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

Human centromeres are poorly understood at both the genetic and the physica l level. In this paper, we have been able to distinguish the alphoid centro meric sequences of chromosome 5 from those of chromosome 19. This result wa s obtained by pulsed-field gel electrophoresis after cutting genomic DNA wi th restriction endonucleases NcoI (chromosome 5) and BamHI (chromosome 19). We could thus define a highly polymorphic marker, representing length vari ations 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 fu ll 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 wh ich were shown to contain the very ends of 5cen on both sides. The p-arm si de of 5cen was shown to contain an alphoid subset (D5Z12) different from th ose described thus far. Two genes and several putative cDNAs could be preci sely located close to the centromere. Several L1 elements were shown to be present within alpha satellites at the boundary between alphoid and nonalph oid sequences on both sides of 5cen, They were used to define STSs that cou ld serve as physical anchor points at the junction of Seen 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 Seen. We could thus estimate recombination rates within a nd around the centromeric region of chromosome 5. Recombination is highly r educed within Been, with zero recombinants in 58 meioses being detected bet ween the two markers located at the two extremities of the centromere. In i ts immediate vicinity, Been indeed exerts a direct negative effect on meiot ic recombination within the proximal chromosomal DNA. This effect is, howev er, less important than expected and is polarized, as different rates are o bserved 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 1.0 2 cM/Mb found throughout the entire chromosome 5. Rates then become close t o the average when one goes further within the arms, Finally, most recombin ants (21/22), irrespective of the arm, are of female origin, thus showing t hat recombination around Been is essentially occurring in the female lineag e, (C) 1999 Academic Press.