Minireview Hotspots of homologous recombination in the human genome: not comment all homologous sequences are equal James R Lupski Address: Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Current address (sabbatical until July 2005): Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK. E-mail: [email protected] Published: 28 September 2004 reviews Genome Biology 2004, 5:242 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2004/5/10/242 © 2004 BioMed Central Ltd reports Abstract Homologous recombination between alleles or non-allelic paralogous sequences does not occur uniformly but is concentrated in ‘hotspots’ with high recombination rates. Recent studies of these hotspots show that they do not share common sequence motifs, but they do have other features in common. deposited research Homologous recombination is the process whereby two DNA this is not the case and have provided evidence for local sequence substrates that share a significant stretch of iden- ‘hotspots’ - short regions of the genome where strand tity are brought together, in an enzyme-catalyzed reaction, exchanges are more common than elsewhere. These obser- and undergo strand exchange to give a product that is a vations come from pedigree studies that examined the novel amalgamation of the two substrates. It occurs during parent-to-offspring transmission of alleles, linkage disequi- meiosis, leading to crossovers between alleles (allelic homol- librium (LD) studies and, more recently, direct DNA refereed research ogous recombination, AHR), and during repair of double- sequencing of the products of recombination using either strand breaks in DNA and other processes, leading to sperm (which represent a large number of recombination recombination between paralogous sequences (non-allelic products from a single meiosis) or junction fragments from homologous recombination, NAHR, also known as ectopic ectopic recombination (NAHR) [4,5]. These recombination recombination). The intermediates of NAHR can be resolved hotspots are a common feature of both AHR and NAHR. to give several products, including deletions, duplications, Such hotspots have important implications for how linked and inversion rearrangements or, as in the case of AHR, the genes and other markers are inherited in haplotypes (their replacement of one sequence by a homologous one (gene amount of LD [4,6-8]) and for studies of LD and haplotypes interactions conversion). When NAHR results in a duplication in one including the International HapMap project [9], as well as product it is usually accompanied by a reciprocal deletion in potentially for disease-association studies and susceptibility the other. Low-copy repeats that can induce NAHR account to rearrangements causing genomic disorders in different for 5-10% of the human genome [1], and rearrangements world populations. between them can result in a class of diseases known as genomic disorders [2,3]. The distribution of meiotic recombination events along chromosomes has been examined at several levels of resolu- tion, from the megabase (Mb) scales of genetic mapping information Finding hotspots (1 Mb is approximately equal to 1 centiMorgan (cM) for It might be thought that homologous recombination is average recombination rates) to the nucleotide levels of reso- driven only by shared sequence identity among substrates. If lution afforded by sequencing of strand-exchange products. this was the case, strand exchange would be expected to High-resolution examination, at the nucleotide sequence occur with equal frequency all the way along a segment of level, defines hotspots as localized sites of recombination homology. Experimental observations suggest, however, that and enables recombination hotspots to be examined for Genome Biology 2004, 5:242 242.2 Genome Biology 2004, Volume 5, Issue 10, Article 242 Lupski http://genomebiology.com/2004/5/10/242 common features. The mechanism underlying the formation shown to induce double-strand breaks (such as palindromes, of recombination hotspots remains obscure, but recent minisatellites and DNA transposons) have often been studies suggest that a ‘punctate’ distribution of recombina- reported near NAHR hotspots (reviewed in [5,23]). tion events (in other words, a hotspot-like pattern of recom- Sequence analyses of the NAHR hotspots [21,22] revealed bination) occurs throughout the human genome [6,10]. proximity to some of these structures, suggesting a link Furthermore, the local positions of recombination hotspots between double-strand breaks and NAHR hotspots [24]. may not be conserved among closely related primate species Hotspots were observed subsequently in all NAHR [11], and in some cases hotspots are characterized by signa- crossovers examined at the nucleotide sequence level [25- tures of concerted evolution [7], whereby duplicated 28]. Like AHR hotspots, common features shared among sequences are more similar to one another than to their NAHR hotspots include clustering within small regions orthologs in a closely related species. (under 1 kb), no obvious sequence similarities with one another, and coincidence with apparent gene conversion The distribution of AHR across the genome has been events. Interestingly, recombination hotspots associated reviewed recently [4,8]. Initial high-resolution analysis of with reciprocal deletion and duplication events coincide; human crossover hotspots characterized using sperm DNA those associated with either the deletion or duplication could studies identified a 1.5 kb region adjacent to the MS32 be used to predict the position of the hotspot associated with minisatellite [12] and several 1-2 kb intervals containing the reciprocal event [20,26]. hotspots across the 210 kb class II region of the major histo- compatibility complex [13,14]. Sperm analysis also identi- fied a hotspot initially inferred from the observed Studying hotspot distribution systematically nonuniform distribution of recombination within the The fine-scale structure of recombination-rate variation human ␤-globin gene cluster [15,16]. These and other AHR throughout the human genome was reported recently hotspots cluster within small regions (1-2 kb), with [6,10]. Both studies used surveys of single-nucleotide poly- crossover breakpoints spread in a normal distribution morphisms (SNPs) in different populations, and both within the narrow hotspot; they have no obvious sequence developed novel statistical methods to infer patterns of similarities with one another, and coincide with gene-con- fine-scale variation in the recombination rate along the version hotspots [4]. The location of AHR hotspots is not genome. One study [10] focused on a 10 Mb region of chro- conserved across distantly related mammalian species mosome 20 in European (Caucasian) and African-Ameri- (human and mouse) [4], consistent with the fact that can populations, whereas the other [6] examined 74 hotspots do not reflect conserved primary sequence motifs. candidate genes to search for hotspots by resequencing DNA from 23 European-Americans and 24 African-Ameri- Jeffreys and colleagues [4] have pointed out that the punctate cans. Both studies [6,10] found evidence for recombina- distribution of human recombination hotspots is very similar tion-rate variation, with hotspots occurring at least every to that of meiotic double-strand breaks in budding yeast [17]; 200 kb and potentially as frequently as every 50 kb, the the latter are sequence-nonspecific and occur at yeast recom- latter value being the same as has been observed in yeast bination hotspots [18,19], suggesting that hotspots could [29]. No single factor was consistently associated with the reflect where recombination is initiated by double-strand presence of hotspots - neither GC content, the frequency of breaks. Furthermore, the observation that a recombination CpG dinucleotides, the presence of (AC)n repeats, nor any reporter placed in different positions in the yeast genome primary DNA sequence motif that had previously been acquires properties of its location is argued [4] to support a hypothesized to influence the existence of hotspots. model in which higher-order chromatin structures and/or Whereas one fine-scale study [6] found extensive recombi- chromosome dynamics contribute to the control of the local nation-rate variations both within and between genes, the frequency of recombination-initiation events. other [10] suggested that recombination occurs preferen- tially outside genes. The degree to which SNPs residing Hotspots have also been observed in association with NAHR within segmental duplications (paralogous sequence (reviewed in [5]). The recombination event can be readily variations or cis-morphisms [3,30-32]) influence the inter- ascertained because the rearrangement (deletion or duplica- pretation of these analyses remains to be determined. tion) conveys a phenotype or produces a genomic disorder. Also, as paralogous sequences are used in NAHR, rather than Both studies [6,10] provided some evidence for differences in allelic homologous sequences as in AHR, paralogous recombination-rate variation among different populations, sequence variations (also known as cis-morphisms [3]) can but to what extent this reflects differences in the genetic back- be used to map crossover sites precisely. NAHR hotspots ground of the populations is not clear. The absence in the were initially observed in diverse populations as the recombi- chimpanzee