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

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 The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

2011 ◽  
Vol 29 (3) ◽  
pp. 1047-1057 ◽  
Author(s):  
D. Kostka ◽  
M. J. Hubisz ◽  
A. Siepel ◽  
K. S. Pollard
Keyword(s):  
Human Genome ◽  
Gene Conversion ◽  
Biased Gene Conversion

DERIVING HAPLOTYPES THROUGH RECOMBINATION AND GENE CONVERSION PATHWAYS

2004 ◽  
Vol 02 (02) ◽  
pp. 241-256 ◽  
Author(s):  
NADIA EL-MABROUK
Keyword(s):  
Human Genome ◽  
Gene Conversion ◽  
Geographic Distribution ◽  
Polynomial Algorithm ◽  
Minimum Energy ◽  
Haplotype Diversity ◽  
Simple Pattern ◽  
Ancestral Haplotypes ◽  
Genetic Events ◽  
Gene Conversions

Retracing the trajectories of past genetic events is crucial to understand the structure of the genome, both in individuals and across populations. A haplotype describes a string of polymorphic sites along a DNA segment. Haplotype diversity is due to mutations creating new variants, and to recombinations and gene conversions that mix and redistribute these variants among individual chromosomes in populations. A number of studies have revealed a relatively simple pattern of haplotype diversity in the human genome, dominated by a few common haplotypes representing founder ancestral ones. New haplotypes are usually rare and have a limited geographic distribution. We propose a method to derive a new haplotype from a set of putative ancestral haplotypes, once mutations in place, through minimal recombination and gene conversion pathways. We describe classes of pathways that represent the whole set of minimal pathways leading to a new haplotype. We show that obtaining this set of pathways can be represented as a problem of finding "secondary structures" of minimum energy. We present a polynomial algorithm solving this folding problem.

scholarly journals Genomic Structure and Evolution of Multigene Families: “Flowers” on the Human Genome

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Hie Lim Kim ◽  
Mineyo Iwase ◽  
Takeshi Igawa ◽  
Tasuku Nishioka ◽  
Satoko Kaneko ◽  
...  
Keyword(s):  
Human Genome ◽  
Gene Conversion ◽  
Genomic Structure ◽  
Gene Families ◽  
Protein Coding ◽  
Average Gene Density ◽  
The Mean ◽  
Average Gene ◽  
Computer Simulation Studies

We report the results of an extensive investigation of genomic structures in the human genome, with a particular focus on relatively large repeats (>50 kb) in adjacent chromosomal regions. We named such structures “Flowers” because the pattern observed on dot plots resembles a flower. We detected a total of 291 Flowers in the human genome. They were predominantly located in euchromatic regions. Flowers are gene-rich compared to the average gene density of the genome. Genes involved in systems receiving environmental information, such as immunity and detoxification, were overrepresented in Flowers. Within a Flower, the mean number of duplication units was approximately four. The maximum and minimum identities between homologs in a Flower showed different distributions; the maximum identity was often concentrated to 100% identity, while the minimum identity was evenly distributed in the range of 78% to 100%. Using a gene conversion detection test, we found frequent and/or recent gene conversion events within the tested Flowers. Interestingly, many of those converted regions contained protein-coding genes. Computer simulation studies suggest that one role of such frequent gene conversions is the elongation of the life span of gene families in a Flower by the resurrection of pseudogenes.

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.

Sign in / Sign up

Export Citation Format

Share Document