Homology requirements for unequal crossing over in humans.

Abstract

To gain insight into mechanisms of unequal homologous recombination in vivo, genes generated by homologous unequal crossovers in the human beta-globin gene cluster were examined by nucleotide sequencing and hybridization experiments. The naturally occurring genes studied included one delta-beta Lepore-Baltimore fusion gene, one delta-beta Lepore-Hollandia fusion gene, 12 delta-beta Lepore-Boston genes, one A gamma-beta fusion Kenya gene, one A gamma-G gamma fusion (the central gene of a triplication) and one G gamma-A gamma fusion. A comparison of the nucleotide sequences of three Lepore-Boston genes indicates that they were derived from at least two independent homologous but unequal crossover events, although the crossovers occurred within the same 58-bp region. Nine additional Lepore-Boston genes from individuals of various ethnic origins were shown, by hybridization to specific oligonucleotide probes, to have been generated by a crossover in the same region as the sequenced genes. Evidence for gene conversion accompanying a homologous unequal crossover event was found in only one case (although some of the single nucleotide differences observed in other genes in this study may be related to the crossover events in ways that we do not presently understand). Thus, as judged by this limited sample, concurrent gene conversions are not commonly associated with homologous but unequal exchange in humans in vivo. Classification of the recombinant chromosomes by their polymorphic restriction sites in the beta-globin gene cluster indicated that the Lepore-Boston genes are found in at least six different haplotype backgrounds. Therefore the total number of independent examples in this study is at least 6, and at most 12. We have shown that in at least six cases of genes that have arisen by homologous but unequal crossing over in vivo, each event occurred in a relatively extensive region of uninterrupted identity between the parental genes. This preference cannot be explained by a mechanism whereby crossovers occur at random within misaligned related but not identical genes. In general, crossovers occur in regions that are among the largest available stretches of identity for a particular pair of mismatched genes. Our data are in agreement with those of other types of studies of homologous recombination, and support the idea that sequence identity, rather than general homology, is a critical factor in homologous recombination.

Novel SPTBN2 gene mutation and first intragenic deletion in early onset spinocerebellar ataxia type 5

“…These sequences of about 300 base pairs share a great level of identity and allow more efficient homologous recombination than sequences with an imperfect identity which would represent an inefficient target 18,19 . The suggested minimum requirement for favorable homologous recombination is 75% of identity between Alu elements 20,21 . In our study, we hypothesize that the de novo deletion of 10895 bp in SPTBN2 gene was generated by an unequal homologous recombination event, due to a misalignment between Alu Sx in intron 12 (5ʹ deletion boundary) of SPTBN2 gene and Alu Sx in intron 20 (3ʹ deletion boundary).…”

“…18,19 The suggested minimum requirement for favorable homologous recombination is 75% of identity between Alu elements. 20,21 In our study, we hypothesize that the de novo deletion of 10895 bp in SPTBN2 gene was generated by an unequal homologous recombination event, due to a misalignment between Alu Sx in intron 12 (5ʹ deletion boundary) of SPTBN2 gene and Alu Sx in intron 20 (3ʹ deletion boundary). Both Alu Sx show 86% sequence identity (91% without gaps) and a microhomology domain of 50 bp.…”

The Alu-Rich Genomic Architecture of SPAST Predisposes to Diverse and Functionally Distinct Disease-Associated CNV Alleles

“…43 However, the short length (<300 bp) and low percent identity (<91%) shared by Alus within each pair may be insufficient to meet the presumed requirements of ectopic homologous recombination derived from observational studies of NAHR at LCRs. 51,52 Furthermore, the three complex Alu-mediated CNVs are inconsistent with formation by NAHR unless a familial Alu polymorphism existed prior to the rearrangement. Some of the Alus at breakpoints of Alu-mediated CNVs contained the 13-nucleotide consensus motif enriched at meiotic recombination hotspots and at some LCRs involved in NAHR.…”

Synaptonemal complexes from DNase-treated rat pachytene chromosomes contain (GT)n and LINE/SINE sequences.

“…In the context of meiosis, the GT repeats are of interest because the repeats and the SCs both show correlations with genetic recombination. The repeats have been found near sites of somatic and germ line recombinants and the positions of the repeats are evolutionarily conserved (BULLOCK, MILLER and BOTCHAN 1986;BOEHM et al 1989;METZENBERG et al 1991). The distribution of the repeats among chromosomes correlates positively with the frequency of meiotic recombination in Drosophila species (LOWENHAUPT, RICH and PARDUE 1989), and in Saccharomyces cerevisiae, meiotic reciprocal recombination is enhanced by the insertion of GT/CA repeats on both homologs (TRECO and ARNHEIM 1986).…”