Unequal Crossing-over Research Articles

Divergence of gene regulation through chromosomal rearrangements.

BackgroundThe molecular mechanisms that modify genome structures to give birth and death to alleles are still not well understood. To investigate the causative chromosomal rearrangements, we took advantage of the allelic diversity of the duplicated p1 and p2 genes in maize. Both genes encode a transcription factor involved in maysin synthesis, which confers resistance to corn earworm. However, p1 also controls accumulation of reddish pigments in floral tissues and has therefore acquired a new function after gene duplication. p1 alleles vary in their tissue-specific expression, which is indicated in their allele designation: the first suffix refers to red or white pericarp pigmentation and the second to red or white glume pigmentation.ResultsComparing chromosomal regions comprising p1-ww[4Co63], P1-rw1077 and P1-rr4B2 alleles with that of the reference genome, P1-wr[B73], enabled us to reconstruct additive events of transposition, chromosome breaks and repairs, and recombination that resulted in phenotypic variation and chimeric regulatory signals. The p1-ww[4Co63] null allele is probably derived from P1-wr[B73] by unequal crossover between large flanking sequences. A transposon insertion in a P1-wr-like allele and NHEJ (non-homologous end-joining) could have resulted in the formation of the P1-rw1077 allele. A second NHEJ event, followed by unequal crossover, probably led to the duplication of an enhancer region, creating the P1-rr4B2 allele. Moreover, a rather dynamic picture emerged in the use of polyadenylation signals by different p1 alleles. Interestingly, p1 alleles can be placed on both sides of a large retrotransposon cluster through recombination, while functional p2 alleles have only been found proximal to the cluster.ConclusionsAllelic diversity of the p locus exemplifies how gene duplications promote phenotypic variability through composite regulatory signals. Transposition events increase the level of genomic complexity based not only on insertions but also on excisions that cause DNA double-strand breaks and trigger illegitimate recombination.

Phylogeny of the rock wallabies, Petrogale (Marsupialia: Macropodidae). Part II: Detection of hybridisation among macropodines

Phylogenetic relationships among rock-wallabies, Petrogale (Marsupialia: Macropodidae), have proven difficult to resolve. Given the documented interspecific hybridisation in the wild and the ease with which hybrids can be bred in captivity, introgression and hybrid speciation are likely explanations for these difficulties. In this paper, an attempt is made at using a phylogenetic approach to identify Petrogale hybrids of known origin. The Hybrid Detection Criterion (HDC) test is applied to DNA–DNA hybridisation data for 15 full species, two natural yard-bred hybrids, and two artificial hybrids from the same pairs of parental species. While the yard-bred hybrids elude detection with this technique, the artificial hybrids, consisting of equimolar mixture of parental extracts, are easily identified. Moreover, splitsgraphs constructed from five pairs of natural and artificial hybrids, including those evaluated with HDC, and their parents show that, in all cases but one, these two kinds of hybrids do not group together. Because the HDC assumes an intermediate phylogenetic position of the hybrid between its postulated parents, it is likely that unequal crossing-over, or another recombination event, affects the results of the test. These conclusions cast some doubt on the possibility of accurately detecting Petrogale hybrids with a phylogenetic approach.

Genetic Analyses of the ChimericCYP11B1/CYP11B2Gene in a Korean Family with Glucocorticoid-Remediable Aldosteronism

Glucocorticoid-remediable aldosteronism (GRA) is an autosomal-dominant inheritable form of hyperaldosteronism with early onset hypertension. GRA is caused by unequal crossing-over of the steroid 11β-hydroxylase (CYP11B1) and aldosterone synthase (CYP11B2) genes. As a result of chimeric gene duplication, aldosterone is ectopically synthesized in the adrenal zona fasciculata under the control of adrenocorticotropin. Here, we describe three cases of GRA in a Korean family. The proband-a 21-yr-old female-was incidentally found to have high blood pressure (170/108 mmHg). Her 46-yr-old father had been treated twice for cerebral hemorrhage at the ages of 29 and 39 yr. Her 15-yr-old brother had a 2-yr history of hypertension; however, he was never treated. Their laboratory test results showed normokalemia, hyporeninemia, hyperaldosteronism, and a high plasma aldosterone concentration-to-plasma renin activity ratio. Normal saline loading failed to suppress aldosterone secretion. However, dexamethasone administration effectively suppressed their plasma aldosterone concentrations. Following genetic analyses with PCR and direct sequencing to document the chimeric gene and crossover site, respectively, we identified CYP11B1/CYP11B2 and determined the breakpoint of unequal crossover to be located between intron 2 of CYP11B1 and exon 3 of CYP11B2.

Relationships between rust resistance genes at the M locus in flax.

Genes at the M locus in flax (Linum usitatissimum) that confer resistance to flax rust (Melampsora lini) occur in complex haplotypes containing up to 15 related genes or gene fragments. We have cloned two additional functional resistance genes at this locus, M1 and M3, by transposon tagging and candidate gene approaches, and investigated the genetic relationships between four genes (M, M1, M3 and M4) by recombination analysis. M1 and M3, like M, are members of the nucleotide binding site, leucine-rich repeat (NBS-LRR) family. Comparisons of the predicted M1 and M3 amino acid sequences with M and L6 reveal that: (i) M1 contains four additional LRRs, probably as a result of an unequal crossover event between duplicated regions; (ii) M1 shares large segments of exact identity with M and M3, indicative of intragenic recombination events; and (iii) a large number of amino acid differences are scattered throughout the M, M1 and M3 proteins. Recombination analysis (here and in previous studies) has revealed that M readily recombines with M1, M3 and M4, whereas these three genes fail to recombine despite large family sizes (>5800) in two test-cross families, suggesting that they may occupy allelic positions in the gene cluster. Several restriction fragment length polymorphism markers within or near the M locus were mapped with respect to seven crossover events between M and M1. The results of this and previous studies provide evidence of structural differences between: (i) homoeologous loci in the different genomes of flax; (ii) different haplotypes at the M locus; (iii) different resistance genes in the M group; and (iv) the flanking regions downstream of M locus resistance genes.

Polyalanine expansion of PHOX2B in congenital central hypoventilation syndrome: rs17884724:A>C is associated with 7-alanine expansion

With congenital central hypoventilation syndrome (CCHS), most patients have a de novo 5-13 polyalanine expansion mutation in PHOX2B. We reported previously that de novo polyalanine expansion mutations were of paternal origin and were derived from unequal sister chromatid exchange during spermatogenesis in six and four informative families, respectively. In this study, we analyzed the relationship between haplotypes and de novo polyalanine expansion in PHOX2B and found that haplotypes carrying rs17884724:A>C were detected frequently in 7-alanine expanded (27-alanine) mutant alleles, which are the most prevalent mutations in CCHS. The allele with rs17884724:A>C made fewer nucleotide mismatches in the misalignment at crossing-over than the allele without rs17884724:A>C. The high frequency of rs17884724:A>C in 7-alanine expansion (27-alanine) mutations also supported the unequal crossover mechanism for polyalanine expansion. We also confirmed the paternal origin of de novo polyalanine expansion mutation and unequal sister chromatid exchange association in three more patients. In spite of paternal bias, the paternal age effect on CCHS incidence was not observed. De novo polyalanine expansion mutations are mainly derived from unequal sister chromatid exchange during spermatogenesis because of replication and/or repair systems that are specific for spermatogenesis.

UNEQUAL CROSSING-OVER IN THE BAR REGION OF DROSOPHILA MELANOGASTER

HereditasVolume 47, Issue 2 p. 357-378 Open Access UNEQUAL CROSSING-OVER IN THE BAR REGION OF DROSOPHILA MELANOGASTER II. INFLUENCE OF TEMPERATURE, X-RAYS AND EDTA MARIANNE RASMUSON, MARIANNE RASMUSON INSTITUTE OF GENETICS, UNIVERSITY OF UPPSALA, SWEDENSearch for more papers by this author MARIANNE RASMUSON, MARIANNE RASMUSON INSTITUTE OF GENETICS, UNIVERSITY OF UPPSALA, SWEDENSearch for more papers by this author First published: September 1961 https://doi.org/10.1111/j.1601-5223.1961.tb01779.xAboutPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Literature cited Darlington, C. D. 1932. Recent advances in cytology. — London . Herskowitz, I. H. and Abrahamson, S. 1957. Induced changes in female germ cells of Drosophila. IV. Dependence of induced crossover-like exchanges in oocytes and oogonia upon X-ray intensity. Genetics 42: 444– 453. Kaplan, W. D. 1960. Autoradiographic and genetic studies of tritiated thymidine in the testes of Drosophila melanogaster. (Abstr.) Genetics 45: 995. LeClerc, G. 1946. Occurrence of mitotic crossing-over without meiotic crossing-over. Science 103: 553– 554. Levine, R. P. 1955. Chromosome structure and the mechanism of crossing-over. Proc. Nat. Acad. Sci.. 41: 727– 730. Mavor, J. W. and Svenson, H. K. 1924. A comparison of the effect of X-rays and temperature on linkage and fertility in Drosophila. Genetics 9: 588– 608. Mitra, S. 1958. Effects of X-rays on chromosomes of Lilium longiflorum during meiosis. Genetics 43: 771– 789. Pritchard, R. H. 1960. The bearing of recombination analysis at high resolution on genetic fine structure in Aspergillus nidulans and the mechanism of recombination in higher organisms. In Hayes and Clowes, Microbial genetics. — Cambridge . Rasmuson, M. 1957. Unequal crossing-over in the Bar region of Drosophila melanogaster. I. High temperature as a means of increasing the frequency. Hereditas 43: 589– 594. Sobels, F. H. and Van Steenis, H. 1957. Chemical induction of crossing-over in Drosophila males. Nature 179: 29– 31. Steffenson, D., Anderson, L. F. and Kase, S. 1956. Crossing-over studies with Drosophila and maize. (Abstr.) Genetics 41: 663. Stehn, C. and Rentschler, V. 1936. The effect of temperature on the frequency of crossing-over in Drosophila melanogaster. Proc. Nat. Acad. Sci.. 22: 451– 453. Sturtevant, A. H. 1928. A further study of so-called mutation at the Bar locus of Drosophila. Genetics 13: 401– 409. Taylor, J. H. 1957. The time and mode of duplication of chromosomes. Amer. Nat.. 91: 209– 221. Whittinghill, M. 1955. Crossover variability and induced crossing-over. J. Cell. and Comp. Physiol. 45, Suppl. 2: 189– 220. Volume47, Issue2September 1961Pages 357-378 ReferencesRelatedInformation

Fork Stalling and Template Switching As a Mechanism for Polyalanine Tract Expansion Affecting the DYC Mutant of HOXD13, a New Murine Model of Synpolydactyly

Polyalanine expansion diseases are proposed to result from unequal crossover of sister chromatids that increases the number of repeats. In this report we suggest an alternative mechanism we put forward while we investigated a new spontaneous mutant that we named "Dyc" for "Digit in Y and Carpe" phenotype. Phenotypic analysis revealed an abnormal limb patterning similar to that of the human inherited congenital disease synpolydactyly (SPD) and to the mouse mutant model Spdh. Both human SPD and mouse Spdh mutations affect the Hoxd13 gene within a 15-residue polyalanine-encoding repeat in the first exon of the gene, leading to a dominant negative HOXD13. Genetic analysis of the Dyc mutant revealed a trinucleotide expansion in the polyalanine-encoding region of the Hoxd13 gene resulting in a 7-alanine expansion. However, unlike the Spdh mutation, this expansion cannot result from a simple duplication of a short segment. Instead, we propose the fork stalling and template switching (FosTeS) described for generation of nonrecurrent genomic rearrangements as a possible mechanism for the Dyc polyalanine extension, as well as for other polyalanine expansions described in the literature and that could not be explained by unequal crossing over.

Rapid detection of the CYP2A6*12 hybrid allele by Pyrosequencing®technology

BackgroundIdentification of CYP2A6 alleles associated with reduced enzyme activity is important in the study of inter-individual differences in drug metabolism. CYP2A6*12 is a hybrid allele that results from unequal crossover between CYP2A6 and CYP2A7 genes. The 5' regulatory region and exons 1–2 are derived from CYP2A7, and exons 3–9 are derived from CYP2A6. Conventional methods for detection of CYP2A6*12 consist of two-step PCR protocols that are laborious and unsuitable for high-throughput genotyping. We developed a rapid and accurate method to detect the CYP2A6*12 allele by Pyrosequencing technology.MethodsA single set of PCR primers was designed to specifically amplify both the CYP2A6*1 wild-type allele and the CYP2A6*12 hybrid allele. An internal Pyrosequencing primer was used to generate allele-specific sequence information, which detected homozygous wild-type, heterozygous hybrid, and homozygous hybrid alleles. We first validated the assay on 104 DNA samples that were also genotyped by conventional two-step PCR and by cycle sequencing. CYP2A6*12 allele frequencies were then determined using the Pyrosequencing assay on 181 multi-ethnic DNA samples from subjects of African American, European Caucasian, Pacific Rim, and Hispanic descent. Finally, we streamlined the Pyrosequencing assay by integrating liquid handling robotics into the workflow.ResultsPyrosequencing results demonstrated 100% concordance with conventional two-step PCR and cycle sequencing methods. Allele frequency data showed slightly higher prevalence of the CYP2A6*12 allele in European Caucasians and Hispanics.ConclusionThis Pyrosequencing assay proved to be a simple, rapid, and accurate alternative to conventional methods, which can be easily adapted to the needs of higher-throughput studies.

Genome-wide analysis of recombination machinery for spliceosomal introns gain

What caused spliceosomal introns gain remains an unsolved problem. To this, defining what spliceosomal introns arise from is critical. Here, the introns density of the genomes is calculated for four species, indicating:(1) sex chromosomes in mammals have lower intron densities, (2) despite that, the proportion of UTRs (untranslated regions) with introns in sex chromosomes is higher than other ones, and (3) AT content of introns is more similar to that of intergenic regions when these regions comprise the majority of a chromosome, and more similar to that of exons, when exons are the majority of the chromosome. On the other hand, introns have been clearly demonstrated to invade genetic sequences in recent times while sex chromosomes evolved from a pair of autosomes within the last 300 millions years. One main difference between sex chromosomes and autosomes in mammalian is that sex chromosomes recombination stopped. Thus, recombination might be the main determinant for eukaryotes gaining spliceosomal introns. To further prove that and avoid giving weak signal, the whole genomes from eight eukaryotic species are analyzed and present strong signal for above the trend (3) in three species (t-test, P = 0.55 for C. elegans, P = 0.72 for D. melanogaster and P = 0.83 for A. thaliana). These results suggest that the genome-wide coincidence as above (3) can only be caused by the large-scale random unequal crossover in eukaryote meiosis, which might have fueled spliceosomal introns but hardly occurred in prokaryotes.

New Insights into Centromere Organization and Evolution from the White-Cheeked Gibbon and Marmoset

The evolutionary history of alpha-satellite DNA, the major component of primate centromeres, is hardly defined because of the difficulty in its sequence assembly and its rapid evolution when compared with most genomic sequences. By using several approaches, we have cloned, sequenced, and characterized alpha-satellite sequences from two species representing critical nodes in the primate phylogeny: the white-cheeked gibbon, a lesser ape, and marmoset, a New World monkey. Sequence analyses demonstrate that white-cheeked gibbon and marmoset alpha-satellite sequences are formed by units of approximately 171 and approximately 342 bp, respectively, and they both lack the high-order structure found in humans and great apes. Fluorescent in situ hybridization characterization shows a broad dispersal of alpha-satellite in the white-cheeked gibbon genome including centromeric, telomeric, and chromosomal interstitial localizations. On the other hand, centromeres in marmoset appear organized in highly divergent dimers roughly of 342 bp that show a similarity between monomers much lower than previously reported dimers, thus representing an ancient dimeric structure. All these data shed light on the evolution of the centromeric sequences in Primates. Our results suggest radical differences in the structure, organization, and evolution of alpha-satellite DNA among different primate species, supporting the notion that 1) all the centromeric sequence in Primates evolved by genomic amplification, unequal crossover, and sequence homogenization using a 171 bp monomer as the basic seeding unit and 2) centromeric function is linked to relatively short repeated elements, more than higher-order structure. Moreover, our data indicate that complex higher-order repeat structures are a peculiarity of the hominid lineage, showing the more complex organization in humans.

Origin and Ascendancy of a Chimeric Fusion Gene: The / -Globin Gene of Paenungulate Mammals

The delta-globin gene (HBD) of eutherian mammals exhibits a propensity for recombinational exchange with the closely linked beta-globin gene (HBB) and has been independently converted by the HBB gene in multiple lineages. Here we report the presence of a chimeric beta/delta fusion gene in the African elephant (Loxodonta africana) that was created by unequal crossing-over between misaligned HBD and HBB paralogs. The recombinant chromosome that harbors the beta/delta fusion gene in elephants is structurally similar to the "anti-Lepore" duplication mutant of humans (the reciprocal exchange product of the hemoglobin Lepore deletion mutant). However, the situation in the African elephant is unique in that the chimeric beta/delta fusion gene supplanted the parental HBB gene and is therefore solely responsible for synthesizing the beta-chain subunits of adult hemoglobin. A phylogenetic survey of beta-like globin genes in afrotherian and xenarthran mammals revealed that the origin of the chimeric beta/delta fusion gene and the concomitant inactivation of the HBB gene predated the radiation of "Paenungulata," a clade of afrotherian mammals that includes three orders: Proboscidea (elephants), Sirenia (dugongs and manatees), and Hyracoidea (hyraxes). The reduced fitness of the human Hb Lepore deletion mutant helps to explain why independently derived beta/delta fusion genes (which occur on an anti-Lepore chromosome) have been fixed in a number of mammalian lineages, whereas the reciprocal delta/beta fusion gene (which occurs on a Lepore chromosome) has yet to be documented in any nonhuman mammal. This illustrates how the evolutionary fates of chimeric fusion genes can be strongly influenced by their recombinational mode of origin.

Alu-Alurecombination underlies the vast majority of largeVHLgermline deletions: Molecular characterization and genotype-phenotype correlations in VHL patients

Von Hippel-Lindau disease (VHL) is an autosomal dominant cancer syndrome. Affected individuals are predisposed to multiple tumors, primarily of the central nervous system (CNS), eyes, adrenals, and kidneys. The VHL tumor suppressor gene on chromosome 3p26-25 is partially or completely deleted in 20 to 30% of families with VHL. We identified deletions ranging from 0.5 kb to 250 kb affecting part of or the entire VHL and flanking genes in 54 families. In 33 of the index patients, the breakpoints were precisely characterized by DNA sequencing. Of the 66 breakpoints, 90% were located in Alu elements, revealing Alu-mediated recombination as the major mechanism for large germline deletions of the VHL gene, which lies in a region of high Alu density. Interestingly, an AluYa5 element in VHL intron 2, the evolutionarily youngest Alu element and the only such element in the entire region, was found to be the most recombinogenic, involved in 7 out of the 33 deletions. In comparison to VHL patients in general, the 54 index cases and their affected relatives showed a higher occurrence of renal cell carcinomas (RCC) and of CNS hemangioblastomas. We not only noted the association of RCC with retention of the HSPC300 gene, but also observed a significant correlation between retention of HSPC300 and the development of retinal angiomas (AR). This study reveals that germline VHL deletions provide a particularly rich source for the study of Alu-mediated unequal crossover events, and provides evidence for a protective role of the loss of the actin-regulator gene HSPC300 for the development of both RCC and AR.

Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species

Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM x DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.

Identification of the first duplication in MYH9-related disease: A hot spot for unequal crossing-over within exon 24 of the MYH9 gene

MYH9-related disease (MYH9RD) is a rare autosomal dominant disorder caused by mutations in MYH9, the gene encoding the heavy chain of non-muscle myosin IIA. All patients present with congenital macrothrombocytopenia and inclusion bodies in neutrophils. Some of them can also develop sensorineural deafness, presenile cataracts, and/or progressive nephritis leading to end-stage renal failure. The spectrum of mutations so far identified is peculiar, consisting of mostly missense mutations. Others are nonsense and frameshift mutations, all localized in the COOH terminus of the protein, or in-frame deletions. We report a family with three affected members carrying a novel mutation, the first duplication (p.E1066_A1072dup), of MYH9. The mutation was localized within exon 24, where the presence of a 16 nucleotide repeat was likely to be responsible for unequal crossing-over. Of note, a deletion of the same amino acids 1066_1072 was also identified in another MHY9RD family. Since two of the four patients with the duplication or the deletion in exon 24 were affected with bilateral neonatal cataracts, we speculate that these mutations might correlate with the ocular defect, which is reported only in 16% of MYH9RD patients.

Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination

Eukaryotes possess mechanisms to limit crossing over during homologous recombination, thus avoiding possible chromosomal rearrangements. We show here that budding yeast Mph1, an ortholog of human FancM helicase, utilizes its helicase activity to suppress spontaneous unequal sister chromatid exchanges and DNA double-strand break-induced chromosome crossovers. Since the efficiency and kinetics of break repair are unaffected, Mph1 appears to channel repair intermediates into a noncrossover pathway. Importantly, Mph1 works independently of two other helicases-Srs2 and Sgs1-that also attenuate crossing over. By chromatin immunoprecipitation, we find targeting of Mph1 to double-strand breaks in cells. Purified Mph1 binds D-loop structures and is particularly adept at unwinding these structures. Importantly, Mph1, but not a helicase-defective variant, dissociates Rad51-made D-loops. Overall, the results from our analyses suggest a new role of Mph1 in promoting the noncrossover repair of DNA double-strand breaks.

Tracing misalignment and unequal crossing over during evolution of the repetitive region of the SM50 gene in sea urchins

The location of misalignment and unequal crossover involved in concerted evolution of tandemly repetitive sequences is difficult to document owing to the homogeneity of sequences that are subject to this process. However, the repetitive domain of the SM50 gene in sea urchins contains variation, within the gene itself, between alleles, and between species that has allowed us to determine where misalignment and unequal crossing over occurred during evolution of this gene. We have therefore analyzed the SM50 repeat regions in a variety of species to determine where recent changes in repeat numbers have occurred, and from this have deduced the mechanisms that lead to these changes. We next tried to determine whether recent misalignment and unequal crossover has produced allelic variation in current populations of sea urchins. We found SM50 alleles within three species that have different numbers of repeats. This marks the first reported documentation of allelic variation in the number of repeats in the SM50 gene. We also show how a single unequal crossover event could have produced the allelic variation. We have found that substitutions and small deletions in the sequences within the repeats can substantially affect how misalignment occurs, resulting in different patterns of repeats after concerted evolution.

Distal 22q11.2 microduplication encompassing the BCR gene

Chromosome 22 band q11.2 has been recognized to be highly susceptible to subtle microdeletions and microduplications, which have been attributed to the presence of several large segmental duplications; also known as low copy repeats (LCRs). These LCRs function as mediators of non-allelic homologous recombination (NAHR), which results in these chromosomal rearrangements as a result of unequal crossover. The four centromeric LCRs at proximal 22q11.2 have been previously implicated in recurrent chromosomal rearrangements including the DiGeorge/Velocardiofacial syndrome (DG/VCFs) microdeletion and its reciprocal microduplication. Recently, we and others have demonstrated that the four telomeric LCRs at distal 22q11.2 are causally implicated in a newly recognized recurrent distal 22q11.2 microdeletion syndrome in the region immediately telomeric to the DG/VCFs typically deleted region. Here we report on the clinical, cytogenetic, and array CGH studies of a 4.5-year-old girl with history of failure to thrive, developmental delay (DD), and relative macrocephaly. She carries a paternally inherited approximately 2.1 Mb microduplication at distal 22q11.2, which spans approximately 34 annotated genes, and is flanked by two of the four telomeric 22q11.2 LCRs. We conclude that the four telomeric LCRs at distal 22q11.2 can mediate both deletions and duplications in this genomic region. Both deletions and duplication of this region present with subtle clinical features including mild to moderate mental retardation, DD, and mild dysmorphic features.

Carrier screening for spinal muscular atrophy

Carrier screening for spinal muscular atrophy

Segmental Duplications Arise from Pol32-Dependent Repair of Broken Forks through Two Alternative Replication-Based Mechanisms

The propensity of segmental duplications (SDs) to promote genomic instability is of increasing interest since their involvement in numerous human genomic diseases and cancers was revealed. However, the mechanism(s) responsible for their appearance remain mostly speculative. Here, we show that in budding yeast, replication accidents, which are most likely transformed into broken forks, play a causal role in the formation of SDs. The Pol32 subunit of the major replicative polymerase Polδ is required for all SD formation, demonstrating that SDs result from untimely DNA synthesis rather than from unequal crossing-over. Although Pol32 is known to be required for classical (Rad52-dependant) break-induced replication, only half of the SDs can be attributed to this mechanism. The remaining SDs are generated through a Rad52-independent mechanism of template switching between microsatellites or microhomologous sequences. This new mechanism, named microhomology/microsatellite-induced replication (MMIR), differs from all known DNA double-strand break repair pathways, as MMIR-mediated duplications still occur in the combined absence of homologous recombination, microhomology-mediated, and nonhomologous end joining machineries. The interplay between these two replication-based pathways explains important features of higher eukaryotic genomes, such as the strong, but not strict, association between SDs and transposable elements, as well as the frequent formation of oncogenic fusion genes generating protein innovations at SD junctions.

New Genes Originated via Multiple Recombinational Pathways in the -Globin Gene Family of Rodents

Species differences in the size or membership composition of multigene families can be attributed to lineage-specific additions of new genes via duplication, losses of genes via deletion or inactivation, and the creation of chimeric genes via domain shuffling or gene fusion. In principle, it should be possible to infer the recombinational pathways responsible for each of these different types of genomic change by conducting detailed comparative analyses of genomic sequence data. Here, we report an attempt to unravel the complex evolutionary history of the beta-globin gene family in a taxonomically diverse set of rodent species. The main objectives were: 1) to characterize the genomic structure of the beta-globin gene cluster of rodents; 2) to assign orthologous and paralogous relationships among duplicate copies of beta-like globin genes; and 3) to infer the specific recombinational pathways responsible for gene duplications, gene deletions, and the creation of chimeric fusion genes. Results of our comparative genomic analyses revealed that variation in gene family size among rodent species is mainly attributable to the differential gain and loss of later expressed beta-globin genes via unequal crossing-over. However, two distinct recombinational mechanisms were implicated in the creation of chimeric fusion genes. In muroid rodents, a chimeric gamma/epsilon fusion gene was created by unequal crossing-over between the embryonic epsilon- and gamma-globin genes. Interestingly, this gamma/epsilon fusion gene was generated in the same fashion as the "anti-Lepore" 5'-delta-(beta/delta)-beta-3' duplication mutant in humans (the reciprocal exchange product of the pathological hemoglobin Lepore deletion mutant). By contrast, in the house mouse, Mus musculus, a chimeric beta/delta fusion pseudogene was created by a beta-globin --> delta-globin gene conversion event. Although the gamma/epsilon and beta/delta fusion genes share a similar chimeric gene structure, they originated via completely different recombinational pathways.