scholarly journals Gene Conversion amongst Alu SINE Elements

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 905
Author(s):  
Liliya Doronina ◽  
Olga Reising ◽  
Jürgen Schmitz
Keyword(s):  
Gene Conversion ◽  
Ribosomal Rna ◽  
Homologous Sequence ◽  
Systematic Screening ◽  
Short Interspersed Elements ◽  
Binding Domains ◽  
Allelic Gene ◽  
New Strategy ◽  
Integrative Process ◽  
Clear Cases

The process of non-allelic gene conversion acts on homologous sequences during recombination, replacing parts of one with the other to make them uniform. Such concerted evolution is best described as paralogous ribosomal RNA gene unification that serves to preserve the essential house-keeping functions of the converted genes. Transposed elements (TE), especially Alu short interspersed elements (SINE) that have more than a million copies in primate genomes, are a significant source of homologous units and a verified target of gene conversion. The consequences of such a recombination-based process are diverse, including multiplications of functional TE internal binding domains and, for evolutionists, confusing divergent annotations of orthologous transposable elements in related species. We systematically extracted and compared 68,097 Alu insertions in various primates looking for potential events of TE gene conversion and discovered 98 clear cases of Alu–Alu gene conversion, including 64 cases for which the direction of conversion was identified (e.g., AluS conversion to AluY). Gene conversion also does not necessarily affect the entire homologous sequence, and we detected 69 cases of partial gene conversion that resulted in virtual hybrids of two elements. Phylogenetic screening of gene-converted Alus revealed three clear hotspots of the process in the ancestors of Catarrhini, Hominoidea, and gibbons. In general, our systematic screening of orthologous primate loci for gene-converted TEs provides a new strategy and view of a post-integrative process that changes the identities of such elements.

scholarly journals Multiple Heterologies Increase Mitotic Double-Strand Break-Induced Allelic Gene Conversion Tract Lengths in Yeast

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 665-679 ◽  
Author(s):  
Jac A Nickoloff ◽  
Douglas B Sweetser ◽  
Jennifer A Clikeman ◽  
Guru Jot Khalsa ◽  
Sarah L Wheeler
Keyword(s):  
Gene Conversion ◽  
Mismatch Repair ◽  
Frameshift Mutation ◽  
Strand Break ◽  
Double Strand Break ◽  
Chromosome Loss ◽  
Allelic Gene ◽  
Break Induced Replication ◽  
Gene Conversion Tract ◽  
Conversion Tract

Abstract Spontaneous and double-strand break (DSB)-induced allelic recombination in yeast was investigated in crosses between ura3 heteroalleles inactivated by an HO site and a +1 frameshift mutation, with flanking markers defining a 3.4-kbp interval. In some crosses, nine additional phenotypically silent RFLP mutations were present at ∼100-bp intervals. Increasing heterology from 0.2 to 1% in this interval reduced spontaneous, but not DSB-induced, recombination. For DSB-induced events, 75% were continuous tract gene conversions without a crossover in this interval; discontinuous tracts and conversions associated with a crossover each comprised ∼7% of events, and 10% also converted markers in unbroken alleles. Loss of heterozygosity was seen for all markers centromere distal to the HO site in 50% of products; such loss could reflect gene conversion, break-induced replication, chromosome loss, or G2 crossovers. Using telomere-marked strains we determined that nearly all allelic DSB repair occurs by gene conversion. We further show that most allelic conversion results from mismatch repair of heteroduplex DNA. Interestingly, markers shared between the sparsely and densely marked interval converted at higher rates in the densely marked interval. Thus, the extra markers increased gene conversion tract lengths, which may reflect mismatch repair-induced recombination, or a shift from restoration- to conversion-type repair.

scholarly journals Evidence of extensive non-allelic gene conversion among LTR elements in the human genome

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Beniamino Trombetta ◽  
Gloria Fantini ◽  
Eugenia D’Atanasio ◽  
Daniele Sellitto ◽  
Fulvio Cruciani
Keyword(s):  
Human Genome ◽  
Gene Conversion ◽  
Allelic Gene

Effect of limited homology on gene conversion in a Saccharomyces cerevisiae plasmid recombination system

1988 ◽  
Vol 8 (6) ◽  
pp. 2442-2448 ◽  
Author(s):  
B Y Ahn ◽  
K J Dornfeld ◽  
T J Fagrelius ◽  
D M Livingston
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Conversion ◽  
Dna Sequences ◽  
Homologous Sequence ◽  
Insertion Mutation ◽  
Base Pairs ◽  
Recombination System ◽  
Plasmid Recombination ◽  
His3 Gene ◽  
Conversion Tract

Plasmids containing heteroallelic copies of the Saccharomyces cerevisiae HIS3 gene undergo intramolecular gene conversion in mitotically dividing S. cerevisiae cells. We have used this plasmid system to determine the minimum amount of homology required for gene conversion, to examine how conversion tract lengths are affected by limited homology, and to analyze the role of flanking DNA sequences on the pattern of exchange. Plasmids with homologous sequences greater than 2 kilobases have mitotic exchange rates as high as 2 x 10(-3) events per cell per generation. As the homology is reduced, the exchange rate decreases dramatically. A plasmid with 26 base pairs (bp) of homology undergoes gene conversion at a rate of approximately 1 x 10(-10) events per cell per generation. These studies have also shown that an 8-bp insertion mutation 13 bp from a border between homologous and nonhomologous sequences undergoes conversion, but that a similar 8-bp insertion 5 bp from a border does not. Examination of independent conversion events which occurred in plasmids with heteroallelic copies of the HIS3 gene shows that markers within 280 bp of a border between homologous and nonhomologous sequences undergo conversion less frequently than the same markers within a more extensive homologous sequence. Thus, proximity to a border between homologous and nonhomologous sequences shortens the conversion tract length.

scholarly journals Rates of gene conversions between Escherichia coli ribosomal operons

2020 ◽  
Author(s):  
Isaac Gifford ◽  
Aurko Dasgupta ◽  
Jeffrey E. Barrick
Keyword(s):  
Escherichia Coli ◽  
Gene Conversion ◽  
Accurate Estimate ◽  
Rrna Genes ◽  
Homologous Sequence ◽  
Rrna Gene ◽  
Potential Donor ◽  
Ribosomal Operons ◽  
High Sequence Conservation ◽  
Gene Conversions

ABSTRACTDue to their universal presence and high sequence conservation, rRNA sequences are used widely in phylogenetics for inferring evolutionary relationships between microbes and in metagenomics for analyzing the composition of microbial communities. Most microbial genomes encode multiple copies of ribosomal RNA (rRNA) genes to supply cells with sufficient capacity for protein synthesis. These copies typically undergo concerted evolution that keeps their sequences identical, or nearly so, due to gene conversion, a type of intragenomic recombination that changes one copy of a homologous sequence to exactly match another. Widely varying rates of rRNA gene conversion have previously been estimated by comparative genomics methods and using genetic reporter assays. To more directly measure rates of rRNA intragenomic recombination, we sequenced the seven Escherichia coli rRNA operons in 15 lineages of cells that were evolved for ~13,750 generations with frequent single-cell bottlenecks that reduce the effects of selection. We identified 34 gene conversion events and estimate an overall rate of intragenomic recombination events between rRNA copies of 3.2 × 10−4 per generation or 5.3 × 10−5 per potential donor sequence. This rate varied only slightly from random expectations between different portions of the rRNA genes and between rRNA operons located at different locations in the genome. This accurate estimate of the rate of rRNA gene conversions fills a gap in our quantitative understanding of how ribosomal sequences and other multicopy elements diversify and homogenize during microbial genome evolution.

scholarly journals Large X-linked palindromes undergo arm-to-arm gene conversion across Mus lineages

2019 ◽  
Author(s):  
Callie M. Swanepoel ◽  
Emma R. Gerlinger ◽  
Jacob L. Mueller
Keyword(s):  
Gene Conversion ◽  
Rapid Evolution ◽  
Genetic Evolution ◽  
Evolutionary Sequence ◽  
Mus Spretus ◽  
High Quality ◽  
Sequence Comparisons ◽  
Allelic Gene ◽  
High Quality Sequence ◽  
Palindromic Sequences

AbstractLarge (>10kb), nearly-identical (>99% nucleotide identity), palindromic sequences are enriched on mammalian sex chromosomes. Primate Y-palindromes undergo high rates of arm-to-arm gene conversion, a proposed mechanism for maintaining their sequence integrity in the absence of X-Y recombination. It is unclear whether X-palindromes, which can freely recombine in females, undergo arm-to-arm gene conversion and, if so, at what rate. We generated high-quality sequence assemblies of Mus molossinus and Mus spretus X-palindromic regions and compared them to orthologous Mus musculus X-palindromes. Our evolutionary sequence comparisons found evidence of X-palindrome arm-to-arm gene conversion at rates comparable to rates of autosomal allelic gene conversion in mice. Mus X-palindrome genes also exhibit higher than expected sequence diversification, indicating gene conversion may facilitate the rapid evolution of palindrome-associated genes. We conclude that in addition to maintaining genes’ sequence integrity via sequence homogenization, arm-to-arm gene conversion can also rapidly drive genetic evolution via sequence diversification.

scholarly journals Frequent non-allelic gene conversion on the human lineage and its effect on the divergence of gene duplicates

2017 ◽  
Author(s):  
Arbel Harpak ◽  
Xun Lan ◽  
Ziyue Gao ◽  
Jonathan K. Pritchard
Keyword(s):  
Gene Conversion ◽  
Genetic Diseases ◽  
Sequence Divergence ◽  
Duplicate Gene ◽  
Gene Families ◽  
Sequence Evolution ◽  
Donor Region ◽  
Allelic Gene ◽  
Order Of Magnitude ◽  
Gene Duplicates

AbstractGene conversion is the copying of genetic sequence from a “donor” region to an “acceptor”. In non-allelic gene conversion (NAGC), the donor and the acceptor are at distinct genetic loci. Despite the role NAGC plays in various genetic diseases and the concerted evolution of gene families, the parameters that govern NAGC are not well-characterized. Here, we survey duplicate gene families and identify converted tracts in 46% of them. These conversions reflect a large GC-bias of NAGC. We develop a sequence evolution model that leverages substantially more information in duplicate sequences than used by previous methods and use it to estimate the parameters that govern NAGC in humans: a mean converted tract length of 250bp and a probability of 2.5×10−7per generation for a nucleotide to be converted (an order of magnitude higher than the point mutation rate). Despite this high baseline rate, we show that NAGC slows down as duplicate sequences diverge—until an eventual “escape” of the sequences from its influence. As a result, NAGC has a small average effect on the sequence divergence of duplicates. This work improves our understanding of the NAGC mechanism and the role that it plays in the evolution of gene duplicates.

scholarly journals Effect of limited homology on gene conversion in a Saccharomyces cerevisiae plasmid recombination system.

1988 ◽  
Vol 8 (6) ◽  
pp. 2442-2448 ◽  
Author(s):  
B Y Ahn ◽  
K J Dornfeld ◽  
T J Fagrelius ◽  
D M Livingston
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Conversion ◽  
Dna Sequences ◽  
Homologous Sequence ◽  
Insertion Mutation ◽  
Base Pairs ◽  
Recombination System ◽  
Plasmid Recombination ◽  
His3 Gene ◽  
Conversion Tract

Plasmids containing heteroallelic copies of the Saccharomyces cerevisiae HIS3 gene undergo intramolecular gene conversion in mitotically dividing S. cerevisiae cells. We have used this plasmid system to determine the minimum amount of homology required for gene conversion, to examine how conversion tract lengths are affected by limited homology, and to analyze the role of flanking DNA sequences on the pattern of exchange. Plasmids with homologous sequences greater than 2 kilobases have mitotic exchange rates as high as 2 x 10(-3) events per cell per generation. As the homology is reduced, the exchange rate decreases dramatically. A plasmid with 26 base pairs (bp) of homology undergoes gene conversion at a rate of approximately 1 x 10(-10) events per cell per generation. These studies have also shown that an 8-bp insertion mutation 13 bp from a border between homologous and nonhomologous sequences undergoes conversion, but that a similar 8-bp insertion 5 bp from a border does not. Examination of independent conversion events which occurred in plasmids with heteroallelic copies of the HIS3 gene shows that markers within 280 bp of a border between homologous and nonhomologous sequences undergo conversion less frequently than the same markers within a more extensive homologous sequence. Thus, proximity to a border between homologous and nonhomologous sequences shortens the conversion tract length.

scholarly journals Homogenization of Tandemly Repeated Nucleotide Sequences by Distance-Dependent Nucleotide Sequence Conversion

Genetics ◽  
1987 ◽  
Vol 116 (3) ◽  
pp. 487-498
Author(s):  
J Dvořák ◽  
D Jue ◽  
M Lassner
Keyword(s):  
Nucleotide Sequence ◽  
Gene Conversion ◽  
Computer Simulations ◽  
Ribosomal Rna ◽  
Crossing Over ◽  
Rolling Circle Replication ◽  
Rolling Circle ◽  
Recurrent Mutations ◽  
Rna Genes ◽  
Heteroduplex Formation

ABSTRACT Previous work revealed that recurrent mutations (=mutation occurring more than once) in the tandemly repeated arrays present in nontranscribed spacers (NTS) of ribosomal RNA genes (rDNA) are clustered, i.e., they most frequently occur in repeats with adjacent or alternate distribution. A possible explanation is that the likelihood of heteroduplex formation, a prerequisite of gene conversion, decreases with the distance between repeats. To test this possibility, evolution of an array of 11 initially homogeneous repeats was computer simulated using three models, two assuming that the likelihood of heteroduplex formation decreases with increasing distance between the repeats and one assuming that it is constant. Patterns of mutations distribution obtained in computer simulations were compared with the distribution of mutations found in the repeated arrays in the NTS of seven rDNA clones. The patterns of mutations generated by the models assuming that the likelihood of heteroduplex formation decreases as distance between the repeats increases agreed with the patterns observed in rDNA; the patterns generated by the model assuming that the likelihood is independent of distance between repeats disagreed with the patterns observed in the rDNA clones. The topology of the heteroduplex formed between DNA in adjacent repeats predicts that the most frequently occurring conversions in the NTS repeated arrays will be shorter than the length of the repeat. The topology of the heteroduplex also predicts that if the heteroduplex leads to crossing over a circular repeat is excised. It is speculated that the circle can transpose or can be amplified via rolling circle replication and subsequently transpose. It is also shown that homogenization of the NTS repeated arrays proceeds at different rates in different species.

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