Genetic and physical analyses of the centromeric and pericentromeric regions of human chromosome 5: recombination across 5cen

Genomics. 1999 Mar 15;56(3):274-87. doi: 10.1006/geno.1999.5742.


Human centromeres are poorly understood at both the genetic and the physical level. In this paper, we have been able to distinguish the alphoid centromeric sequences of chromosome 5 from those of chromosome 19. This result was obtained by pulsed-field gel electrophoresis after cutting genomic DNA with restriction endonucleases NcoI (chromosome 5) and BamHI (chromosome 19). We could thus define a highly polymorphic marker, representing length variations of the D5Z1 domain located at the q arm boundary of the chromosome 5 centromere. The centromeric region of chromosome 5 was then analyzed in full detail. We established an approximately 4.6-Mb physical map of the whole region with five rare-cutting enzymes by using nonchimeric YACs, two of which were shown to contain the very ends of 5cen on both sides. The p-arm side of 5cen was shown to contain an alphoid subset (D5Z12) different from those described thus far. Two genes and several putative cDNAs could be precisely located close to the centromere. Several L1 elements were shown to be present within alpha satellites at the boundary between alphoid and nonalphoid sequences on both sides of 5cen. They were used to define STSs that could serve as physical anchor points at the junction of 5cen with the p and q arms. Some STSs were placed on a radiation hybrid map. One was polymorphic and could therefore be used as a second centromeric genetic marker at the p arm boundary of 5cen. We could thus estimate recombination rates within and around the centromeric region of chromosome 5. Recombination is highly reduced within 5cen, with zero recombinants in 58 meioses being detected between the two markers located at the two extremities of the centromere. In its immediate vicinity, 5cen indeed exerts a direct negative effect on meiotic recombination within the proximal chromosomal DNA. This effect is, however, less important than expected and is polarized, as different rates are observed on both arms if one compares the 0 cM/Mb of the p proximal first 5.5 Mb and the 0.64 cM/Mb of the q proximal first 5 Mb to the sex-average 1.02 cM/Mb found throughout the entire chromosome 5. Rates then become close to the average when one goes further within the arms. Finally, most recombinants (21/22), irrespective of the arm, are of female origin, thus showing that recombination around 5cen is essentially occurring in the female lineage.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blotting, Southern
  • Centromere / genetics*
  • Chromosomes, Artificial, Yeast
  • Chromosomes, Human, Pair 5 / genetics*
  • Contig Mapping
  • Electrophoresis, Gel, Pulsed-Field
  • Humans
  • Models, Genetic
  • Molecular Sequence Data
  • Nucleic Acid Hybridization
  • Oligonucleotide Probes
  • Pedigree
  • Physical Chromosome Mapping
  • Recombination, Genetic*
  • Restriction Mapping
  • Sequence Analysis, DNA
  • Sequence Tagged Sites
  • Temperature


  • Oligonucleotide Probes

Associated data

  • GENBANK/AF023528
  • GENBANK/AJ007751
  • GENBANK/AJ007752
  • GENBANK/AJ007753
  • GENBANK/AJ007754
  • GENBANK/AJ007755
  • GENBANK/AJ007756
  • GENBANK/AJ007757
  • GENBANK/AJ007758
  • GENBANK/AJ007759
  • GENBANK/AJ007760
  • GENBANK/AJ007761
  • GENBANK/AJ007762