Abstract
Several recurrent common chromosomal deletion and duplication breakpoints have been localized to large, highly homologous, low-copy repeats (LCRs). The mechanism responsible for these rearrangements, viz., non-allelic homologous recombination between LCR copies, has been well established. However, fewer studies have examined the mechanisms responsible for non-recurrent rearrangements with non-homologous breakpoint regions. Here, we have analyzed four uncommon deletions of 17p11.2, involving the Smith–Magenis syndrome region. Using somatic cell hybrid lines created from patient lymphoblasts, we have utilized a strategy based on the polymerase chain reaction to refine the deletion breakpoints and to obtain sequence data at the deletion junction. Our analyses have revealed that two of the four deletions are a product of Alu/Alu recombination, whereas the remaining two deletions result from a non-homologous end-joining mechanism. Of the breakpoints studied, three of eight are located in LCRs, and five of eight are within repetitive elements, including Alu and MER5B sequences. These findings suggest that higher-order genomic architecture, such as LCRs, and smaller repetitive sequences, such as Alu elements, can mediate chromosomal deletions via homologous and non-homologous mechanisms. These data further implicate homologous recombination as the predominant mechanism of deletion formation in this genomic interval.
Similar content being viewed by others
References
Babcock M, Pavlicek A, Spiteri E, Kashork CD, Ioshikhes I, Shaffer LG, Jurka J, Morrow BE (2003) Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. Genome Res 13:2519–2532
Bailey JA, Liu G, Eichler EE (2003) An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet 73:823–834
Barbouti A, Stankiewicz P, Nusbaum C, Cuomo C, Cook A, Hoglund M, Johansson B, Hagemeijer A, Park SS, Mitelman F, Lupski JR, Fioretos T (2004) The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats. Am J Hum Genet 74:1–10
Bi W, Park SS, Shaw CJ, Withers MA, Patel PI, Lupski JR (2003) Reciprocal crossovers and a positional preference for strand exchange in recombination events resulting in deletion or duplication of chromosome 17p11.2. Am J Hum Genet 73:1302–1315
Caceres M, Ranz JM, Barbadilla A, Long M, Ruiz A (1999) Generation of a widespread Drosophila inversion by a transposable element. Science 285:415–418
Chen KS, Manian P, Koeuth T, Potocki L, Zhao Q, Chinault AC, Lee CC, Lupski JR (1997) Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome. Nat Genet 17:154–163
Deininger PL, Batzer MA (1999) Alu repeats and human disease. Mol Genet Metab 67:183–193
Guzzetta V, Franco B, Trask BJ, Zhang H, Saucedo-Cardenas O, Montes de Oca-Luna R, Greenberg F, Chinault AC, Lupski JR, Patel PI (1992) Somatic cell hybrids, sequence-tagged sites, simple repeat polymorphisms, and yeast artificial chromosomes for physical and genetic mapping of proximal 17p. Genomics 13:551–559
Inoue K, Osaka H, Thurston VC, Clarke JT, Yoneyama A, Rosenbarker L, Bird TD, Hodes ME, Shaffer LG, Lupski JR (2002) Genomic rearrangements resulting in PLP1 deletion occur by nonhomologous end joining and cause different dysmyelinating phenotypes in males and females. Am J Hum Genet 71:838–853
Kazazian HH Jr (2004) Mobile elements: drivers of genome evolution. Science 303:1626–1632
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Lieber MR, Ma Y, Pannicke U, Schwarz K (2003) Mechanism and regulation of human non-homologous DNA end-joining. Nat Rev Mol Cell Biol 4:712–720
Lim JK, Simmons MJ (1994) Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster. Bioessays 16:269–275
Lupski JR (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 14:417–422
Nobile C, Toffolatti L, Rizzi F, Simionati B, Nigro V, Cardazzo B, Patarnello T, Valle G, Danieli GA (2002) Analysis of 22 deletion breakpoints in dystrophin intron 49. Hum Genet 110:418–421
Shaw CJ, Lupski JR (2004) Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum Mol Genet 13 (Suppl 1):R57–R64
Shaw CJ, Bi W, Lupski JR (2002) Genetic proof of unequal meiotic crossovers in reciprocal deletion and duplication of 17p11.2. Am J Hum Genet 71:1072–1081
Shaw CJ, Withers MA, Lupski JR (2004) Uncommon deletions of the Smith–Magenis syndrome region can be recurrent when alternate low-copy repeats act as homologous recombination substrates. Am J Hum Genet 75:75–81
Stankiewicz P, Lupski JR (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet 18:74–82
Stankiewicz P, Shaw CJ, Dapper JD, Wakui K, Shaffer LG, Withers M, Elizondo L, Park SS, Lupski JR (2003) Genome architecture catalyzes nonrecurrent chromosomal rearrangements. Am J Hum Genet 72:1101–1116
Toffolatti L, Cardazzo B, Nobile C, Danieli GA, Gualandi F, Muntoni F, Abbs S, Zanetti P, Angelini C, Ferlini A, Fanin M, Patarnello T (2002) Investigating the mechanism of chromosomal deletion: characterization of 39 deletion breakpoints in introns 47 and 48 of the human dystrophin gene. Genomics 80:523–530
Venturin M, Gervasini C, Orzan F, Bentivegna A, Corrado L, Colapietro P, Friso A, Tenconi R, Upadhyaya M, Larizza L, Riva P (2004) Evidence for non-homologous end joining and non-allelic homologous recombination in atypical NF1 microdeletions. Hum Genet 115:69–80
Zhang J, Peterson T (1999) Genome rearrangements by nonlinear transposons in maize. Genetics 153:1403–1410
Lupski JR (2004) Hotspots of homologous recombination in the human genome: not all homologous sequences are equal. Genome Biol 5:242
Stankiewicz P, Shaw CJ, Withers M, Inoue K, Lupski JR (2004) Serial segmental duplications during primate evolution result in complex human genome architecture. Genome Res: 14: 2209–2220
Acknowledgements
We thank the patients and their parents for participation. We are also grateful to Dr. K. Inoue and Dr. P. Stankiewicz for critical reviews, and Marjorie Withers for technical assistance. This work was supported in part by grants from the National Institute of Child Health and Human Development (PO1 HD39420) and the Mental Retardation Research Center (HD24064).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Shaw, C.J., Lupski, J.R. Non-recurrent 17p11.2 deletions are generated by homologous and non-homologous mechanisms. Hum Genet 116, 1–7 (2005). https://doi.org/10.1007/s00439-004-1204-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00439-004-1204-9