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Crossing Over01:30

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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,...
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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.
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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...
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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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DNA Distortion and Damage
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Structural basis for human PRDM9 action at recombination hot spots.

Anamika Patel1, John R Horton1, Geoffrey G Wilson2

  • 1Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA;

Genes & Development
|February 3, 2016
PubMed
Summary

The PRDM9 protein binds DNA sequences to guide meiotic recombination hot spots. Structural and allele-specific binding studies reveal how PRDM9 adapts to sequence variations, influencing recombination patterns.

Keywords:
PRDM9crystallographyrecombination hot spotszinc finger arrays

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Area of Science:

  • Genetics and Epigenetics
  • Molecular Biology
  • Structural Biology

Background:

  • PRDM9 (PRD1-BF1-RIZ1 homologous domain-containing 9) is a key regulator of meiotic recombination hot spot localization.
  • It functions through sequence-specific DNA binding and histone modifications.
  • The common human PRDM9 allele A (hPRDM9A) recognizes a specific DNA consensus sequence.

Purpose of the Study:

  • To determine the crystal structure of the zinc finger (ZnF) 8-12 domains of hPRDM9A bound to a hot spot DNA sequence.
  • To investigate the binding affinities of different hPRDM9 alleles to various hot spot sequences.
  • To understand the structural basis for PRDM9's sequence specificity and adaptability in regulating meiotic recombination.

Main Methods:

  • Cocrystallization of hPRDM9A ZnF8-12 domains with a hot spot oligonucleotide.
  • X-ray crystallography to determine the protein-DNA complex structure.
  • In vitro binding assays to compare the affinities of different hPRDM9 alleles for various DNA sequences.

Main Results:

  • The crystal structure revealed that ZnF8-11 of hPRDM9A bind DNA via major groove interactions, with α helices forming hydrogen bonds with bases.
  • Specific residues in ZnF8, ZnF9, ZnF11, and ZnF10 mediate interactions with consensus and variable DNA bases, showing adaptability to sequence variations.
  • Different hPRDM9 alleles exhibit varying binding affinities and sequence preferences, with allele C showing higher affinity for C-specific sites than allele A for A-specific sites.

Conclusions:

  • The structural analysis elucidates the molecular mechanisms underlying PRDM9's sequence recognition and its adaptability to DNA variations.
  • Allelic differences in binding affinity and specificity contribute to the observed variations in meiotic recombination hot spot locations and activities.
  • These findings provide insights into the genetic control of meiosis and potential implications for human fertility and evolution.