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Nature May 2023Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data....
Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have 'relocated' on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences.
Topics: Humans; Gene Conversion; Genome, Human; Mutation; Segmental Duplications, Genomic; Polymorphism, Single Nucleotide; Haplotypes; Exons; Cytosine; Guanine; CpG Islands
PubMed: 37165237
DOI: 10.1038/s41586-023-05895-y -
Genes Jun 2021The 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...
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 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 insertions in various primates looking for potential events of TE gene conversion and discovered 98 clear cases of - gene conversion, including 64 cases for which the direction of conversion was identified (e.g., S conversion to Y). 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 s 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.
Topics: Alu Elements; Animals; Evolution, Molecular; Gene Conversion; Humans; Primates
PubMed: 34208107
DOI: 10.3390/genes12060905 -
Genetics Aug 2022Recombination can occur either as a result of crossover or gene conversion events. Population genetic methods for inferring the rate of recombination from patterns of...
Recombination can occur either as a result of crossover or gene conversion events. Population genetic methods for inferring the rate of recombination from patterns of linkage disequilibrium generally assume a simple model of recombination that only involves crossover events and ignore gene conversion. However, distinguishing the 2 processes is not only necessary for a complete description of recombination, but also essential for understanding the evolutionary consequences of inversions and other genomic partitions in which crossover (but not gene conversion) is reduced. We present heRho, a simple composite likelihood scheme for coestimating the rate of crossover and gene conversion from individual diploid genomes. The method is based on analytic results for the distance-dependent probability of heterozygous and homozygous states at 2 loci. We apply heRho to simulations and data from the house mouse Mus musculus castaneus, a well-studied model. Our analyses show (1) that the rates of crossover and gene conversion can be accurately coestimated at the level of individual chromosomes and (2) that previous estimates of the population scaled rate of recombination ρ=4Ner under a pure crossover model are likely biased.
Topics: Animals; Biological Evolution; Chromosomes; Gene Conversion; Genome; Linkage Disequilibrium; Mice
PubMed: 35771626
DOI: 10.1093/genetics/iyac100 -
Molecular Biology and Evolution Sep 2023Following a duplication, the resulting paralogs tend to diverge. While mutation and natural selection can accelerate this process, they can also slow it. Here, we...
Following a duplication, the resulting paralogs tend to diverge. While mutation and natural selection can accelerate this process, they can also slow it. Here, we quantify the paralog homogenization that is caused by point mutations and interlocus gene conversion (IGC). Among 164 duplicated teleost genes, the median percentage of postduplication codon substitutions that arise from IGC rather than point mutation is estimated to be between 7% and 8%. By differentiating between the nonsynonymous codon substitutions that homogenize the protein sequences of paralogs and the nonhomogenizing nonsynonymous substitutions, we estimate the homogenizing nonsynonymous rates to be higher for 163 of the 164 teleost data sets as well as for all 14 data sets of duplicated yeast ribosomal protein-coding genes that we consider. For all 14 yeast data sets, the estimated homogenizing nonsynonymous rates exceed the synonymous rates.
Topics: Gene Conversion; Saccharomyces cerevisiae; Amino Acid Sequence; Genes, Duplicate; Magnoliopsida; Selection, Genetic
PubMed: 37675606
DOI: 10.1093/molbev/msad198 -
PLoS Biology Dec 2021Highly efficient gene conversion systems have the potential to facilitate the study of complex genetic traits using laboratory mice and, if implemented as a "gene...
Highly efficient gene conversion systems have the potential to facilitate the study of complex genetic traits using laboratory mice and, if implemented as a "gene drive," to limit loss of biodiversity and disease transmission caused by wild rodent populations. We previously showed that such a system of gene conversion from heterozygous to homozygous after a sequence targeted CRISPR/Cas9 double-strand DNA break (DSB) is feasible in the female mouse germline. In the male germline, however, all DSBs were instead repaired by end joining (EJ) mechanisms to form an "insertion/deletion" (indel) mutation. These observations suggested that timing Cas9 expression to coincide with meiosis I is critical to favor conditions when homologous chromosomes are aligned and interchromosomal homology-directed repair (HDR) mechanisms predominate. Here, using a Cas9 knock-in allele at the Spo11 locus, we show that meiotic expression of Cas9 does indeed mediate gene conversion in the male as well as in the female germline. However, the low frequency of both HDR and indel mutation in both male and female germlines suggests that Cas9 may be expressed from the Spo11 locus at levels too low for efficient DSB formation. We suggest that more robust Cas9 expression initiated during early meiosis I may improve the efficiency of gene conversion and further increase the rate of "super-mendelian" inheritance from both male and female mice.
Topics: Animals; CRISPR-Associated Protein 9; CRISPR-Cas Systems; DNA Breaks, Double-Stranded; DNA Repair; Female; Gene Conversion; Gene Editing; Gene Expression; Gene Expression Regulation, Developmental; Genetic Engineering; Germ Cells; Male; Meiosis; Mice; RNA, Guide, CRISPR-Cas Systems; Recombinational DNA Repair
PubMed: 34941868
DOI: 10.1371/journal.pbio.3001478 -
BMC Biology Jan 2022The application of CRISPR/Cas9 technology in human induced pluripotent stem cells (hiPSC) holds tremendous potential for basic research and cell-based gene therapy....
CRISPR/Cas9-mediated gene knockout and interallelic gene conversion in human induced pluripotent stem cells using non-integrative bacteriophage-chimeric retrovirus-like particles.
BACKGROUND
The application of CRISPR/Cas9 technology in human induced pluripotent stem cells (hiPSC) holds tremendous potential for basic research and cell-based gene therapy. However, the fulfillment of these promises relies on the capacity to efficiently deliver exogenous nucleic acids and harness the repair mechanisms induced by the nuclease activity in order to knock-out or repair targeted genes. Moreover, transient delivery should be preferred to avoid persistent nuclease activity and to decrease the risk of off-target events. We recently developed bacteriophage-chimeric retrovirus-like particles that exploit the properties of bacteriophage coat proteins to package exogenous RNA, and the benefits of lentiviral transduction to achieve highly efficient, non-integrative RNA delivery in human cells. Here, we investigated the potential of bacteriophage-chimeric retrovirus-like particles for the non-integrative delivery of RNA molecules in hiPSC for CRISPR/Cas9 applications.
RESULTS
We found that these particles efficiently convey RNA molecules for transient expression in hiPSC, with minimal toxicity and without affecting the cell pluripotency and subsequent differentiation. We then used this system to transiently deliver in a single step the CRISPR-Cas9 components (Cas9 mRNA and sgRNA) to generate gene knockout with high indel rate (up to 85%) at multiple loci. Strikingly, when using an allele-specific sgRNA at a locus harboring compound heterozygous mutations, the targeted allele was not altered by NHEJ/MMEJ, but was repaired at high frequency using the homologous wild type allele, i.e., by interallelic gene conversion.
CONCLUSIONS
Our results highlight the potential of bacteriophage-chimeric retrovirus-like particles to efficiently and safely deliver RNA molecules in hiPSC, and describe for the first time genome engineering by gene conversion in hiPSC. Harnessing this DNA repair mechanism could facilitate the therapeutic correction of human genetic disorders in hiPSC.
Topics: Alleles; Bacteriophages; CRISPR-Cas Systems; Gene Conversion; Gene Editing; Gene Knockout Techniques; Humans; Induced Pluripotent Stem Cells; RNA; Retroviridae
PubMed: 34996449
DOI: 10.1186/s12915-021-01214-x -
Genome Biology and Evolution Jul 2019Nature has found many ways to utilize transposable elements (TEs) throughout evolution. Many molecular and cellular processes depend on DNA-binding proteins recognizing... (Review)
Review
Nature has found many ways to utilize transposable elements (TEs) throughout evolution. Many molecular and cellular processes depend on DNA-binding proteins recognizing hundreds or thousands of similar DNA motifs dispersed throughout the genome that are often provided by TEs. It has been suggested that TEs play an important role in the evolution of such systems, in particular, the rewiring of gene regulatory networks. One mechanism that can further enhance the rewiring of regulatory networks is nonallelic gene conversion between copies of TEs. Here, we will first review evidence for nonallelic gene conversion in TEs. Then, we will illustrate the benefits nonallelic gene conversion provides in rewiring regulatory networks. For instance, nonallelic gene conversion between TE copies offers an alternative mechanism to spread beneficial mutations that improve the network, it allows multiple mutations to be combined and transferred together, and it allows natural selection to work efficiently in spreading beneficial mutations and removing disadvantageous mutations. Future studies examining the role of nonallelic gene conversion in the evolution of TEs should help us to better understand how TEs have contributed to evolution.
Topics: DNA Transposable Elements; Gene Conversion; Gene Regulatory Networks; Humans; Mutation
PubMed: 31209488
DOI: 10.1093/gbe/evz124 -
Trends in Parasitology Nov 2016While some amoebae reproduce sexually, many amoebae (e.g., Acanthamoeba, Naegleria) reproduce asexually and therefore, according to popular doctrine, are likely to have... (Review)
Review
While some amoebae reproduce sexually, many amoebae (e.g., Acanthamoeba, Naegleria) reproduce asexually and therefore, according to popular doctrine, are likely to have been genetically disadvantaged as a consequence. In the absence of sex, mutations are proposed to accumulate by a mechanism known as Muller's ratchet. I hypothesise that amoebae can escape the ravages of accumulated mutation by virtue of their being polyploid. The polyploid state reduces spontaneous mutation accumulation by gene conversion, the freshly mutated copy being corrected by the presence of the many other wild-type copies. In this manner these amoebae reap the benefits of an asexual reproductive existence: principally, that it is rapid and convenient. Evidence for this mechanism comes from polyploid plants, bacteria, and archaea.
Topics: Amoeba; Gene Conversion; Mutation; Polyploidy; Reproduction, Asexual
PubMed: 27599632
DOI: 10.1016/j.pt.2016.08.006 -
Genome Biology and Evolution May 2021Recombination reshuffles the alleles of a population through crossover and gene conversion. These mechanisms have considerable consequences on the evolution and...
Recombination reshuffles the alleles of a population through crossover and gene conversion. These mechanisms have considerable consequences on the evolution and maintenance of genetic diversity. Crossover, for example, can increase genetic diversity by breaking the linkage between selected and nearby neutral variants. Bias in favor of G or C alleles during gene conversion may instead promote the fixation of one allele over the other, thus decreasing diversity. Mutation bias from G or C to A and T opposes GC-biased gene conversion (gBGC). Less recognized is that these two processes may-when balanced-promote genetic diversity. Here, we investigate how gBGC and mutation bias shape genetic diversity patterns in wood white butterflies (Leptidea sp.). This constitutes the first in-depth investigation of gBGC in butterflies. Using 60 resequenced genomes from six populations of three species, we find substantial variation in the strength of gBGC across lineages. When modeling the balance of gBGC and mutation bias and comparing analytical results with empirical data, we reject gBGC as the main determinant of genetic diversity in these butterfly species. As alternatives, we consider linked selection and GC content. We find evidence that high values of both reduce diversity. We also show that the joint effects of gBGC and mutation bias can give rise to a diversity pattern which resembles the signature of linked selection. Consequently, gBGC should be considered when interpreting the effects of linked selection on levels of genetic diversity.
Topics: Animals; Base Composition; Butterflies; Evolution, Molecular; Gene Conversion; Genetic Variation; Genome, Insect; Models, Genetic; Mutation; Selection, Genetic
PubMed: 33760095
DOI: 10.1093/gbe/evab064 -
Genetics Jul 2020Reduction of fitness due to deleterious mutations imposes a limit to adaptive evolution. By characterizing features that influence this genetic load we may better...
Reduction of fitness due to deleterious mutations imposes a limit to adaptive evolution. By characterizing features that influence this genetic load we may better understand constraints on responses to both natural and human-mediated selection. Here, using whole-genome, transcriptome, and methylome data from >600 individuals, we set out to identify important features influencing selective constraint. Our analyses reveal that multiple factors underlie the accumulation of maladaptive mutations, including gene expression level, gene network connectivity, and gene-body methylation. We then focus on a feature with major effect, nucleotide composition. The ancestral derived status of segregating alleles suggests that GC-biased gene conversion, a recombination-associated process that increases the frequency of G and C nucleotides regardless of their fitness effects, shapes sequence patterns in Through estimation of mutational effects, we present evidence that biased gene conversion hinders the purging of deleterious mutations and contributes to a genome-wide signal of decreased efficacy of selection. By comparing these results to two outcrossing relatives, and , we find that protein evolution in is as strongly affected by biased gene conversion as in the outcrossing species. Last, we perform simulations to show that natural levels of outcrossing in are sufficient to facilitate biased gene conversion despite increased homozygosity due to selfing. Together, our results show that even predominantly selfing taxa are susceptible to biased gene conversion, suggesting that it may constitute an important constraint to adaptation among plant species.
Topics: Adaptation, Physiological; Arabidopsis; Arabidopsis Proteins; Epigenome; Evolution, Molecular; Gene Conversion; Genetic Fitness; Genome, Plant; Mutation; Selection, Genetic; Transcriptome
PubMed: 32414868
DOI: 10.1534/genetics.120.303335