1
|
Ahmad T, Neville M, Marshall SE, Armuzzi A, Mulcahy-Hawes K, Crawshaw J, Sato H, Ling KL, Barnardo M, Goldthorpe S, Walton R, Bunce M, Jewell DP, Welsh KI. Haplotype-specific linkage disequilibrium patterns define the genetic topography of the human MHC. Hum Mol Genet 2003. [PMID: 12620970 DOI: 10.1093/hmg/ddg066] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Detailed knowledge of linkage disequilibrium (LD) is regarded as a prerequisite for population-based disease gene mapping. Variable patterns across the human genome are now recognized, both between regions and populations. Here, we demonstrate that LD may also vary within a genomic region in a haplotype-specific manner. In 864 Caucasian unrelated individuals, we describe haplotype-specific LD patterns across the human MHC by the construction of gene-specific allelic haplotypes at 25 loci between HLA-A and Tapasin. Strong and extensive LD is found across both common and rare haplotypes, suggesting that haplotype structure is influenced by factors other than genetic drift, including both selection and differential haplotype recombination. Knowledge of haplotype-specific LD in the HLA may explain the apparent discrepant data from previous studies of global LD, help delineate key areas in mapping HLA-associated diseases and, together with recombination data, provide valuable information about a population's demographic history and the selective pressures operating on it.
Collapse
Affiliation(s)
- Tariq Ahmad
- Gastroenterology Unit, University of Oxford, Gibson Laboratories, Radcliffe Infirmary, Woodstock Road, Oxford, OX2 6HE, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Cullen M, Perfetto SP, Klitz W, Nelson G, Carrington M. High-resolution patterns of meiotic recombination across the human major histocompatibility complex. Am J Hum Genet 2002; 71:759-76. [PMID: 12297984 PMCID: PMC378534 DOI: 10.1086/342973] [Citation(s) in RCA: 171] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2002] [Accepted: 06/27/2002] [Indexed: 11/03/2022] Open
Abstract
Definitive characteristics of meiotic recombination events over large (i.e., >1 Mb) segments of the human genome remain obscure, yet they are essential for establishing the haplotypic structure of the genome and for efficient mapping of complex traits. We present a high-resolution map of recombination at the kilobase level across a 3.3-Mb interval encompassing the major histocompatibility complex (MHC). Genotyping of 20,031 single sperm from 12 individuals resulted in the identification and fine mapping of 325 recombinant chromosomes within genomic intervals as small as 7 kb. Several principal characteristics of recombination in this region were observed: (1) rates of recombination can differ significantly between individuals; (2) intense hot spots of recombination occur at least every 0.8 Mb but are not necessarily evenly spaced; (3) distribution in the location of recombination events can differ significantly among individuals; (4) between hot spots, low levels of recombination occur fairly evenly across 100-kb segments, suggesting the presence of warm spots of recombination; and (5) specific sequence motifs associate significantly with recombination distribution. These data provide a plausible model for recombination patterns of the human genome overall.
Collapse
Affiliation(s)
- Michael Cullen
- Basic Research Program, SAIC–Frederick, National Cancer Institute, Frederick, MD; Graduate Genetics Program, Institute for Biomedical Sciences, The George Washington University, Washington DC; USA Program Vaccine Research Center, National Institutes of Health, Bethesda; Children’s Hospital Oakland Research Institute, Oakland, CA; and School of Public Health, University of California, Berkeley
| | - Stephen P. Perfetto
- Basic Research Program, SAIC–Frederick, National Cancer Institute, Frederick, MD; Graduate Genetics Program, Institute for Biomedical Sciences, The George Washington University, Washington DC; USA Program Vaccine Research Center, National Institutes of Health, Bethesda; Children’s Hospital Oakland Research Institute, Oakland, CA; and School of Public Health, University of California, Berkeley
| | - William Klitz
- Basic Research Program, SAIC–Frederick, National Cancer Institute, Frederick, MD; Graduate Genetics Program, Institute for Biomedical Sciences, The George Washington University, Washington DC; USA Program Vaccine Research Center, National Institutes of Health, Bethesda; Children’s Hospital Oakland Research Institute, Oakland, CA; and School of Public Health, University of California, Berkeley
| | - George Nelson
- Basic Research Program, SAIC–Frederick, National Cancer Institute, Frederick, MD; Graduate Genetics Program, Institute for Biomedical Sciences, The George Washington University, Washington DC; USA Program Vaccine Research Center, National Institutes of Health, Bethesda; Children’s Hospital Oakland Research Institute, Oakland, CA; and School of Public Health, University of California, Berkeley
| | - Mary Carrington
- Basic Research Program, SAIC–Frederick, National Cancer Institute, Frederick, MD; Graduate Genetics Program, Institute for Biomedical Sciences, The George Washington University, Washington DC; USA Program Vaccine Research Center, National Institutes of Health, Bethesda; Children’s Hospital Oakland Research Institute, Oakland, CA; and School of Public Health, University of California, Berkeley
| |
Collapse
|
3
|
Snoek M, Teuscher C, van Vugt H. Molecular Analysis of the Major MHC Recombinational Hot Spot Located Within the G7c Gene of the Murine Class III Region That Is Involved in Disease Susceptibility. THE JOURNAL OF IMMUNOLOGY 1998. [DOI: 10.4049/jimmunol.160.1.266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
Recombination within the MHC does not occur at random, but crossovers are clustered in hot spots. We previously described a recombinational hotspot within the 50-kb Hsp70.3–G7 interval in the class III region of the mouse MHC. The parental haplotypes of recombinants with crossovers in this region represent the majority of the laboratory haplotypes (a, b, d, dx, k, m, p, px, q, s, and u). Using microsatellite markers and sequence-based nucleotide polymorphisms, the breakpoint intervals of 30 recombinants were mapped to a 5-kb-long interval within the G7c gene adjacent to G7a. Recombination within the G7c hot spot does not appear to be restricted to certain haplotypes. Sequence motifs that had been suggested to be associated with site-restricted meiotic recombination were absent in the vicinity of the G7c hot spot, and hence, these sequence motifs are no prerequisite for meiotic recombination. The G7c hot spot resides in a region to which a number of disease susceptibility loci have been mapped, including susceptibility to cleft palate, experimental autoimmune allergic orchitis, and chemically induced alveolar lung tumors. The exact localization of crossovers in recombinants that have been used in functional studies is important for mapping susceptibility genes and limits the number of candidate genes.
Collapse
Affiliation(s)
- Margriet Snoek
- *Division of Molecular Genetics, The Netherlands Cancer Institute (Antoni van Leeuwenhoek), Amsterdam, The Netherlands; and
| | - Cory Teuscher
- †Department of Veterinary Pathobiology, University of Illinois, Urbana, IL 61801
| | - Huub van Vugt
- *Division of Molecular Genetics, The Netherlands Cancer Institute (Antoni van Leeuwenhoek), Amsterdam, The Netherlands; and
| |
Collapse
|
4
|
Wahls WP, Moore PD. Recombination hotspot activity of hypervariable minisatellite DNA requires minisatellite DNA binding proteins. SOMATIC CELL AND MOLECULAR GENETICS 1998; 24:41-51. [PMID: 9776980 PMCID: PMC3151739 DOI: 10.1007/bf02677494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Hypervariable minisatellite DNA repeats are found at tens of thousands of loci in the mammalian genome. These sequences stimulate homologous recombination in mammalian cells [Cell 60:95-103]. To test the hypothesis that protein-DNA interaction is required for hotspot function in vivo, we determined whether a second protein binding nearby could abolish hotspot activity. Intermolecular recombination between pairs of plasmid substrates was measured in the presence or absence of the cis-acting recombination hotspot and in the presence or absence of the second trans-acting DNA binding protein. Minisatellite DNA had hotspot activity in two cell lines, but lacked hotspot activity in two closely related cell lines expressing a site-specific helicase that bound to DNA adjacent to the hotspot. Suppression of hotspot function occurred for both replicating and non-replicating recombination substrates. These results indicate that hotspot activity in vivo requires site occupancy by minisatellite DNA binding proteins.
Collapse
Affiliation(s)
- W P Wahls
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | | |
Collapse
|
7
|
Yoshino M, Sagai T, Moriwaki K, Shiroishi T. Meiotic recombination at the Lmp2 hotspot tolerates minor sequence divergence between homologous chromosomes. Immunogenetics 1995; 43:80-2. [PMID: 8537128 DOI: 10.1007/bf00186609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- M Yoshino
- Mammalian Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | | | | | | |
Collapse
|