Nonhomologous Crossover Research Articles

Abnormal hemoglobin anti-Lepore Hong Kong compound with β0-thalassemia ameliorate thalassemia severity when co-inherited with α-thalassemia

Abnormal hemoglobin anti-Lepore Hong Kong is a rare βδ fusion variants resulting from non-homologous crossover during meiosis. Anti-Lepore Hong Kong is known to consistently exhibit significantly increased level of HbA2. In this study, we used multiplex ligation-dependent probe amplification (MLPA) and single molecular real-time (SMRT) sequencing, as well as Sanger sequencing, to identify variants in five unrelated families with abnormal elevated HbA2 level. All probands in these five families were found to be heterozygous for anti-Lepore Hong Kong. Among them, two families showed co-occurrence of β0-thalassemia and α-thalassemia (–SEA/ or αCSα/). Heterozygotes for anti-Lepore Hong Kong displayed an average HbA2 level of 17.7% and behaved normal. However, when combined with β0-thalassemia and α-thalassemia, the probands exhibited higher HbA2 level (30.2–40.8%) and behaved with β-thalassemia trait. Furthermore, determination of the α/β-mRNA ratio revealed a slight downregulation of β-globin, similar to that of β-thalassemia minor. Our study is the first to identify compound heterozygotes for anti-Lepore Hong Kong, β0-thalassemia and α-thalassemia, provide valuable information for prenatal counseling.

Effects of Identity Minimization on Moloney Murine Leukemia Virus Template Recognition and Frequent Tertiary Template-Directed Insertions during Nonhomologous Recombination

Homology requirements for Moloney murine leukemia virus recombination were addressed in this study by monitoring titer defects observed when acceptor/donor template identity lengths were systematically reduced. Recombination acceptors with at least 16 contiguous bases of donor template identity were recognized as efficiently as longer acceptors. In contrast, a sharp 1-log titer drop was observed for an acceptor of only 15 bases long, with an additional 1-log titer decline for an 8-base acceptor and further decreases for shorter acceptors. Eighty-three independent nonhomologous recombination products were sequenced to examine recombination template selection in the absence of significant sequence identity. These replication products contained a total of 152 nonhomologous crossover junctions. Forced copy choice models predict that forced nonhomologous recombination should result in DNA synthesis to the donor template's 5' end, followed by microidentity-guided acceptor template selection. However, only a single product displayed this structure. The majority of examined nonhomologous recombination products contained junction-associated sequence insertions. Most insertions resulted from the use of one or more tertiary templates, recognizable as discontiguous portions of viral or host RNA or minus-strand DNA. The donor/acceptor template microidentity evident at most crossovers reconfirmed the remarkable capability of the reverse transcription machinery to recognize short regions of sequence identity. These results demonstrate that recruitment of discontiguous host or viral sequences is a common way for retroviruses to resolve nonhomologous recombination junctions and provide experimental support for the role of splinting templates in the generation of retroviral insertions.

A Novel beta-delta Globin Gene Fusion Leads to Over-Expression of Delta Globin Chain and a Mild Thalassemia Intermedia Phenotype When Co-Inherited with β0-Thalassemia.

Anti-Lepore hemoglobins are rare βδ fusion variants that arise from nonhomologous crossover during meiosis, resulting in a δ-βδ-β configuration in the β globin cluster on the short arm of chromosome 11. No such variant has previously been reported in Chinese. We studied 2 unrelated Chinese families with anti-Lepore due to a novel βδ fusion. A moderate increase of Hb A2 to between 16.8 and 19.2% of total Hb was seen in 4 clinically and hematologically normal carriers, while in 1 patient with concurrent β thalassemia allele and mild thalassemia intermedia phenotype, the Hb A2 was markedly raised to 42.2%. Potential βδ fusion gene was amplified using PCR with primer 5′ to β globin gene Cap site and 3′ to δ globin gene poly A region in these 5 subjects. Direct sequencing of the PCR products revealed a crossover between the β and δ globin gene within a 54 bp region spanning the junction of CAP and exon 1 in all 5 subjects. Active transcription of this novel βδ fusion gene was studied in 2 subjects (1 normal carrier and the patient with thalassemia intermedia). Using primer pair 5′ to β globin gene Cap site and at the 3′ end of δ globin gene exon 3, a 655 bp PCR product was obtained from cDNA in both subjects. Direct sequencing confirmed the presence of a βδ fusion mRNA. The predicted protein product of this fusion gene was identical to δ globin, since only the 5′ untranslated region was β specific. Determination of α/β mRNA ratios by quantitative real-time PCR was performed in 2 normal carriers (ratio 3.28 and 3.95) and the patient with thalassemia intermedia (ratio 25.59). These were compared with ratios ± standard deviation from 20 normal controls (1.92±0.55), 5 unrelated patients with β thalassaemia minor (17.23±5.38) and 3 unrelated patients with β thalassemia major (139.21±39.50). Mild down-regulation of the β gene in cis due to this interposed βδ fusion gene was demonstrated. Although heterozygotes of this novel anti-Lepore Hb had normal red cell indices and were clinically silent, compound heterozygotes with β0 mutation in trans produced a mild thalassemia intermedia phenotype with a markedly raised Hb A2 level that might mimic clinically mild Hb E-β+ thalassemia. Awareness of this new anti-Lepore Hb will help to resolve diagnostic problems in regions with significant prevalence of globin disorders.

A novel beta‐delta globin gene fusion, anti‐Lepore Hong Kong, leads to overexpression of delta globin chain and a mild thalassaemia intermedia phenotype when co‐inherited with β0‐thalassaemia

Anti-Lepore haemoglobins (Hb) are rare betadelta fusion variants that arise from non-homologous crossover during meiosis, resulting in a delta-betadelta-beta configuration. A novel anti-Lepore mutation (anti-Lepore Hong Kong) was found in two Chinese families with raised Hb A(2). Direct sequencing revealed a crossover within a 54-bp region spanning the junction of cap site (CAP) and exon 1, which predicted the production of normal delta-globin. Determination of alpha/beta-mRNA ratios by quantitative real-time polymerase chain reaction demonstrated downregulation of the beta gene in cis due to the interposed betadelta fusion gene. Although heterozygotes have normal red cell indices and are clinically silent, compound heterozygotes with beta(0) mutation in trans produce a mild thalassaemia intermedia phenotype with a markedly raised Hb A(2) level that may mimic clinically mild Hb E-beta(+)-thalassaemia. Awareness of the presence of anti-Lepore Hong Kong will help to resolve diagnostic problems in regions with significant prevalence of globin disorders.

Enhanced crossover SCRATCHY: construction and high-throughput screening of a combinatorial library containing multiple non-homologous crossovers.

SCRATCHY is a methodology for the construction of libraries of chimeras between genes that display low sequence homology. We have developed a strategy for library creation termed enhanced crossover SCRATCHY, that significantly increases the number of clones containing multiple crossovers. Complementary chimeric gene libraries generated by incremental truncation (ITCHY) of two distinct parental sequences are created, and are then divided into arbitrarily defined sections. The respective sections are amplified by skewed sets of primers (i.e. a combination of gene A specific forward primer and gene B specific reverse primer, etc.) allowing DNA fragments containing non-homologous crossover points to be amplified. The amplified chimeric sections are then subjected to a DNA shuffling process generating an enhanced crossover SCRATCHY library. We have constructed such a library using the rat theta 2 glutathione transferase (rGSTT2) and the human theta 1 glutathione transferase (hGSTT1) genes (63% DNA sequence identity). DNA sequencing analysis of unselected library members revealed a greater diversity than that obtained by canonical family shuffling or with conventional SCRATCHY. Expression and high-throughput flow cytometric screening of the chimeric GST library identified several chimeric progeny that retained rat-like parental substrate specificity.

Unusual organization of the human T-cell receptor beta-chain gene complex is linked to recombination hotspots.

Two rare Sfi I polymorphisms of 360 kb and 280 kb present within the human T-cell antigen receptor beta-chain gene complex were revealed by pulsed-field gel electrophoresis. They represent allelic variants of the polymorphic 330- and 300-kb Sfi I fragments previously described. The 360-kb polymorphism results from duplication of the 30-kb DNA fragment responsible for the 330/300-kb insertion/deletion-related polymorphism. The 280-kb polymorphism results from a 20-kb deletion from the 300-kb SfiI allele. The rare polymorphisms also map on either side of a Sal I site located near a recombination hotspot, suggesting that germline duplications and deletions arose from nonhomologous crossover events.

Gene replacement with one-sided homologous recombination.

Homologous recombination is now routinely used in mammalian cells to replace endogenous chromosomal sequences with transferred DNA. Vectors for this purpose are traditionally constructed so that the replacement segment is flanked on both sides by DNA sequences which are identical to sequences in the chromosomal target gene. To test the importance of bilateral regions of homology, we measured recombination between transferred and chromosomal immunoglobulin genes when the transferred segment was homologous to the chromosomal gene only on the 3' side. In each of the four recombinants analyzed, the 5' junction was unique, suggesting that it was formed by nonhomologous, i.e., random or illegitimate, recombination. In two of the recombinants, the 3' junction was apparently formed by homologous recombination, while in the other two recombinants, the 3' junction as well as the 5' junction might have involved a nonhomologous crossover. As reported previously, we found that the frequency of gene targeting increases monotonically with the length of the region of homology. Our results also indicate that targeting with fragments bearing one-sided homology can be as efficient as with fragments with bilateral homology, provided that the overall length of homology is comparable. The frequency of these events suggests that the immunoglobulin locus is particularly susceptible to nonhomologous recombination. Vectors designed for one-sided homologous recombination might be advantageous for some applications in genetic engineering.

Gene Replacement with One-Sided Homologous Recombination

Homologous recombination is now routinely used in mammalian cells to replace endogenous chromosomal sequences with transferred DNA. Vectors for this purpose are traditionally constructed so that the replacement segment is flanked on both sides by DNA sequences which are identical to sequences in the chromosomal target gene. To test the importance of bilateral regions of homology, we measured recombination between transferred and chromosomal immunoglobulin genes when the transferred segment was homologous to the chromosomal gene only on the 3' side. In each of the four recombinants analyzed, the 5' junction was unique, suggesting that it was formed by nonhomologous, i.e., random or illegitimate, recombination. In two of the recombinants, the 3' junction was apparently formed by homologous recombination, while in the other two recombinants, the 3' junction as well as the 5' junction might have involved a nonhomologous crossover. As reported previously, we found that the frequency of gene targeting increases monotonically with the length of the region of homology. Our results also indicate that targeting with fragments bearing one-sided homology can be as efficient as with fragments with bilateral homology, provided that the overall length of homology is comparable. The frequency of these events suggests that the immunoglobulin locus is particularly susceptible to nonhomologous recombination. Vectors designed for one-sided homologous recombination might be advantageous for some applications in genetic engineering.

Hemoglobin Miyada: DNA analysis of the anti-Lepore beta delta fusion gene.

Hemoglobin Miyada, an anti-Lepore hemoglobin, represents the protein product of a nonhomologous crossover between beta and delta genes. The mutant globin is beta-like from the N terminus to amino acid 12, and delta-like from amino acid 22 through the C terminus, thus predicting a crossover site in the first coding region of the gene. DNA analysis, using multiple restriction endonucleases and hybridization to delta and beta globin gene-specific probes, confirms that the beta delta hybrid gene 1) is located on a single chromosomal fragment between normal delta and beta genes, and 2) has 5' beta promoter sequences, delta IVS 1 and 2, and 3' coding and flanking sequences.

The junctions between the repetitive and the short unique sequences of the herpes simplex virus genome are determined by the polypeptide-coding regions of two spliced immediate-early mRNAs.

Immediate-early (IE) mRNAs-4 and -5 of herpes simplex virus type 2 (HSV-2) are transcribed from the IRs/TRs genome regions towards the Us region. Each of these spliced mRNAs has an untranslated leader sequence of 249 bases and a single intron of approximately 540 bases which are contained entirely within TRs/IRs sequences. The DNA sequence of the intron largely comprises tandem reiterations of three distinct short sequences. Upstream of the common 5' mRNA termini the DNA sequence contains regions of homology with the equivalent region of HSV-1. Comparison of the polypeptides encoded by these HSV-2 mRNAs with those of HSV-1 shows blocks of conserved amino acids. The locations of the first initiator ATG triplets of these two HSV-2 mRNAs suggest that the IRs/TRs regions of HSV expand, by gene conversion or by equal though non-homologous crossover, to an extent determined by the functions of the DNA sequences which are duplicated or deleted as a result of the crossover. This mechanism for expansion of repeats may apply to other herpesviruses which have a genome structure similar to that of HSV.

Hemoglobin Parchman: double crossover within a single human gene.

Structural analysis of a new variant hemoglobin revealed tryptic peptides with the amino acid composition of normal delta-globin, except for two internal peptides, which had the compositions of normal beta-globin. The most likely explanation for these findings is that a double, nonhomologous crossover between the delta-and beta-globin genes had occurred.

Linkage of alpha G-Philadelphia to alpha-thalassemia in African-Americans .

We have studied the inheritance of the alpha-chain hemoglobin variant Hb G-Philadelphia (alpha 2(68 Asn leads to Lys)Beta 2) in two African-American families. Expression of the alpha-globin loci was monitored by the percentage of Hb G in these individuals. The variant represented approximately 33% of the total adult hemoglobin in some and 50% in others. alpha-Globin gene fragments were analyzed by using restricton endonucleases that cleave outside (EcoRI), within (HindIII), and between (Bgl II) the normal duplicated alpha-globin loci (alpha alpha/alpha alpha). Individuals having 33% variant lack one functioning alpha gene (alpha G/alpha alpha); those with 50% variant lack two genes, one missing on each chromosome (alpha G/alpha). Inheritance of alpha G was therefore linked to that of a chromosome with only one functional alpha-globin gene locus. This locus is probably the result of a nonhomologous crossover. Our results also suggest equal expression of the alpha-globin loci in humans because the percentages of the variant could be explained solely on the basis of the total number of alpha genes present. The percentages of Hb G as well as other hematologic data all were consistent with the number of alpha-globin genes identified by restriction endonuclease mapping. Gene mapping yields a more precise determination of the number of alpha-globin genes than does study of globin synthesis.

Triplicated alpha-globin loci in humans.

We have identified 12 individuals who are heterozygous for a chromosome with three alpha-globin genes. We determined the presence of the third alpha-globin locus by restriction endonuclease digestion and hybridization with alpha-globin cDNA probes. The three alpha-globin loci resided in an elongated fragment on digestion with EcoRI, BamHI, and Xba I, and the third locus was present in an additional 3.7-kilobase fragment on digestion with Hpa I, Sac I, and Bgl II. The locations of the restriction sites are compatible with a nonhomologous crossover mechanism producing the triple alpha loci. The frequency of the triple alpha loci was 0.0036 in American blacks and less than 0.004 in Sardinians, but was higher in Greek Crypriots (0.05). Individuals with five alpha-globin genes (alpha alpha/alpha alpha alpha) apparently showed no clinical or hematologic abnormalities.

Hemoglobin Lincoln Park: a betadelta fusion (anti-Lepore) variant with an amino acid deletion in the delta chain-derived segment.

An electrophoretically slow-moving hemoglobin variant was identified in three members of a family originating from Southern Mexico. The variant, Hb Lincoln Park, made up approximately 14% of the total hemoglobin and appeared to have normal stability and functional properties. None of the individuals in whom the abnormal hemoglobin was present was anemic, but each had a mildly elevated reticulocyte count. Structural data suggest that the non-alpha chain of Hb Lincoln Park represents a betadelta gene-fusion product, with normal beta chain structure of the amino-terminal portion of the chain and delta sequences subsequently, the crossover point occurring between animo acid residues 22 and 50. An additional abnormality is the deletion of valine-137, a component of the delta gene-derived segment of the betadelta chain. To account for the development of this abnormal globin chain, a series of intergenic crossovers is proposed; the first, a nonhomologous crossover between the beta and delta genes, presumably gave rise to the betadelta fusion gene; two additional crossovers, one of them unequal, may then have occurred between the same beta and delta genes to produce the amino acid deletion.

Hemoglobin Cranston, an unstable variant having an elongated beta chain due to nonhomologous crossover between two normal beta chain genes.

An asymptomatic woman was found to have a compensated hemolytic state due to an unstable hemoglobin variant, comprising 35% of the total. Peptide maps of tryptic digests of the abnormal beta chain were identical to those of beta A except that tryptic peptide 15 (Tyr-His-COOH) was absent and a new peptide was detected, containing equivalent amounts of Ser, Ile, Thr, and Lys. Its sequence was determined by manual Edman degradation. An additional hydrophobic peptide isolated by counter-current distribution contained: Asx, Ser, Ala, Tyr, 2 Phe, and 3 Leu. Its sequence was determined on an automatic solid phase sequencer. Digestion with carboxypeptidase A confirmed the C-terminal sequence. Hemoglobin Cranston has an elongated beta chain with the following structure: (see article). This variant is the first "adult" human hemoglobin known to contain isoleucine. It is likely that hemoglobin Cranston arose because of a nonhomologous crossover of two normal beta chain genes, probably during meiosis, with the insertion of two nucleotides (AG) at position 144, resulting in a frame shift. Hemoglobin Cranston provides new information on the structure of the beta chain gene as well as an explanation of both the structure and genetic basis of hemoglobin Tak, the only other elongated beta chain variant that has been described.