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Human Molecular Genetics Advance Access published online on September 22, 2004
Human Molecular Genetics, doi:10.1093/hmg/ddh310
© 2004 by Oxford University Press
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Article

Evidence and characteristics of putative human {alpha} recombination hotspots

Jing Zhang 1, Fei Li 2, Jun Li 2, Michael Q. Zhang 3, and Xuegong Zhang 1*

1 MOE Key Laboratory of Bioinformatics/Department of Automation, Tsinghua University, Beijing 100084, China; Chinese National Human Genome Center, Beijing 100176, China
2 MOE Key Laboratory of Bioinformatics/Department of Automation, Tsinghua University, Beijing 100084, China
3 MOE Key Laboratory of Bioinformatics/Department of Automation, Tsinghua University, Beijing 100084, China; Cold Spring Harbor Laboratory, New York, USA

* To whom correspondence should be addressed. E-mail: zhangxg{at}tsinghua.edu.cn.


  Abstract

Understanding recombination rate variation is very important for studying genome diversity and evolution and for investigation of phenotypic association and genetic diseases. Recombination hotspots have been observed in many species and are well studied in yeast. Recent study demonstrated that recombination hotspots are also a ubiquitous feature of the human genome. But the nature of human hotspots remains largely unknown. We have developed and validated a novel computational method for testing the existence of hotspots as well as for localizing them with either unphased or phased genotyping data. To study the characteristics of hotspots within or close to genes, we scanned for unusually high levels of recombination using the European population samples in the SeattleSNPs database, and found evidence for the existence of human {alpha} hotspots similar to those of yeast. This type of hotspots, found at promoter regions, accounts for about half of the total detected and appears to depend on some specific transcription factor binding sites (such as CGCCCCCGC). These characteristics can explain the observed weak correlation between hotspots and GC-content and their variation may contribute to the diversity of hotspot distribution among different individuals and species. And these long-sought putative human {alpha} recombination hotspots should deserve further experimental investigations.


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