
[56]
Saxonov S, Berg P, Brutlag D. L (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 103: 1412–1417.
[57]
Khaitovich P, Hellmann I, Enard W, Nowick K, Leinweber M, et al. (2005) Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309: 1850–1854.
[58]
She X, Cheng Z, Zollner S, Church D. M, Eichler E. E (2008) Mouse segmental duplication and copy number variation. Nat Genet 40: 909–914.
[59]
Brunetti-Pierri N, Berg J. S, Scaglia F, Belmont J, Bacino C. A, et al. (2008) Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities. Nat Genet 40: 1466–1471.
[60]
Shinawi M, Liu P, Kang S. H, Shen J, Belmont J. W, et al. (2010) Recurrent reciprocal 16p11.2 rearrangements associated with global developmental delay, behavioral problems, dysmorphism, epilepsy, and abnormal head size. J Med Genet 47: 332–341.
[61]
McCarthy S. E, Makarov V, Kirov G, Addington A. M, McClellan J, et al. (2009) Microduplications of 16p11.2 are associated with schizophrenia. Nat Genet 41: 1223–1227.
[62]
Consortium (2008) Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature 455: 237–241.
[63]
Stefansson H, Rujescu D, Cichon S, Pietilainen O. P, Ingason A, et al. (2008) Large recurrent microdeletions associated with schizophrenia. Nature 455: 232–236.
[64]
Mefford H. C, Sharp A. J, Baker C, Itsara A, Jiang Z, et al. (2008) Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med 359: 1685–1699.
[65]
Weiss L. A, Shen Y, Korn J. M, Arking D. E, Miller D. T, et al. (2008) Association between microdeletion and microduplication at 16p11.2 and autism. N Engl J Med 358: 667–675.
[66]
Walters R. G, Jacquemont S, Valsesia A, de Smith A. J, Martinet D, et al. (2010) A new highly penetrant form of obesity due to deletions on chromosome 16p11.2. Nature 463: 671–675.
[67]
Bochukova E. G, Huang N, Keogh J, Henning E, Purmann C, et al. (2010) Large, rare chromosomal deletions associated with severe early-onset obesity. Nature 463: 666–670.
[68]
Consortium T. I. S (2008) Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature 455: 237–241.
[69]
Walsh T, McClellan J. M, McCarthy S. E, Addington A. M, Pierce S. B, et al. (2008) Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science 320: 539–543.
[70]
Bijlsma E. K, Gijsbers A. C, Schuurs-Hoeijmakers J. H, van Haeringen A, Fransen van de Putte D. E, et al. (2009) Extending the phenotype of recurrent rearrangements of 16p11.2: deletions in mentally retarded patients without autism and in normal individuals. Eur J Med Genet 52: 77–87.
[71]
Kumar R. A, KaraMohamed S, Sudi J, Conrad D. F, Brune C, et al. (2008) Recurrent 16p11.2 microdeletions in autism. Hum Mol Genet 17: 628–638.
[72]
Marshall C. R, Noor A, Vincent J. B, Lionel A. C, Feuk L, et al. (2008) Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet 82: 477–488.
[73]
Crespi B, Badcock C (2008) Psychosis and autism as diametrical disorders of the social brain. Behav Brain Sci 31: 241–261; discussion 261–320.
[74]
Crespi B, Stead P, Elliot M (2010) Evolution in health and medicine Sackler colloquium: comparative genomics of autism and schizophrenia. Proc Natl Acad Sci U S A 107: Suppl 11736–1741.
[75]
Crespi B, Summers K, Dorus S (2009) Genomic sister-disorders of neurodevelopment: an evolutionary approach. Evolutionary Applications 2: 81–100.
[76]
Girirajan S, Patel N, Slager R. E, Tokarz M. E, Bucan M, et al. (2008) How much is too much? Phenotypic consequences of Rai1 overexpression in mice. Eur J Hum Genet 16: 941–954.
[77]
De Leersnyder H (2006) Inverted rhythm of melatonin secretion in Smith-Magenis syndrome: from symptoms to treatment. Trends Endocrinol Metab 17: 291–298.
[78]
Gropman A. L, Elsea S, Duncan W. C Jr, Smith A. C (2007) New developments in Smith-Magenis syndrome (del 17p11.2). Curr Opin Neurol 20: 125–134.
[79]
Gabellini D, Green M. R, Tupler R (2002) Inappropriate gene activation in FSHD: a repressor complex binds a chromosomal repeat deleted in dystrophic muscle. Cell 110: 339–348.
[80]
Lettice L. A, Horikoshi T, Heaney S. J, van Baren M. J, van der Linde H. C, et al. (2002) Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proc Natl Acad Sci U S A 99: 7548–7553.
[81]
Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, et al. (2007) Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 17: 746–759.
[82]
Finlan L. E, Sproul D, Thomson I, Boyle S, Kerr E, et al. (2008) Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 4: e1000039. doi:10.1371/journal.pgen.1000039.
[83]
Deng W, Blobel G. A (2010) Do chromatin loops provide epigenetic gene expression states? Curr Opin Genet Dev 20: 548–554.
[84]
Harewood L, Schutz F, Boyle S, Perry P, Delorenzi M, et al. (2010) The effect of translocation-induced nuclear reorganization on gene expression. Genome Res 20: 554–564.
[85]
McCarroll S. A (2008) Extending genome-wide association studies to copy-number variation. Hum Mol Genet 17: R135–R142.
