Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome

Nature Genetics

Volumn 43, Issue 11, 2011, Pages 1074-1081

  Carvalho, Claudia M B ^a   Ramocki, Melissa B ^a,b   Pehlivan, Davut ^a   Franco, Luis M ^a   Gonzaga Jauregui, Claudia ^a   Fang, Ping ^a   McCall, Alanna ^a   Pivnick, Eniko Karman ^c   Hines Dowell, Stacy ^d   Seaver, Laurie H ^e,i   Friehling, Linda ^f   Lee, Sansan ^e   Smith, Rosemarie ^g   Del Gaudio, Daniela ^a   Withers, Marjorie ^a   Liu, Pengfei ^a   Cheung, Sau Wai ^a   Belmont, John W ^a   Zoghbi, Huda Y ^a,b,h   Hastings, P J ^a   Lupski, James R ^a,b   more..

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b TEXAS CHILDREN S HOSPITAL   (United States)

^c UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

^d LE BONHEUR CHILDREN S HOSPITAL   (United States)

^e Kapiolani Medical Specialists   (United States)

^f Maine Medical Center ^*

^g MAINE MEDICAL CENTER   (United States)

^h HOWARD HUGHES MEDICAL INSTITUTE   (United States)

ⁱ UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA REPLICATION; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE; GENE DOSAGE; GENE DUPLICATION; GENE LOCUS; GENE REARRANGEMENT; HELA CELL; HUMAN; HUMAN CELL; HUMAN GENOME; MALE; MECP2 GENE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTHERN BLOTTING;

GENE REARRANGEMENT; GENOME, HUMAN; HUMANS; METHYL-CPG-BINDING PROTEIN 2; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 80055003130     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.944     Document Type: Article

References (42)

1. Carvalho, C.M. et al. Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching. Hum. Mol. Genet. 18, 2188-2203 (2009).
2. Morrow, D.M., Connelly, C. & Hieter, P. "Break copy" duplication: a model for chromosome fragment formation in Saccharomyces cerevisiae. Genetics 147, 371-382 (1997). (Pubitemid 27418552)
3. Smith, C.E., Llorente, B. & Symington, L.S. Template switching during break-induced replication. Nature 447, 102-105 (2007). (Pubitemid 46685835)
4. McEachern, M.J. & Haber, J.E. Break-induced replication and recombinational telomere elongation in yeast. Annu. Rev. Biochem. 75, 111-135 (2006). (Pubitemid 44118028)
5. Hastings, P.J., Ira, G. & Lupski, J.R. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet. 5, e1000327 (2009).
6. Hastings, P.J., Lupski, J.R., Rosenberg, S.M. & Ira, G. Mechanisms of change in gene copy number. Nat. Rev. Genet. 10, 551-564 (2009).
7. Lee, J.A., Carvalho, C.M. & Lupski, J.R. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131, 1235-1247 (2007). (Pubitemid 350297419)
8. Slack, A., Thornton, P.C., Magner, D.B., Rosenberg, S.M. & Hastings, P.J. On the mechanism of gene amplification induced under stress in Escherichia coli. PLoS Genet. 2, e48 (2006).
9. del Gaudio, D. et al. Increased MECP2 gene copy number as the result of genomic duplication in neurodevelopmentally delayed males. Genet. Med. 8, 784-792 (2006). (Pubitemid 44973767)
10. Small, K., Iber, J. & Warren, S.T. Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats. Nat. Genet. 16, 96-99 (1997). (Pubitemid 27198164)
11. Deem, A. et al. Break-induced replication is highly inaccurate. PLoS Biol. 9, e1000594 (2011).
12. (Pubitemid 43202498)
13. Lee, J.A. et al. Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect. Ann. Neurol. 59, 398-403 (2006). (Pubitemid 43202498)
14. Ramocki, M.B., Tavyev, Y.J. & Peters, S.U. The MECP2 duplication syndrome. Am. J. Med. Genet. A. 152A, 1079-1088 (2010).
15. Bailey, J.A. et al. Recent segmental duplications in the human genome. Science 297, 1003-1007 (2002). (Pubitemid 34856032)
16. Hu, X.Y., Ray, P.N., Murphy, E.G., Thompson, M.W. & Worton, R.G. Duplicational mutation at the Duchenne muscular dystrophy locus: its frequency, distribution, origin, and phenotype-genotype correlation. Am. J. Hum. Genet. 46, 682-695 (1990).
17. Mimault, C. et al. Proteolipoprotein gene analysis in 82 patients with sporadic Pelizaeus-Merzbacher disease: duplications, the major cause of the disease, originate more frequently in male germ cells, but point mutations do not. The Clinical European Network on Brain Dysmyelinating Disease. Am. J. Hum. Genet. 65, 360-369 (1999). (Pubitemid 30462994)
18. Whibley, A.C. et al. Fine-scale survey of X chromosome copy number variants and indels underlying intellectual disability. Am. J. Hum. Genet. 87, 173-188 (2010).
19. Bartsch, O. et al. Four unrelated patients with Lubs X-linked mental retardation syndrome and different Xq28 duplications. Am. J. Med. Genet. A. 152A, 305-312 (2010).
20. Lieber, M.R. The mechanism of human nonhomologous DNA end joining. J. Biol. Chem. 283, 1-5 (2008).
21. Sheen, C.R. et al. Double complex mutations involving F8 and FUNDC2 caused by distinct break-induced replication. Hum. Mutat. 28, 1198-1206 (2007). (Pubitemid 350250384)
22. Zhang, F., Carvalho, C.M. & Lupski, J.R. Complex human chromosomal and genomic rearrangements. Trends Genet. 25, 298-307 (2009).
23. Zhang, F. et al. The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat. Genet. 41, 849-853 (2009).
24. Yatsenko, S.A. et al. Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Hum. Mol. Genet. 18, 1924-1936 (2009).
25. Vialard, F. et al. Mechanism of intrachromosomal triplications 15q11-q13: a new clinical report. Am. J. Med. Genet. A. 118A, 229-234 (2003). (Pubitemid 37063931)
26. Wang, J. et al. Intrachromosomal triplication of 2q11.2-q21 in a severely malformed infant: case report and review of triplications and their possible mechanism. Am. J. Med. Genet. 82, 312-317 (1999). (Pubitemid 29075778)
27. Reddy, K.S. & Logan, J.J. Intrachromosomal triplications: molecular cytogenetic and clinical studies. Clin. Genet. 58, 134-141 (2000).
28. Lebofsky, R. & Bensimon, A. DNA replication origin plasticity and perturbed fork progression in human inverted repeats. Mol. Cell Biol. 25, 6789-6797 (2005). (Pubitemid 41023249)
29. Voineagu, I., Narayanan, V., Lobachev, K.S. & Mirkin, S.M. Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins. Proc. Natl. Acad. Sci. USA 105, 9936-9941 (2008).
30. Paek, A.L. et al. Fusion of nearby inverted repeats by a replication-based mechanism leads to formation of dicentric and acentric chromosomes that cause genome instability in budding yeast. Genes Dev. 23, 2861-2875 (2009).
31. Mizuno, K., Lambert, S., Baldacci, G., Murray, J.M. & Carr, A.M. Nearby inverted repeats fuse to generate acentric and dicentric palindromic chromosomes by a replication template exchange mechanism. Genes Dev. 23, 2876-2886 (2009).
32. Kitamura, E., Blow, J.J. & Tanaka, T.U. Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories. Cell 125, 1297-1308 (2006). (Pubitemid 43929088)
33. Mirkin, E.V. & Mirkin, S.M. Mechanisms of transcription-replication collisions in bacteria. Mol. Cell Biol. 25, 888-895 (2005). (Pubitemid 40165798)
34. Merrikh, H., Machon, C., Grainger, W.H., Grossman, A.D. & Soultanas, P. Co-directional replication-transcription conflicts lead to replication restart. Nature 470, 554-557 (2011).
35. Cáceres, M., Sullivan, R.T. & Thomas, J.W. A recurrent inversion on the eutherian X chromosome. Proc. Natl. Acad. Sci. USA 104, 18571-18576 (2007). (Pubitemid 350210738)
36. Lee, J.A., Cheung, S.W., Ward, P.A., Inoue, K. & Lupski, J.R. Prenatal diagnosis of PLP1 copy number by array comparative genomic hybridization. Prenat. Diagn. 25, 1188-1191 (2005). (Pubitemid 43164737)
37. Singleton, A.B. et al. α-Synuclein locus triplication causes Parkinson's disease. Science 302, 841 (2003). (Pubitemid 37339619)
38. Beunders, G. et al. A triplication of the Williams-Beuren syndrome region in a patient with mental retardation, a severe expressive language delay, behavioral problems and dysmorphisms. J. Med. Genet. 47, 271-275 (2010).
39. Lee, J.A. et al. Role of genomic architecture in PLP1 duplication causing Pelizaeus-Merzbacher disease. Hum. Mol. Genet. 15, 2250-2265 (2006). (Pubitemid 43985516)
40. Allen, R.C., Zoghbi, H.Y., Moseley, A.B., Rosenblatt, H.M. & Belmont, J.W. Methylation of HpaII and HhaI sites near the polymorphic CAG repeat in the human androgen-receptor gene correlates with X chromosome inactivation. Am. J. Hum. Genet. 51, 1229-1239 (1992). (Pubitemid 23001082)
41. Ramocki, M.B. et al. Autism and other neuropsychiatric symptoms are prevalent in individuals with MECP2 duplication syndrome. Ann. Neurol. 66, 771-782 (2009).
42. Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265 (2005). (Pubitemid 40202029)