Low copy repeats or segmental duplications are duplicated blocks of genomic DNA ranging in size from 1 to 200 kb. They result from interchromosomal or intrachromosomal duplications.
Keywords: low-copy repeats; duplicon; paralogy; evolution; diseases
Chromosome‐specific Repeats (Low‐copy Repeats)
M‐C Potier, CNRS UMR 7637, Paris, France
G Golfier, CNRS UMR 7637, Paris, France
EE Eichler, Case Western University School of Medicine, Cleveland, OH, USA
Published online: December 2007
DOI: 10.1002/9780470015902.a0005033.pub2
|
Figure 1. Possible genomic rearrangements mediated by chromosome-specific repeats. (a, b) Interchromosomal (a) and intrachromatid (b) rearrangements of direct repeats, which result in the formation of microdeletions, microduplications and an episomal circle for genes. (c, d) Possible outcomes of interchromosomal (c) and intrachromatid (d) rearrangements between repeats in an inverted configuration, resulting in acentric, dicentric and an inverted orientation of genes.
|
| References | |
| Amos-Landgraf JM, Ji Y, Gottlieb W et al. (1999) Chromosome breakage in the Prader–Willi and Angelman syndromes involves recombination between large, transcribed repeats at proximal and distal breakpoints. American Journal of Human Genetics 65: 370–386. | |
| Chen K, Manian P, Koeuth T et al. (1997) Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome. Nature Genetics 17: 154–163. | |
| Edelmann L, Pandita RK and Morrow BE (1999) Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome. American Journal of Human Genetics 64: 1076–1086. | |
| Eichler EE, Budarf ML, Rocchi M et al. (1997) Interchromosomal duplications of the adrenoleukodystrophy locus: a phenomenon of pericentromeric plasticity. Human Molecular Genetics 6: 991–1002. | |
| Francke U (1999) Williams–Beuren syndrome: genes and mechanisms. Human Molecular Genetics 8: 1947–1954. | |
| Golfier G, Chibon F, Aurias A et al. (2003) The 200-kb segmental duplication on human chromosome 21 originates from a pericentromeric dissemination involving human chromosomes 2, 18 and 13. Gene 312: 51–59. | |
| Horvath JE, Schwartz S and Eichler EE (2000) The mosaic structure of human pericentromeric DNA: a strategy for characterizing complex regions of the human genome. Human Molecular Genetics 9: 113–123. | |
| Jackson MS, Rocchi M, Thompson G et al. (1999) Sequences flanking the centromere of human chromosome 10 are a complex patchwork of arm-specific sequences, stable duplications, and unstable sequences with homologies to telomeric and other centromeric locations. Human Molecular Genetics 8: 205–215. | |
| Nickerson E and Nelson DL (1998) Molecular definition of pericentric inversion breakpoints occurring during the evolution of humans and chimpanzees. Genomics 50: 368–372. | |
| Potier M-C, Dutriaux A, Orti R et al. (1998) Two sequence-ready contigs spanning the two copies of a 200-kb duplication on human 21q: partial sequence and polymorphisms. Genomics 51: 417–426. | |
| Régnier V, Meddeb M, Lecointre G et al. (1997) Emergence and scattering of multiple neurofibromatosis (NF1)-related sequences during hominoid evolution suggest a process of pericentromeric interchromosomal transposition. Human Molecular Genetics 6: 9–16. | |
| Reiter L, Murakami T, Koeuth T et al. (1997) A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element. Nature Genetics 12: 288–297. | |
| Further Reading | |
| Alexandrov IA, Mitkevich SP and Yurov YB (1988) The phylogeny of human chromosome specific alpha satellites. Chromosoma 96: 443–453. | |
| Christian SL, Fantes JA, Mewborn SK, Huang B and Ledbetter DH (1999) Large genomic duplicons map to sites of instability in the Prader–Willi/Angelman syndrome chromosome region (15q11–q13). Human Molecular Genetics 8: 1025–1037. | |
| Eichler EE (2001) Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends in Genetics 17: 661–669. | |
| Eichler EE (2001) Segmental duplications: what's missing, misassigned, and misassembled – and should we care? Genome Research 11: 653–656. | |
| Eichler EE, Archidiacono N and Rocchi M (1999) CAGGG repeats and the pericentromeric duplication of the hominoid genome. Genome Research 9: 1048–1058. | |
| Emanuel BS and Shaikh TH (2001) Segmental duplications: an expanding role in genomic instability and disease. Nature Reviews Genetics 2: 791–800. | |
| Giglio S, Broman KW, Matsumoto N et al. (2001) Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements. American Journal of Human Genetics 68: 874–883. | |
| Guy J, Spalluto C, McMurray A et al. (2000) Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10q. Human Molecular Genetics 9: 2029–2042. | |
| Horvath JE, Bailey JA, Locke DP and Eichler EE (2001) Lessons from the human genome: transitions between euchromatin and heterochromatin. Human Molecular Genetics 10: 2215–2223. | |
| International Human Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–920. | |
| Ji Y, Eichler EE, Schwartz S and Nicholls RD (2000) Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Research 10: 597–610. | |
| Ji Y, Rebert NA, Joslin JM et al. (2000) Structure of the highly conserved HERC2 gene and of multiple partially duplicated paralogs in human. Genome Research 10: 319–329. | |
| Luijten M, Wang Y, Smith BT et al. (2000) Mechanism of spreading of the highly related neurofibromatosis type 1 (NF1) pseudogenes on chromosomes 2, 14 and 22. European Journal of Human Genetics 8: 209–214. | |
| Lupski JR (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends in Genetics 14: 417–422. | |
| Sprenger R, Schlagenhaufer R, Kerb R et al. (2000) Characterization of the glutathione S-transferase GSTT1 deletion: discrimination of all genotypes by polymerase chain reaction indicates a trimodular genotype–phenotype correlation. Pharmacogenetics 10: 557–565. | |
| Tilford CA, Kuroda-Kawaguchi T, Skaletsky H et al. (2001) A physical map of the human Y chromosome. Nature 409: 943–945. | |
