PMID- 24454780
OWN - NLM
STAT- MEDLINE
DCOM- 20140918
LR  - 20240320
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 9
IP  - 1
DP  - 2014
TI  - Diversity of Prdm9 zinc finger array in wild mice unravels new facets of the 
      evolutionary turnover of this coding minisatellite.
PG  - e85021
LID - 10.1371/journal.pone.0085021 [doi]
LID - e85021
AB  - In humans and mice, meiotic recombination events cluster into narrow hotspots 
      whose genomic positions are defined by the PRDM9 protein via its DNA binding 
      domain constituted of an array of zinc fingers (ZnFs). High polymorphism and 
      rapid divergence of the Prdm9 gene ZnF domain appear to involve positive 
      selection at DNA-recognition amino-acid positions, but the nature of the 
      underlying evolutionary pressures remains a puzzle. Here we explore the 
      variability of the Prdm9 ZnF array in wild mice, and uncovered a high allelic 
      diversity of both ZnF copy number and identity with the caracterization of 113 
      alleles. We analyze features of the diversity of ZnF identity which is mostly due 
      to non-synonymous changes at codons -1, 3 and 6 of each ZnF, corresponding to 
      amino-acids involved in DNA binding. Using methods adapted to the minisatellite 
      structure of the ZnF array, we infer a phylogenetic tree of these alleles. We 
      find the sister species Mus spicilegus and M. macedonicus as well as the three 
      house mouse (Mus musculus) subspecies to be polyphyletic. However some 
      sublineages have expanded independently in Mus musculus musculus and M. m. 
      domesticus, the latter further showing phylogeographic substructure. Compared to 
      random genomic regions and non-coding minisatellites, none of these patterns 
      appears exceptional. In silico prediction of DNA binding sites for each allele, 
      overlap of their alignments to the genome and relative coverage of the different 
      families of interspersed repeated elements suggest a large diversity between 
      PRDM9 variants with a potential for highly divergent distributions of 
      recombination events in the genome with little correlation to evolutionary 
      distance. By compiling PRDM9 ZnF protein sequences in Primates, Muridae and 
      Equids, we find different diversity patterns among the three amino-acids most 
      critical for the DNA-recognition function, suggesting different diversification 
      timescales.
FAU - Buard, Jerome
AU  - Buard J
AD  - Institute of Human Genetics, UPR 1142, Centre National de la Recherche 
      Scientifique, Montpellier, France.
FAU - Rivals, Eric
AU  - Rivals E
AD  - Laboratoire d'Informatique, de Robotique et de Microelectronique de Montpellier, 
      UMR 5506, Universite Montpellier 2, Centre National de la Recherche Scientifique, 
      Montpellier, France ; Institut de Biologie Computationnelle, Montpellier, France.
FAU - Dunoyer de Segonzac, Denis
AU  - Dunoyer de Segonzac D
AD  - Institute of Human Genetics, UPR 1142, Centre National de la Recherche 
      Scientifique, Montpellier, France ; Institut des Sciences de l'Evolution 
      Montpellier, Universite Montpellier 2, Centre National de la Recherche 
      Scientifique, Institut de Recherche pour le Developpement, Montpellier, France.
FAU - Garres, Charlotte
AU  - Garres C
AD  - Institute of Human Genetics, UPR 1142, Centre National de la Recherche 
      Scientifique, Montpellier, France ; Institut des Sciences de l'Evolution 
      Montpellier, Universite Montpellier 2, Centre National de la Recherche 
      Scientifique, Institut de Recherche pour le Developpement, Montpellier, France.
FAU - Caminade, Pierre
AU  - Caminade P
AD  - Institut des Sciences de l'Evolution Montpellier, Universite Montpellier 2, 
      Centre National de la Recherche Scientifique, Institut de Recherche pour le 
      Developpement, Montpellier, France.
FAU - de Massy, Bernard
AU  - de Massy B
AD  - Institute of Human Genetics, UPR 1142, Centre National de la Recherche 
      Scientifique, Montpellier, France.
FAU - Boursot, Pierre
AU  - Boursot P
AD  - Institut des Sciences de l'Evolution Montpellier, Universite Montpellier 2, 
      Centre National de la Recherche Scientifique, Institut de Recherche pour le 
      Developpement, Montpellier, France.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140113
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Amino Acids)
RN  - EC 2.1.1.43 (Histone-Lysine N-Methyltransferase)
SB  - IM
MH  - Alleles
MH  - Amino Acids/genetics
MH  - Animals
MH  - Binding Sites
MH  - *Evolution, Molecular
MH  - Gene Dosage
MH  - *Genetic Variation
MH  - Genome/genetics
MH  - Geography
MH  - Heterozygote
MH  - Histone-Lysine N-Methyltransferase/chemistry/*genetics
MH  - Mice
MH  - Minisatellite Repeats/*genetics
MH  - Nucleotide Motifs/genetics
MH  - Open Reading Frames/*genetics
MH  - Phylogeny
MH  - Protein Structure, Tertiary
MH  - Sequence Analysis, DNA
MH  - Species Specificity
MH  - Zinc Fingers/*genetics
PMC - PMC3890296
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2014/01/24 06:00
MHDA- 2014/09/19 06:00
PMCR- 2014/01/13
CRDT- 2014/01/24 06:00
PHST- 2013/10/26 00:00 [received]
PHST- 2013/11/20 00:00 [accepted]
PHST- 2014/01/24 06:00 [entrez]
PHST- 2014/01/24 06:00 [pubmed]
PHST- 2014/09/19 06:00 [medline]
PHST- 2014/01/13 00:00 [pmc-release]
AID - PONE-D-13-43883 [pii]
AID - 10.1371/journal.pone.0085021 [doi]
PST - epublish
SO  - PLoS One. 2014 Jan 13;9(1):e85021. doi: 10.1371/journal.pone.0085021. eCollection 
      2014.