Ectopic recombination

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Ectopic recombination is an atypical form of recombination in which a crossing over takes place between two homologous DNA sequences located at non-allelic chromosomal positions. Such recombination often results in dramatic chromosomal rearrangement, which is generally harmful to the organism. [1] Some research, however, has suggested that ectopic recombination can result in mutated chromosomes that benefit the organism. [2] Ectopic recombination can occur during both meiosis and mitosis, although it is more likely occur during meiosis. [3] It occurs relatively frequently—in at least one yeast species (Saccharomyces cerevisiae) the frequency of ectopic recombination is roughly on par with that of allelic (or traditional) recombination. [4] If the alleles at two loci are heterozygous, then ectopic recombination is relatively likely to occur, whereas if the alleles are homozygous, they will almost certainly undergo allelic recombination. [4] Ectopic recombination does not require loci involved to be close to one another; it can occur between loci that are widely separated on a single chromosome, and has even been known to occur across chromosomes. [5] Neither does it require high levels of homology between sequences—the lower limit required for it to occur has been estimated at as low as 2.2 kb of homologous stretches of DNA nucleotides. [4]

In tobacco plant somatic cells, DNA double-strand break-induced recombination between ectopic homologous sequences appears to serve as a minor DNA repair pathway for double-strand breaks. [6]

The role of transposable elements in ectopic recombination is an area of active inquiry. Transposable elements—repetitious sequences of DNA that can insert themselves into any part of the genome—can encourage ectopic recombination at repeated homologous sequences of nucleotides. However, according to one proposed model, ectopic recombination might serve as an inhibitor of high transposable element copy numbers. [1] The frequency of ectopic recombination of transposable elements has been linked to both higher copy numbers of transposable elements and the longer lengths of those elements. [7] Since ectopic recombination is generally deleterious, anything that increases its odds of occurring is selected against, including the aforementioned higher copy numbers and longer lengths. This model, however, can only be applied to single families of transposable elements in the genome, as the probability of ectopic recombination occurring in one TE family is independent of it occurring in another. It follows that transposable elements that are shorter, transpose themselves less often, and have mutation rates high enough to disrupt the homology between transposable element sequences sufficiently to prevent ectopic recombination from occurring are selected for. [7]

Related Research Articles

<span class="mw-page-title-main">Transposable element</span> Semiparasitic DNA sequence

A transposable element is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition often results in duplication of the same genetic material. In the human genome, L1 and Alu elements are two examples. Barbara McClintock's discovery of them earned her a Nobel Prize in 1983. Its importance in personalized medicine is becoming increasingly relevant, as well as gaining more attention in data analytics given the difficulty of analysis in very high dimensional spaces.

Selfish genetic elements are genetic segments that can enhance their own transmission at the expense of other genes in the genome, even if this has no positive or a net negative effect on organismal fitness. Genomes have traditionally been viewed as cohesive units, with genes acting together to improve the fitness of the organism. However, when genes have some control over their own transmission, the rules can change, and so just like all social groups, genomes are vulnerable to selfish behaviour by their parts.

<span class="mw-page-title-main">Chromosomal crossover</span> Cellular process

Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs in the pachytene stage of prophase I of meiosis during a process called synapsis. Synapsis begins before the synaptonemal complex develops and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

<span class="mw-page-title-main">Genetic recombination</span> Production of offspring with combinations of traits that differ from those found in either parent

Genetic recombination is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) interchromosomal recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes ; & (2) intrachromosomal recombination, occurring through crossing over.

<span class="mw-page-title-main">Homologous chromosome</span> Chromosomes that pair in fertilization

A pair of homologous chromosomes, or homologs, are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during fertilization. Homologs have the same genes in the same loci, where they provide points along each chromosome that enable a pair of chromosomes to align correctly with each other before separating during meiosis. This is the basis for Mendelian inheritance, which characterizes inheritance patterns of genetic material from an organism to its offspring parent developmental cell at the given time and area.

Gene duplication is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.

<span class="mw-page-title-main">Mosaic (genetics)</span> Condition in multi-cellular organisms

Mosaicism or genetic mosaicism is a condition in which a multicellular organism possesses more than one genetic line as the result of genetic mutation. This means that various genetic lines resulted from a single fertilized egg. Mosaicism is one of several possible causes of chimerism, wherein a single organism is composed of cells with more than one distinct genotype.

Gene conversion is the process by which one DNA sequence replaces a homologous sequence such that the sequences become identical after the conversion event. Gene conversion can be either allelic, meaning that one allele of the same gene replaces another allele, or ectopic, meaning that one paralogous DNA sequence converts another.

Intragenomic conflict refers to the evolutionary phenomenon where genes have phenotypic effects that promote their own transmission in detriment of the transmission of other genes that reside in the same genome. The selfish gene theory postulates that natural selection will increase the frequency of those genes whose phenotypic effects cause their transmission to new organisms, and most genes achieve this by cooperating with other genes in the same genome to build an organism capable of reproducing and/or helping kin to reproduce. The assumption of the prevalence of intragenomic cooperation underlies the organism-centered concept of inclusive fitness. However, conflict among genes in the same genome may arise both in events related to reproduction and altruism.

Transvection is an epigenetic phenomenon that results from an interaction between an allele on one chromosome and the corresponding allele on the homologous chromosome. Transvection can lead to either gene activation or repression. It can also occur between nonallelic regions of the genome as well as regions of the genome that are not transcribed.

Subtelomeres are segments of DNA between telomeric caps and chromatin.

<span class="mw-page-title-main">Mating of yeast</span> Biological process

The yeast Saccharomyces cerevisiae is a simple single-celled eukaryote with both a diploid and haploid mode of existence. The mating of yeast only occurs between haploids, which can be either the a or α (alpha) mating type and thus display simple sexual differentiation. Mating type is determined by a single locus, MAT, which in turn governs the sexual behaviour of both haploid and diploid cells. Through a form of genetic recombination, haploid yeast can switch mating type as often as every cell cycle.

<span class="mw-page-title-main">Sister chromatids</span> Two identical copies of a chromosome joined at the centromere

A sister chromatid refers to the identical copies (chromatids) formed by the DNA replication of a chromosome, with both copies joined together by a common centromere. In other words, a sister chromatid may also be said to be 'one-half' of the duplicated chromosome. A pair of sister chromatids is called a dyad. A full set of sister chromatids is created during the synthesis (S) phase of interphase, when all the chromosomes in a cell are replicated. The two sister chromatids are separated from each other into two different cells during mitosis or during the second division of meiosis.

<span class="mw-page-title-main">Holliday junction</span> Branched nucleic acid structure

A Holliday junction is a branched nucleic acid structure that contains four double-stranded arms joined. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the junction. The structure is named after Robin Holliday, the molecular biologist who proposed its existence in 1964.

Mitotic recombination is a type of genetic recombination that may occur in somatic cells during their preparation for mitosis in both sexual and asexual organisms. In asexual organisms, the study of mitotic recombination is one way to understand genetic linkage because it is the only source of recombination within an individual. Additionally, mitotic recombination can result in the expression of recessive alleles in an otherwise heterozygous individual. This expression has important implications for the study of tumorigenesis and lethal recessive alleles. Mitotic homologous recombination occurs mainly between sister chromatids subsequent to replication. Inter-sister homologous recombination is ordinarily genetically silent. During mitosis the incidence of recombination between non-sister homologous chromatids is only about 1% of that between sister chromatids.

<span class="mw-page-title-main">Sister chromatid exchange</span>

Sister chromatid exchange (SCE) is the exchange of genetic material between two identical sister chromatids.

The mating-type locus is a specialized region in the genomes of some yeast and other fungi, usually organized into heterochromatin and possessing unique histone methylation patterns. The genes in this region regulate the mating type of the organism and therefore determine key events in its life cycle, such as whether it will reproduce sexually or asexually. In fission yeast such as S. pombe, the formation and maintenance of the heterochromatin organization is regulated by RNA-induced transcriptional silencing, a form of RNA interference responsible for genomic maintenance in many organisms. Mating type regions have also been well studied in budding yeast S. cerevisiae and in the fungus Neurospora crassa.

Chromosome segregation is the process in eukaryotes by which two sister chromatids formed as a consequence of DNA replication, or paired homologous chromosomes, separate from each other and migrate to opposite poles of the nucleus. This segregation process occurs during both mitosis and meiosis. Chromosome segregation also occurs in prokaryotes. However, in contrast to eukaryotic chromosome segregation, replication and segregation are not temporally separated. Instead segregation occurs progressively following replication.

<span class="mw-page-title-main">Unequal crossing over</span> Chromosomal crossover resulting in gene duplication or deletion

Unequal crossing over is a type of gene duplication or deletion event that deletes a sequence in one strand and replaces it with a duplication from its sister chromatid in mitosis or from its homologous chromosome during meiosis. It is a type of chromosomal crossover between homologous sequences that are not paired precisely. Normally genes are responsible for occurrence of crossing over. It exchanges sequences of different links between chromosomes. Along with gene conversion, it is believed to be the main driver for the generation of gene duplications and is a source of mutation in the genome.

<span class="mw-page-title-main">Synthesis-dependent strand annealing</span>

Synthesis-dependent strand annealing (SDSA) is a major mechanism of homology-directed repair of DNA double-strand breaks (DSBs). Although many of the features of SDSA were first suggested in 1976, the double-Holliday junction model proposed in 1983 was favored by many researchers. In 1994, studies of double-strand gap repair in Drosophila were found to be incompatible with the double-Holliday junction model, leading researchers to propose a model they called synthesis-dependent strand annealing. Subsequent studies of meiotic recombination in S. cerevisiae found that non-crossover products appear earlier than double-Holliday junctions or crossover products, challenging the previous notion that both crossover and non-crossover products are produced by double-Holliday junctions and leading the authors to propose that non-crossover products are generated through SDSA.

References

  1. 1 2 Montgomery, E., B. Charlesworth, and C. H. Langley. 1987. A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila melanogaster. Genet. Res. 49:31–41
  2. ↑ Bush, G.L., S.M. Case, A.C. Wilson and J.L. Patton. 1977. Rapid speciation and chromosomal evolution in mammals. Proc. Natl. Acad. Sci. USA 74: 3942-3946
  3. ↑ Montgomery, E., S.M. Huang, C.H. Langley, and B.H. Judd. 1991. Chromosome rearrangement by ectopic recombination in drosophila melanogaster: genome structure and evolution. Genetics 129: 1085-1098
  4. 1 2 3 Licthen, M, R.H. Borts, and J.E. Haber. 1986. Meiotic gene conversion and crossing over between dispersed homologous sequences occurs frequently in saccharomyces cerevisiae. Genetics 115: 233-246
  5. ↑ Harris, S, K.S. Rudnicki, and J.E. Haber. 1993. Gene conversions and crossing over during homologous and homeologous ectopic recombination in saccharomyces cerevisiae. Genetics 135: 5-16
  6. ↑ Puchta H. Double-strand break-induced recombination between ectopic homologous sequences in somatic plant cells. Genetics. 1999 Jul;152(3):1173-81. doi: 10.1093/genetics/152.3.1173. PMID 10388832; PMCID: PMC1460648
  7. 1 2 Petrov, D.A, Y.T. Aminetzach, J.C. Davis, D. Bensasson, and A.E. Hirsh. 2003. Size matters: non-LTR retrotransposable elements and ectopic recombination in drosophila. Mol Bio Evol 20: 880-892
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