Sequence features of HLA-DRB1 locus define putative basis for gene conversion and point mutations

  • Jenny von Salomé2, 3, 4 and

    Affiliated with

    • Jyrki P Kukkonen1, 3, 4Email author

      Affiliated with

      BMC Genomics20089:228

      DOI: 10.1186/1471-2164-9-228

      Received: 07 November 2007

      Accepted: 19 May 2008

      Published: 19 May 2008



      HLA/MHC class II molecules show high degree of polymorphism in the human population. The individual polymorphic motifs have been suggested to be propagated and mixed by transfer of genetic material (recombination, gene conversion) between alleles, but no clear molecular basis for this has been identified as yet. A large number of MHC class II allele sequences is publicly available and could be used to analyze the sequence features behind the recombination, revealing possible basis for such recombination processes both in HLA class II genes and other genes, which recombination acts upon.


      In this study we analyzed the vast dataset of human allelic variants (49 full coding sequences, 374 full exon 2 sequences) of the most polymorphic MHC class II locus, HLA-DRB1, and identified many previously unknown sequence features possibly contributing to the recombination. The CpG-dinucleotide content of exon 2 (containing the antigen-binding sites and subsequently a high degree of polymorphism) was much elevated as compared to the other exons despite similar overall G+C content. Furthermore, the CpG pattern was highly conserved. We also identified more complex, highly conserved sequence motifs in exon 2. Some of these can be identified as putative recombination motifs previously found in other genes, but most are previously unidentified.


      The identified sequence features could putatively act in recombination allowing either less (CpG dinucleotides) or more specific DNA cleavage (complex sequences) or homologous recombination (complex sequences).


      Over the last few years our knowledge of the mechanism of recombination has increased substantially. Still, the knowledge is to a large extent based on simple organisms such as E. coli and yeasts, as the vertebrate genome is not equally readily or rapidly monitored or manipulated. It is well known that homologous pairing and strand exchange involved in recombination in the eukaryotic cell is promoted by specific recombination proteins [1], and that recombination is tightly linked to DNA replication and repair. For example, double strand breaks are repaired by recombination using information from homologous DNA molecules. Moreover, stalled replication can be re-started by forming a recombination intermediate with assistance from recombination proteins at the replication fork [2]. Recombination also generates diversity essential for, e.g., the vertebrate adaptive immune system (immunoglobulins and T-cell receptor genes) and long-term genome evolution. The term illegitimate recombination was coined to describe one type of "novel" recombination, which, in contrast to the classical (homologous) recombination, requires no or only short stretches of sequence homology [reviewed in [35]]. Despite recent advances in the investigation of eukaryotic recombination, little is known about the mechanisms of illegitimate recombination, except for some specific cases like the immunoglobulin gene rearrangements.

      The major histocompatibility complex (MHC) class II loci encode heterodimeric cell surface receptors that present peptide antigens to helper T-cells so that an appropriate immune response can be induced. In man, the by-far most polymorphic MHC class II locus is HLA-DRB1; as of march 2008 the HLA-DRB1 locus had over 540 alleles [6, 7] and is thus one of the most polymorphic loci in the human genome. A large number of low-frequency alleles is apparently maintained in the human population by balancing selection. The peptide fragments are bound by interactions with the peptide backbone and amino acid side chains in the second exon-coded part of HLA-DRB1 (DRB1-e2), termed antigen recognition sites (ARS). Each individual carries a maximum number of two different inherited alleles per locus (assuming heterozygocity), while the greater allelic diversity is present in the population, putatively allowing population adaptation to pathogens.

      ARS polymorphisms are thought to be created by point mutations, which are propagated by some recombination events, e.g. gene conversion. This view is based on the observed patchwork pattern of apparently exchanged motifs and the fact that synonymous substitutions are also much elevated in the DRB1-e2 (hitch-hiking with the non-synonymous substitutions) [811]. However, there is little direct evidence for any recombination in MHC class II ARS, and no clear recombinogenic motifs or mechanisms have as yet been identified. Since the multiple ARS of DRB1-e2 are spread over a small region of 200 bp only, exchange of very small blocks of DNA is needed to create the pattern of polymorphism seen. This, again, is in sharp contrast to the classical (homologous) recombination, which requires significant stretches of sequence homology and exchanges relatively large blocks of generic material. Therefore, due to the apparent high activity of illegitimate recombination in DRB1-e2 and the large number of allelic sequences known, DRB1-e2 seems to be a uniquely suitable target for investigations of mechanisms behind illegitimate recombination. As it is known that specific DNA sequences can enhance or mediate recombination, we have in this study targeted the vast database of known human HLA-DRB1 alleles in the quest for possible sequence motifs that would enable recombination. The analyses identify strongly conserved sequence features as well as recombinogenic motifs previously recognized in other genes, which may thus lie at the basis of recombination events creating new alleles.


      Diversity in the antigen-binding exon

      DRB1-e2 displays much higher degree of sequence diversity than the other exons in DRB1 (Fig. 1A), independently of whether gross-diversity or non-synonymous (aminoacid-changing) diversity is analyzed [12]. As seen in earlier studies [see e.g. [12]], the synonymous diversity is also elevated in exon 2 (Fig. 1B), supporting the view that recombination, e.g. gene conversion is involved in creating polymorphism in this exon [13, 14, 10]. Consequently, synonymous substitutions would "hitch-hike" within the same exchanged DNA blocks as the non-synonymous substitutions and remain conserved due to selection forces acting on the non-synonymous substitutions. Indeed, synonymous substitutions were mainly found either in the same codons as the non-synonymous ones (Fig. 1C, the "complex" trace in its entity and the overlap of the non-synonymous and synonymous traces) or in their close vicinity (Fig. 1C).
      Figure 1

      The HLA-DRB1 exon diversity. A, DRB1 exon 2 diversity compared to the rest of the coding region (fused exons 1, 3, 4, 5 and 6) in the dataset including the entire DRB1 coding region (49 sequences). Mean ± sem is shown. B, synonymous and non-synonymous diversity in the DRB1 coding region in the dataset including the entire DRB1 coding region. In the short exon 5 (24 bp) half of the alleles have G instead of C at the nucleotide position 22, resulting in high apparent diversity for the whole exon. Mean ± sem is shown. C, sliding window analysis of non-synonymous, synonymous and complex substitutions in the DRB1-e2 in the dataset including the complete DRB1-e2. Complex stands for complex combinations of non-synonymous and synonymous substitutions in the same codon. The graph illustrates the contribution of these different components in d, which is not equal to d synonymous and d non-synonymous (d, as calculated here does not take into consideration the capability of the codon to mutate in synonymous and non-synonymous manner).

      Frequency of transitions and transversions in the coding region

      The higher diversity of DRB1-e2 is also reflected by a higher frequency of both transitions (T↔C, A↔G) and transversions (T↔A, T↔G, C↔A, C↔G), as compared to the rest of the DRB1 exons (Fig. 2). In general, transitions occur at higher frequencies than transversions in our genome [15]. However, while the transition/transversion-ratio was about 2 in the fused other exons (between 2 and 3 in the separate exons 1, 3 and 4, which have a length comparable to exon 2), it was 0.8 in exon 2. The results using the full dataset of 374 complete DRB1-e2 (transitions = 3.4 ± 0.0%, transversions = 4.2 ± 0.1%, ratio = 0.8) were similar to the 49 complete coding sequences (Fig. 2). The transition/transversion ratio near unity in DRB1-e2 is logical in the light of previous studies, which show that when sequences diverge and mutations accumulate, the transition/transversion-ratio decreases finally approaching 1 due to transition saturation [16, 17].
      Figure 2

      Transitions and transversions in HLA-DRB1, based on the dataset including the entire DRB1 coding region (49 sequences). Mean ± sem is shown.

      CpG dinucleotide enrichment and conservation in DRB1-e2

      The G+C level was similar across all DRB1 exons (Fig. 3). At the determined G+C content of the whole of DRB1 of 60%, the theoretical level of CpG should under neutral conditions be 9% (see below). When present in the CpG-dinucleotide, cytosine is often methylated. Methyl-cytosine can then deaminate to uracil, and thus lead to the transition C→T or, if occurring in the complementary strand, a G→A transition. Thus, CG may mutate to TG or CA, and genes regularly have a lower than mathematically expected level of CpG dinucleotides. The high propensity of CpG to mutate may also effectively engage DNA repair. DNA repair induces double strand breaks and may support recombination events, which may explain why CpG-rich sequences have been identified to display high recombination activity.
      Figure 3

      G+C content in HLA-DRB1 exons 1–6, based on the dataset including the entire DRB1 coding region (49 sequences). The dotted line indicates the overall average G+C. Mean ± sem is shown.

      Theoretically, CpG content = ((G+C content/100%)/2)2 * 100% (e.g. for G+C content of 50%, CpG content = 6.25%). The actual CpG content depends on the age of the gene, but in average the content would be below one third of the theoretical (e.g. for G+C content of 50%, CpG content < 2%) [18]. As expected, the determined CpG content of DRB1-e1, and -3-6 was well below the theoretical level of 9% (Fig. 4A; in average ~1/6 of the theoretical level [dotted line in Fig. 4B]). In contrast, CpG content of DRB1-e2 was surprisingly high, about 8% (Fig. 4A), which suggests that the CpG level is almost fully preserved in DRB1-e2 (see also Fig. 4B). In addition, the distribution of CpG dinucleotides in DRB1-e2 was to a very high extent conserved in all alleles (Fig. 5AB).
      Figure 4

      CpG-dinucleotide content in HLA-DRB1 exons 1–6, based on the dataset including the entire DRB1 coding region (49 sequences). A, the observed CpG-dinucleotide content. B, the observed CpG level (as in A) divided by the mathematically estimated CpG content (based on the total G+C level). Mean ± sem is shown. The ratios were separately calculated for each allele and then averaged.
      Figure 5

      CpG distribution in DRB1-e2, based on the dataset including the 374 complete DRB1-e2 sequences. A, each individual sequence lined under each other in the consensus numbering order starting from DRB1*010101. Black boxes indicate CpG dinucleotides and gray boxes other dinucleotides. B, CpG frequency for each nucleotide position. The dotted line indicates 100%.

      Motifs potentially involved in site-specific recombination

      There is a number of sequence features or motifs proposed to be recognized by specific nuclease complexes, resulting in double strand breaks and increased recombination rate [19, 20]. We further analyzed the sequence data sets to explore the possibility that specific recombination motifs are involved in creating polymorphism in DRB1-e2 (Table 1).
      Table 1

      Motifs used in the screening of DRB1-e2.

      Motif description

      Motif sequence


      Polypurine/-pyrimidine tract


      [47, 19, 48, 49]

      Alternating purine-pyrimidine tract


      [19, 50]

      Immunoglobulin heavy chain class switch repeats


      [51, 49]










      DNA polymerase arrest site



      Deletion hotspot consensus


      [28, 49]

      Heptamer recombination signal



      Nonamer recombination signal



      Chi-like sequence


      [40, 52]

      Chi-like sequence


      [53, 54]

      Chi-like sequence



      Topoisomerase I consensus cleavage sites








      DNA polymerase A pause site core sequence






      DNA polymerase A/B frameshift hotspots


      [58, 59]

      Vertebrate topoisomerase II consensus cleavage site


      [60, 61]




      Human hypervariable minisatellite core sequence



      DNA polymerase A frameshift hotspots


      [59, 63]

      DNA polymerase B frameshift hotspots



      Indel hotspot



      Hotspot motif



      Repeat element motif



      Double strand break-generating motif



      The sequences of the complementary strands are separated by "/". The ambiguity code symbols are: R = A/G, Y = C/T, K = G/T, M = A/C, S = G/C, W = A/T, N = A/C/G/T.

      Recombination signal sequences (RSSs) are involved in the diversification of antibody genes, initiated by DNA double-strand breaks introduced in the vicinity of RSSs. The RSSs are composed of conserved heptamer and nonamer motifs separated by a spacer of 12 or 23 bp [21]. The heptamer motifs, especially the first three bases (CAC), are the most influential on recombination efficiency and are usually the most conserved [22]. We found a heptamer-like motif (5'-CACGGTG-3', the bold letter is replaced in 7% of the alleles) at position 254–260 in exon 2.

      Class switch recombination (CSR) refers to the event when a lymphocyte changes the type of immunoglobulin it produces [23]. Also CSR involves recombination via DNA double strand breaks at switch regions containing repetitive elements (predominantly, 5'-GAGCT-3' and 5'-GGGGT-3'). The immunoglobulin heavy chain class switch repeat GAGCT was present at position 145–149 and 248–252 in all but one (DRB1*0423) of 374 DRB1 alleles (Table 2). Another immunoglobulin heavy chain class switch repeat (5'-TGGGG-3') was present in all alleles except for alleles in the lineage DRB1*07 (Table 2). This immunoglobulin heavy chain class switch repeats was also present in the exon 2 sequences excluded from the analysis due to missing bases in either the 3' or 5' end (see Additional file 1).
      Table 2

      Motifs previously identified in other genes found in the DRB1-e2

      Motif description

      Motif sequence


      Not present in

      Polypurine tract










      Polypyrimidine tract






      Immunoglobulin heavy chain class switch repeat











      Deletion hotspot consensus










      Chi-like sequence














      Topoisomerase I consensus cleavage site





      DRB1*0423, *0452





















      DNA polymerase a pause site core sequence







      246–251 (2×)











      Deletion hotspot









      Only the motifs present in at least an (almost) entire allelic family are presented; some less common motifs are presented in the text. The ambiguity code symbols are: R = A/G, Y = C/T, K = G/T, M = A/C, S = G/C, W = A/T, N = A/C/G/T.

      amotif ± 1 bp

      b motif in non-coding strand corresponding to these bases in the coding strand.

      Chi (crossover hotspot instigator, χ) is an octamer recombination hotspot (5'-GCTGGTGG-3') of the major recombination pathway in E. coli [reviewed in [24]]. Recombination by this pathway is initiated by double-strand breaks occurring at chi sequences. Variants of this motif are suggested to have partial recombinogenic activity, and chi-like sequences have been speculated to be involved in both deletion and translocation events in man [2527]. A chi-like sequences at nucleotide position 143–149 in exon 2 was found in all alleles except for the DRB1*07 allelic lineage (Table 2). The chi-like sequence in DRB1-e2 was overlapping with a motif reported to be a deletion hotspot consensus sequence (5'-TGRRKM-3'), suggested to be involved in illegitimate recombination [28, 29]. We located this hotspot sequence at positions 145–150 in all alleles except for the allelic lineage DRB1*07 (Table 2). Moreover, this sequence was present in the non-coding strand of all alleles at coding strand position 37–42 (Table 2).

      Several types of the recombination motifs screened for were also found in the other exons of DRB1 (the dataset of 49 complete coding sequences) (not shown).

      Conserved sequence stretches and motifs in DRB1-e2

      Despite the high degree of variability in DRB1-e2 we could, to our surprise, find 19 stretches of a length 3–13 bp that have no variation at all among different DRB1-e2 (Table 3 and Fig. 6). Some of these fully conserved bases corresponded to the known motifs as identified above (Table 3).
      Table 3

      Fully conserved stretches of a minimum of 3 bp in all DRB1-e2 sequences


      Sequence (underlined letters corresponding to motif in table 2)

      Corresponding motif in Table 2



      Polypyrimidine tract







      Deletion hotspot consensus sequence (5'-TGAAGA-3') in non-coding strand

      Polypyrimidine tract (5'-TTCTTC-3')















      Polypurine tract



      Part of the immunoglobulin heavy chain class switch repeat (5'-GAGCT-3')a



      Part of the chi-like sequence (5'-GCTGGGG-3')a



      Part of deletion hotspot consensus sequence (5'-TGRRKM-3')a



      Part of the chi-like sequence (5'-GCTGGGG-3')a


















      Polypurine trac



      Part of the immunoglobulin heavy chain class switch repeat (5'-GAGCT-3')a



      Deletion hotspot consensus sequence







      athe full motif as in Table 2
      Figure 6

      Sliding window analysis of nucleotide diversity in HLA-DRB1 exon 2, displaying stretches of totally conserved bases in the 374 DRB1-e2 sequences (of the length ≥ 3 bp; thick grey lines below the abscissa). Also indicated are the previously identified ARS-coding codons (thick black lines above the diversity graph).


      In this study we identify several distinct features of exon 2 of DRB1. One of these is its high CpG content, possibly leading to a high degree of a) point mutations and b) DNA repair. However, not only is the CpG level high in DRB1-e2, but also the CpG pattern is highly conserved in DRB-e2. It therefore appears unlikely that CpG-dinucleotides would support ARS polymorphism by point mutations. More likely is that the conserved CpG pattern is explained by frequent DNA repair, which, by introducing double-strand DNA cleavage followed by non-homologous end-joining, is one of the suggested mechanisms of gene conversion [reviewed in [3, 5, 30]]. Earlier studies of MHC class I nucleotide sequences in mice have proposed that regions with high levels of CpG dinucleotides are involved in non-reciprocal recombination (gene conversion) [31]. Analyzes of human MHC class I and II sequences also have reported increased CpG dinucleotide levels in regions suggested to be involved in gene conversion [32]. CpG nucleotide could be preserved if the repair system had a bias towards G:C pairs instead of A:T pairs [33] as suggested for regions with high recombination activity [34]. However, it should be born in mind that unmethylated CpG dinucleotides, in contrast to the cytosine-methylated CpG:s, mutate at normal rates and regions with high CpG contents may have low levels of methylation [35]. Conservation of CpG dinucleotides may therefore be a result of either low germ-line methylation or a specific selection against the loss of CpGs [36]. However, the highly significant pattern of conserved CpG in HLA-DRB1-e2 can be considered unlikely even if the CpG dinucleotides were unmethylated and mutated at the rate of other bases.

      A few eukaryotic endonucleases with specific DNA recognition sequences involved in DNA recombination, such as topoisomerase I [37], Endo.SceI [38] and homing endonucleases [reviewed in [39]], have been identified. The enzymes have in common that they recognize a more or less strictly defined DNA sequence and cleave at it or some distance from it. In addition, a number of other conserved sequence motifs associated with high recombination activity (such as the chi-like sequences) but without a pinpointed endonuclease/recombinase have been recognized [40, 19, 41]. In this study, we screened DRB1-e2 for "known" recombination, translocation and deletion motifs. A heptamer-like motif was found in all investigated DRB1 alleles and an immunoglobulin heavy chain class switch repeat was found in all but one of the DRB1 alleles. Moreover, a chi-like sequence and a deletion hotspot consensus sequence were present in all alleles except for the *07 lineage. It is thinkable that the DRB1*07 allelic lineage, which contains least alleles of all the lineages, may have lost one of these motifs and therefore gained a limited ability to recombine. This may also be true for other, even less frequent motifs, also including conserved CpGs. Currently, not enough is known about the function of the specific motifs found in order to speculate further on their function. Interspersed among the highly polymorphic areas of DRB1-e2, we found multiple short stretches of bases that have no variation at all between the DRB1 alleles in the dataset. Conserved amino acid motifs can be important for the maintenance of the overall structure of the antigen-binding groove, but as these stretches also lack synonymous substitutions they may have a function in allowing recombination between alleles via illegitimate recombination. This could occur either by offering homology for recombination, by allowing cleavage by some specific enzymes or by stabilization of DNA's secondary structure. Comparison of these sequences to known sequence motifs associated with recombination (see above) produced no hits, which is by no means surprising as indeed only few motifs are known and even fewer verified.

      It should be born in mind that the specific sequence motifs screened for are for the most part very short and may thus appear in a random fashion in any sequence analyzed. Indeed, some motifs were found in the other exons of HLA-DRB1, not subject to recombination. However, the fact that exon 2 is subject to high rate of recombination - in contrast to the other exons which are highly conserved - makes random conservation of such stretches unlikely, especially in such a large pool of allelic sequences. Yet the most remarkable features of DRB1-e2 are, rather than the known recombinogenic motifs found, a) the fully conserved sequence stretches and b) high CpG content and the conserved CpG pattern.


      We have identified in DRB1-e2 both some known recombination motifs and multiple putative motifs. The latter include both the conserved CpG pattern and other fully conserved sequence motifs. Although the role of these sequence features in the recombination processes in DRB1 is speculative, it is obvious that the known recombination motifs identified here cannot be enough to support the full spectrum of recombination. 22 variable and 15 conserved DRB1-e2 ARS-coding codons, spread over 245 bp (Fig. 6), are known, and each of the variable ARS codons should probably be able to recombine separately from the others, theoretically requiring 23 recombination breakpoints. Whether this indeed is the case, will be deduced from full mapping of the DRB1-e2 recombination profile, which is currently in progress. If the conserved sequence motifs identified here indeed are important in recombination, they would likely be present in other regions of the genome with high recombination activity. This will also be addressed in future studies.


      Nucleotide sequences used

      For the analysis, sequences from the IMGT/HLA database [6, 7] were used. The datasets analyzed were the 374 complete exon 2 sequences and 49 complete coding sequences (exons 1–6). Full descriptions of the datasets can be found in the Additional files 2 and 3.

      Analysis of diversity, transition/transversion-ratios, G+C and CpG contents

      The sequences were aligned using ClustalW [42]. The mean synonymous and non-synonymous diversities (d) were estimated by pairwise comparison of the number of nucleotide substitutions using the Jukes-Cantor method [43] with the MEGA3.1 software [44]. Sliding-window analyses of the nucleotide diversities were performed using DnaSP 4.10.9 [45] Analyses of the transition/transversion-ratios and the G+C and CpG contents were done with SWAAP 1.0.2 [46] and MEGA3.1. The sliding window analyses of the CpG content were performed using Microsoft Excel.

      Analysis of motifs potentially involved in site-specific recombination

      Recombination has been suggested to be promoted by common sequence features or motifs [20], known or postulated to be recognized by specific nuclease complexes, leading to double strand break and increased recombination rate. We screened DRB1-e2 (coding and non-coding strands) in MEGA3.1 for sequence motifs previously shown to be involved in recombination, to explore the possibility that specific motifs are involved in creating new polymorphisms. The motifs screened for are listed in Table 1.

      List of abbreviations


      antigen-recognition site(s)




      crossover hotspot instigator


      CG-dinucleotide (in DNA)


      class switch recombination


      nucleotide diversity

      G+C content: 

      content of guanine and cytosine nucleotides (in DNA), DRB1-e2: exon 2 of the HLA-DRB1 gene


      human leukocyte antigen


      major histocompatibility complex


      recombination signal sequences.



      This study was supported by grants from the Novo Nordisk Foundation, the Sigrid Jusélius Foundation, the Magnus Ehrnrooth Foundation, the K. Albin Johansson Foundation, the Swedish Research Council, Uppsala University, Åbo Akademi University and the University of Helsinki Research Funds.

      Authors’ Affiliations

      Department of Basic Veterinary Sciences, University of Helsinki
      Department of Clinical Genetics, Karolinska University Hospital
      Department of Biology, Åbo Akademi University
      Department of Neuroscience, Uppsala University


      1. Gruss A, Michel B: The replication-recombination connection: insights from genomics. Curr Opin Microbiol 2001,4(5):595–601.View ArticlePubMed
      2. West SC: Molecular views of recombination proteins and their control. Nat Rev Mol Cell Biol 2003,4(6):435–445.View ArticlePubMed
      3. Haber JE: Recombination: a frank view of exchanges and vice versa. Curr Opin Cell Biol 2000,12(3):286–292.View ArticlePubMed
      4. van Rijk A, Bloemendal H: Molecular mechanisms of exon shuffling: illegitimate recombination. Genetica 2003,118(2–3):245–249.View ArticlePubMed
      5. Wurtele H, Little KC, Chartrand P: Illegitimate DNA integration in mammalian cells. Gene Ther 2003,10(21):1791–1799.View ArticlePubMed
      6. Robinson J, Waller MJ, Parham P, de Groot N, Bontrop R, Kennedy LJ, Stoehr P, Marsh SG: IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res 2003,31(1):311–314.View ArticlePubMed
      7. IMGT/HLA Database [http://​www.​ebi.​ac.​uk/​imgt/​hla]
      8. Hogstrand K, Bohme J: A determination of the frequency of gene conversion in unmanipulated mouse sperm. Proc Natl Acad Sci U S A 1994,91(21):9921–9925.View ArticlePubMed
      9. Titus-Trachtenberg EA, Rickards O, De Stefano GF, Erlich HA: Analysis of HLA class II haplotypes in the Cayapa Indians of Ecuador: a novel DRB1 allele reveals evidence for convergent evolution and balancing selection at position 86. Am J Hum Genet 1994,55(1):160–167.PubMed
      10. Ohta T: Gene conversion vs point mutation in generating variability at the antigen recognition site of major histocompatibility complex loci. J Mol Evol 1995,41(2):115–119.View ArticlePubMed
      11. Zangenberg G, Huang MM, Arnheim N, Erlich H: New HLA-DPB1 alleles generated by interallelic gene conversion detected by analysis of sperm. Nat Genet 1995,10(4):407–414.View ArticlePubMed
      12. von Salome J, Gyllensten U, Bergstrom TF: Full-length sequence analysis of the HLA-DRB1 locus suggests a recent origin of alleles. Immunogenetics 2007,59(4):261–271.View Article
      13. Gorski J, Mach B: Polymorphism of human Ia antigens: gene conversion between two DR beta loci results in a new HLA-D/DR specificity. Nature 1986,322(6074):67–70.View ArticlePubMed
      14. Gyllensten UB, Sundvall M, Erlich HA: Allelic diversity is generated by intraexon sequence exchange at the DRB1 locus of primates. Proc Natl Acad Sci U S A 1991,88(9):3686–3690.View ArticlePubMed
      15. Wakeley J: Substitution-rate variation among sites and the estimation of transition bias. Mol Biol Evol 1994,11(3):436–442.PubMed
      16. Purvis A, Bromham L: Estimating the transition/transversion ratio from independent pairwise comparisons with an assumed phylogeny. J Mol Evol 1997,44(1):112–119.View ArticlePubMed
      17. Yang Z, Yoder AD: Estimation of the transition/transversion rate bias and species sampling. J Mol Evol 1999,48(3):274–283.View ArticlePubMed
      18. Sved J, Bird A: The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc Natl Acad Sci U S A 1990,87(12):4692–4696.View ArticlePubMed
      19. Abeysinghe SS, Chuzhanova N, Krawczak M, Ball EV, Cooper DN: Translocation and gross deletion breakpoints in human inherited disease and cancer I: Nucleotide composition and recombination-associated motifs. Hum Mutat 2003,22(3):229–244.View ArticlePubMed
      20. Ball EV, Stenson PD, Abeysinghe SS, Krawczak M, Cooper DN, Chuzhanova NA: Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat 2005,26(3):205–213.View ArticlePubMed
      21. Ramsden DA, McBlane JF, van Gent DC, Gellert M: Distinct DNA sequence and structure requirements for the two steps of V(D)J recombination signal cleavage. Embo J 1996,15(12):3197–3206.PubMed
      22. Cuomo CA, Mundy CL, Oettinger MA: DNA sequence and structure requirements for cleavage of V(D)J recombination signal sequences. Mol Cell Biol 1996,16(10):5683–5690.PubMed
      23. Dunnick W, Hertz GZ, Scappino L, Gritzmacher C: DNA sequences at immunoglobulin switch region recombination sites. Nucleic Acids Res 1993,21(3):365–372.View ArticlePubMed
      24. Smith GR: Homologous recombination near and far from DNA breaks: alternative roles and contrasting views. Annu Rev Genet 2001, 35:243–274.View ArticlePubMed
      25. Wyatt RT, Rudders RA, Zelenetz A, Delellis RA, Krontiris TG: BCL2 oncogene translocation is mediated by a chi-like consensus. J Exp Med 1992,175(6):1575–1588.View ArticlePubMed
      26. Veljkovic E, Dzodic R, Neskovic G, Stanojevic B, Milovanovic Z, Opric M, Dimitrijevic B: Sequence variant in the intron 10 of the RET oncogene in a patient with microfollicular thyroid carcinoma with medullar differentiation: implications for newly generated chi-like sequence. Med Oncol 2004,21(4):319–324.View ArticlePubMed
      27. Xie F, Wang X, Cooper DN, Chuzhanova N, Fang Y, Cai X, Wang Z, Wang H: A novel Alu-mediated 61-kb deletion of the von Willebrand factor (VWF) gene whose breakpoints co-locate with putative matrix attachment regions. Blood Cells Mol Dis 2006,36(3):385–391.View ArticlePubMed
      28. Krawczak M, Cooper DN: Gene deletions causing human genetic disease: mechanisms of mutagenesis and the role of the local DNA sequence environment. Hum Genet 1991,86(5):425–441.View ArticlePubMed
      29. Schmucker B, Krawczak M: Meiotic microdeletion breakpoints in the BRCA1 gene are significantly associated with symmetric DNA-sequence elements. Am J Hum Genet 1997,61(6):1454–1456.View ArticlePubMed
      30. Helleday T, Lo J, van Gent DC, Engelward BP: DNA double-strand break repair: From mechanistic understanding to cancer treatment. DNA Repair (Amst) 2007,6(7):923–935.View Article
      31. Jaulin C, Perrin A, Abastado JP, Dumas B, Papamatheakis J, Kourilsky P: Polymorphism in mouse and human class I H-2 and HLA genes is not the result of random independent point mutations. Immunogenetics 1985,22(5):453–470.View ArticlePubMed
      32. Hogstrand K, Bohme J: Gene conversion of major histocompatibility complex genes is associated with CpG-rich regions. Immunogenetics 1999,49(5):446–455.View ArticlePubMed
      33. Marais G: Biased gene conversion: implications for genome and sex evolution. Trends Genet 2003,19(6):330–338.View ArticlePubMed
      34. Duret L, Eyre-Walker A, Galtier N: A new perspective on isochore evolution. Gene 2006, 385:71–74.View ArticlePubMed
      35. Takai D, Jones PA: Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A 2002,99(6):3740–3745.View ArticlePubMed
      36. Tanay A, O'Donnell AH, Damelin M, Bestor TH: Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci U S A 2007,104(13):5521–5526.View ArticlePubMed
      37. Zhu J, Schiestl RH: Topoisomerase I involvement in illegitimate recombination in Saccharomyces cerevisiae. Mol Cell Biol 1996,16(4):1805–1812.PubMed
      38. Nakagawa K, Morishima N, Shibata T: An endonuclease with multiple cutting sites, Endo.SceI, initiates genetic recombination at its cutting site in yeast mitochondria. Embo J 1992,11(7):2707–2715.PubMed
      39. Stoddard BL: Homing endonuclease structure and function. Q Rev Biophys 2005,38(1):49–95.View ArticlePubMed
      40. Amor M, Parker KL, Globerman H, New MI, White PC: Mutation in the CYP21B gene (Ile-172----Asn) causes steroid 21-hydroxylase deficiency. Proc Natl Acad Sci U S A 1988,85(5):1600–1604.View ArticlePubMed
      41. Blanco MG, Boan F, Barros P, Castano JG, Gomez-Marquez J: Generation of DNA double-strand breaks by two independent enzymatic activities in nuclear extracts. J Mol Biol 2005,351(5):995–1006.View ArticlePubMed
      42. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994,22(22):4673–4680.View ArticlePubMed
      43. Jukes TH, Cantor CR: Evolution of protein molecules. Mammalian Protein Metabolism (Edited by: Munro, H.N). New York, Academic Press 1969, 21–32.
      44. Kumar S, Tamura K, Nei M: MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 2004,5(2):150–163.View ArticlePubMed
      45. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R: DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003,19(18):2496–2497.View ArticlePubMed
      46. Pride DT: SWAAP - A tool for analyzing substitutions and similarity in multiple alignments. [http://​www.​bacteriamuseum.​org/​SWAAP/​SwaapPage.​htm]
      47. Simonsson T: G-quadruplex DNA structures--variations on a theme. Biol Chem 2001,382(4):621–628.View ArticlePubMed
      48. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S: Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 2006,34(19):5402–5415.View ArticlePubMed
      49. Ferec C, Casals T, Chuzhanova N, Macek M Jr., Bienvenu T, Holubova A, King C, McDevitt T, Castellani C, Farrell PM, Sheridan M, Pantaleo SJ, Loumi O, Messaoud T, Cuppens H, Torricelli F, Cutting GR, Williamson R, Ramos MJ, Pignatti PF, Raguenes O, Cooper DN, Audrezet MP, Chen JM: Gross genomic rearrangements involving deletions in the CFTR gene: characterization of six new events from a large cohort of hitherto unidentified cystic fibrosis chromosomes and meta-analysis of the underlying mechanisms. Eur J Hum Genet 2006,14(5):567–576.View ArticlePubMed
      50. Tsai CL, Chatterji M, Schatz DG: DNA mismatches and GC-rich motifs target transposition by the RAG1/RAG2 transposase. Nucleic Acids Res 2003,31(21):6180–6190.View ArticlePubMed
      51. van Gent DC, Hoeijmakers JH, Kanaar R: Chromosomal stability and the DNA double-stranded break connection. Nat Rev Genet 2001,2(3):196–206.View ArticlePubMed
      52. Lee HH, Niu DM, Lin RW, Chan P, Lin CY: Structural analysis of the chimeric CYP21P/CYP21 gene in steroid 21-hydroxylase deficiency. J Hum Genet 2002,47(10):517–522.View ArticlePubMed
      53. Chou CL, Morrison SL: A common sequence motif near nonhomologous recombination breakpoints involving Ig sequences. J Immunol 1993,150(12):5350–5360.PubMed
      54. Borgato L, Bonizzato A, Lunardi C, Dusi S, Andrioli G, Scarperi A, Corrocher R: A 1.1-kb duplication in the p67-phox gene causes chronic granulomatous disease. Hum Genet 2001,108(6):504–510.View ArticlePubMed
      55. Krowczynska AM, Rudders RA, Krontiris TG: The human minisatellite consensus at breakpoints of oncogene translocations. Nucleic Acids Res 1990,18(5):1121–1127.View ArticlePubMed
      56. Bullock P, Champoux JJ, Botchan M: Association of crossover points with topoisomerase I cleavage sites: a model for nonhomologous recombination. Science 1985,230(4728):954–958.View ArticlePubMed
      57. Fry M, Loeb LA: A DNA polymerase alpha pause site is a hot spot for nucleotide misinsertion. Proc Natl Acad Sci U S A 1992,89(2):763–767.View ArticlePubMed
      58. Kunkel TA: The mutational specificity of DNA polymerase-beta during in vitro DNA synthesis. Production of frameshift, base substitution, and deletion mutations. J Biol Chem 1985,260(9):5787–5796.PubMed
      59. Kunkel TA: The mutational specificity of DNA polymerases-alpha and -gamma during in vitro DNA synthesis. J Biol Chem 1985,260(23):12866–12874.PubMed
      60. Sander M, Hsieh TS: Drosophila topoisomerase II double-strand DNA cleavage: analysis of DNA sequence homology at the cleavage site. Nucleic Acids Res 1985,13(4):1057–1072.View ArticlePubMed
      61. Gale KC, Osheroff N: Intrinsic intermolecular DNA ligation activity of eukaryotic topoisomerase II. Potential roles in recombination. J Biol Chem 1992,267(17):12090–12097.PubMed
      62. Jeffreys AJ, Wilson V, Thein SL: Hypervariable 'minisatellite' regions in human DNA. Nature 1985,314(6006):67–73.View ArticlePubMed
      63. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P: A fine-scale map of recombination rates and hotspots across the human genome. Science 2005,310(5746):321–324.View ArticlePubMed
      64. Chuzhanova NA, Anassis EJ, Ball EV, Krawczak M, Cooper DN: Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat 2003,21(1):28–44.View ArticlePubMed


      © von Salomé and Kukkonen. 2008

      This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.