We use genotype data generated by the International HapMap Project to dissect the relationship between sequence features and the degree of linkage disequilibrium in the genome. We show that variation in linkage disequilibrium is broadly similar across Populations and examine sequence landscape in regions of strong and weak disequilibrium. Linkage disequilibrium is generally low within similar to 15 Mb of the telomeres of each chromosome and noticeably elevated in large, duplicated regions of the genome as well as within similar to 5 Mb of centromeres and other heterochromatic regions. At a broad scale (100-1000 kb resolution), Our results show that regions of strong linkage disequilibrium are typically GC poor and have reduced polymorphism. In addition, these regions are enriched for LINE repeats, but have fewer SINE, DNA, and simple repeats than the rest of the genome. At a fine scale, we examine the sequence composition of "hotspots" for the rapid breakdown of linkage disequilibrium and show that they are enriched in SINEs, in simple repeats, and in sequences that are conserved between species. Regions of high and low linkage disequilibrium (the top and bottom quartiles of the genome) have a higher density of genes and coding bases than the rest of the genome. Closer examination of the data shows that whereas some types of genes (including genes involved in immune response and sensory perception) are typically located in regions of low linkage disequilibrium, other genes (including those involved in DNA and RNA metabolism, response to DNA damage, and the cell cycle) are preferentially located in regions of strong linkage disequilibrium. Our results provide a detailed analysis of the relationship between sequence features and linkage disequilibrium and Suggest an evolutionary justification for the heterogeneity in linkage disequilibrium in the genome.
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Blanchette, M
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Kent, WJ
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Kent, WJ
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Riemer, C
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Riemer, C
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Elnitski, L
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Elnitski, L
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Smit, AFA
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Smit, AFA
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Roskin, KM
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Roskin, KM
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Baertsch, R
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Baertsch, R
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Rosenbloom, K
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Rosenbloom, K
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Clawson, H
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Clawson, H
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Green, ED
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Green, ED
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Haussler, D
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Haussler, D
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Miller, W
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Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Blanchette, M
;
Kent, WJ
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Kent, WJ
;
Riemer, C
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Riemer, C
;
Elnitski, L
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Elnitski, L
;
Smit, AFA
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h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Smit, AFA
;
Roskin, KM
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h-index: 0
机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Roskin, KM
;
Baertsch, R
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Baertsch, R
;
Rosenbloom, K
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Rosenbloom, K
;
Clawson, H
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Clawson, H
;
Green, ED
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Green, ED
;
Haussler, D
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机构:Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
Haussler, D
;
Miller, W
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机构:
Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USAPenn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA