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Related Concept Videos

Crossing Over01:30

Crossing Over

Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I, duplicated...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Viral Recombination00:57

Viral Recombination

Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.

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Related Experiment Video

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Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

Identifying the important HIV-1 recombination breakpoints.

John Archer1, John W Pinney, Jun Fan

  • 1Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

Plos Computational Biology
|September 13, 2008
PubMed
Summary
This summary is machine-generated.

Recombinant HIV-1 genomes drive pandemic diversity. A probabilistic model reveals natural selection influences recombination patterns, particularly around the env gene, suggesting only a minority of events significantly impact HIV-1 evolution.

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Area of Science:

  • Virology
  • Molecular Biology
  • Evolutionary Genetics

Background:

  • Recombinant Human Immunodeficiency Virus type 1 (HIV-1) genomes are key drivers of viral diversity and the ongoing HIV/AIDS pandemic.
  • Circulating Recombinant Forms (CRFs) are prevalent, suggesting some mosaic genomes possess advantageous properties.

Purpose of the Study:

  • To investigate whether recombination breakpoint distributions in the HIV-1 genome deviate from a probabilistic null model.
  • To identify genomic regions under natural selection influencing HIV-1 recombination patterns and viral evolution.

Main Methods:

  • Development of a probabilistic model for HIV-1 copy-choice recombination.
  • Comparison of predicted breakpoint distributions with empirical data from the HIV/AIDS pandemic.
  • Analysis of breakpoint frequencies across the HIV-1 genome, focusing on specific genes like env, gag, and pol.

Main Results:

  • A probabilistic model accurately predicted recombination breakpoint frequencies across large portions of the HIV-1 genome.
  • Significant deviations from the null model were observed in specific regions, notably an over-representation of breakpoints flanking the env gene and an under-representation within gag, pol, and most of env.
  • The env gene region showed a paucity of breakpoints, suggesting reduced success for recombinants generated there.

Conclusions:

  • Natural selection demonstrably influences HIV-1 recombination patterns, particularly in regions like the env gene.
  • The env gene and its flanking regions appear to be under selection, with recombination events in these areas potentially conferring a selective advantage.
  • Despite extensive viral diversity, only a subset of recombination events significantly contributes to the evolutionary trajectory of HIV-1.