Molecular Mechanisms of Exon Shuffling: Illegitimate Recombination

  title={Molecular Mechanisms of Exon Shuffling: Illegitimate Recombination},
  author={Anke van Rijk and Hans Bloemendal},
Illegitimate recombination (IR) is a process that takes place far more often than homologous recombination and is characterized by the recombination between non-homologous or short homologous sequences. The consequences of IR frequently emerge after the introduction of DNA in cell lines because it more frequently integrates in non-homologous than in homologous regions of the host genome. As a result, unexpected truncated or elongated products may be found. By not discarding those products as… 
The role of DNA gyrase in illegitimate recombination
It is shown that DNA gyrase can undergo subunit exchange, and that this seems to occur within higherorder oligomers of the enzyme, which have not been investigated before.
Origination of an X-Linked Testes Chimeric Gene by Illegitimate Recombination in Drosophila
A case of a young chimeric gene that has originated by illegitimate recombination in Drosophila that has evolved lineage-specifically with evidence for positive selection acting along the D. simulans branch.
Repetitive Element-Mediated Recombination as a Mechanism for New Gene Origination in Drosophila
The dataset strongly suggests an important role for REs in the generation of chimeric genes within these species, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes.
The revolution of the biology of the genome
Sequence data of entire eukaryotic genomes and their detailed comparison have provided new evidence on genome evolution and mechanisms to decrease genome sizes and, in particular, to remove specific DNA sequences appear to involve the action of RNA interference (RNAi).
Origination of chimeric genes through DNA-level recombination.
A short review of the reported mechanisms that have been identified for chimeric gene formations, excluding retroposition-related cases, and several of the evolutionary analyses carried out on them are provided.
Exon-domain correlation and its corollaries
It is demonstrated that correlation between the borders of protein domains and their encoding exons is a genome-wide phenomenon in multiple eukaryotic organisms and probably contributed more to the expansion and diversification of proteomes than other domains as a result of duplications and exon shuffling.
Current topics in genome evolution: Molecular mechanisms of new gene formation
Recent genome-wide DNA and EST analyses are reviewed, and the three major molecular mechanisms of gene formation are discussed, including atypical spicing, both within and between genes, followed by adaptation, and retrotransposition events.
Alternative splicing and evolution: diversification, exon definition and function
The current knowledge of alternative splicing and evolution is summarized and insights into some of these unresolved questions are provided.
Quantifying the mechanisms of domain gain in animal proteins
The interplay of gene duplication and domain gain demonstrates an important mechanism for fast neofunctionalization of genes.


Illegitimate Recombination in Bacteria
The stimulation of transposon excision by rolling-circle replication adds to the long list of indirect evidence that supports the occurrence of the replication slippage events in vivo.
Processing of DNA prior to illegitimate recombination in mouse cells
It is concluded that DNA is frequently subjected to 5'-->3' exonuclease digestion prior to integration by illegitimate recombination and that the length of DNA removed by exonuclelease digestion can be extensive.
Palindrome resolution and recombination in the mammalian germ line.
It is proposed that the ability of mammalian cells to eliminate the perfect symmetry in a palindromic sequence may be an important DNA repair pathway, with implications regarding the metabolism of palindromaic repeats, the mutability of quasipalindromo triplet repeats, and the early steps in gene amplification events.
Role of DNA ligase in the illegitimate recombination that generates lambdabio-transducing phages in Escherichia coli.
The hypothesis that the illegitimate recombination that generates lambdabio-transducing phages is mediated by the DNA break-and-join mechanism is supported, at least after UV irradiation.
Molecular mechanisms of nucleic acid integration
  • J. Coffin
  • Biology
    Journal of medical virology
  • 1990
Only the first of the three mechanisms employed by retroviruses and related elements is at all relevant from a standpoint of vaccine safety, and it results in a predictable, stable association between virus and cell DNA with only minor sequence changes.
Topoisomerase I involvement in illegitimate recombination in Saccharomyces cerevisiae
In vivo evidence is provided that a general eukaryotic topoisomerase I enzyme nicks DNA and ligates nonhomologous ends, leading to illegitimate recombination.
A common sequence motif near nonhomologous recombination breakpoints involving Ig sequences.
Intriguingly, this tetranucleotide is also found to be associated with the breakpoints of VH gene replacement and isotype switching, suggesting that common pathways may be involved in all three B cell processes.
Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair
  • D. Leach
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 1994
Observations lead to the proposal that cells may have evolved a post‐replicative mechanism for the elimination and/or repair of large DNA secondary structures.
High-frequency illegitimate integration of transfected DNA at preintegrated target sites in a mammalian genome
A cell system that selects for integration events in defined genomic regions suggests that transfected DNA may preferentially integrate at unstable mammalian loci.
Chromosomal insertion of foreign DNA.
The main route and, in most species, the only reliable route to the generation of transgenic animals is by microinjecting DNA into an early embryo, generally one of the pronuclei of a newly