Human centromeric alphoid domains are periodically homogenized so that they vary substantially between homologues. Mechanism and implications for centromere functioning

Sequence analysis of alphoid repeats from human chromosomes 17, 21 and 13 reveals recurrent diagnostic variant nucleotides. Their combinations define haplotypes, with higher order repeats (HORs) containing identical or closely-related haplotypes tandemly arranged into separate domains. The haplotypes found on homologues can be totally different, while HORs remain 99.8% homogeneous both intrachromosomally and between homologues. These results support the hypothesis, never before demonstrated, that unequal crossovers between sister chromatids accumulate to produce homogenization and amplification into tandem alphoid repeats. I propose that the molecular basis of this involves the diagnostic variant nucleotides, which enable pairing between HORs with identical or closely-related haplotypes. Domains are thus periodically renewed to maintain high intrachromosomal and interhomologue homogeneity. The capacity of a domain to form an active centromere is maintained as long as neither retrotransposons nor significant numbers of mutations affect it. In the presented model, a chromosome with an altered centromere can be transiently rescued by forming a neocentromere, until a restored, fully-competent domain is amplified de novo or rehomogenized through the accumulation of unequal crossovers

Molecular and evolutionary characteristics of the fraction of human alpha satellite DNA associated with CENP-A at the centromeres of chromosomes 1, 5, 19, and 21

<p>Abstract</p> <p>Background</p> <p>The mode of evolution of the highly homogeneous Higher-Order-Repeat-containing alpha satellite arrays is still subject to discussion. This is also true of the CENP-A associated repeats where the centromere is formed.</p> <p>Results</p> <p>In this paper, we show that the molecular mechanisms by which these arrays evolve are identical in multiple chromosomes: i) accumulation of crossovers that homogenise and expand the arrays into different domains and subdomains that are mostly unshared between homologues and ii) sporadic mutations and conversion events that simultaneously differentiate them from one another. Individual arrays are affected by these mechanisms to different extents that presumably increase with time. Repeats associated with CENP-A, where the centromere is formed, are subjected to the same evolutionary mechanisms, but constitute minor subsets that exhibit subtle sequence differences from those of the bulk repeats. While the DNA sequence <it>per se </it>is not essential for centromere localisation along an array, it appears that certain sequences can be selected against. On chromosomes 1 and 19, which are more affected by the above evolutionary mechanisms than are chromosomes 21 and 5, CENP-A associated repeats were also recovered from a second homogeneous array present on each chromosome. This could be a way for chromosomes to sustain mitosis and meiosis when the normal centromere locus is ineluctably undermined by the above mechanisms.</p> <p>Conclusion</p> <p>We discuss, in light of these observations, possible scenarios for the normal evolutionary fates of human centromeric regions.</p

Genomic structure of a copy of the human TPTE gene which encompasses 87kb on the short arm of chromosome 21

Abstract.: The testis-expressed human TPTE is a putative transmembrane tyrosine phosphatase, probably involved in signal transduction pathways of the endocrine and/or the spermatogenetic function of the testis. TPTE was mapped to the pericentromeric region of human chromosomes 21 and 13, and to chromosomes 15, 22, and Y. It is unknown which of the TPTE copies are transcribed, contain intronic sequences, and/or have open reading frames. Here, in silico analysis of the genomic sequence of human chromosome 21 allowed the determination of the genomic structure of a copy of the TPTE gene. This copy consists of 24 exons and spans approximately 87kb. The mapping position of this copy of TPTE on the short arm of chromosome 21 was confirmed by FISH using the BAC 15L0C0 clone as a probe that contains almost the entire TPTE gene. This is the first description of the genomic sequence of a non-RNR gene on the short arm of human acrocentric chromosome

A nuclease from Neurospora crassa specific for d(A-T) rich regions in double stranded DNA

A nuclease from N. crassa has been prepared to the hydroxylapatite stage of purification described by Rabin and Fraser (1). It degrades single stranded DNA in an essentially exonucleolytic process. It does not give any appreciable acid soluble material with double stranded DNA as substrate. This shows its high degree of specificity towards single stranded DNA. An extra activity which makes double strand breaks in the AT rich regions of DNA is described. A limited number of breaks are observed with calf or mouse DNAs, as judged by the decrease of sedimentation velocity in alkaline or neutral sucrose gradients. The number of breaks decreases with increasing the ionic strength. λ DNA is broken in half at the AT rich middle region of the molecule. The circular replicative form of fd DNA is converted to linear pieces of a rather homogeneous length. It is concluded from these results that it is an endonuclease activity specific for d(A-T) rich regions in double stranded DNA

Analysis of eucaryotic DNAs with a restriction endonuclease from H.influenzae: isolation of “hidden” satellite DNAs

The restriction enzymes from H. influenzae have been used to study various eucaryotic DNAs. Fractions resistant to the action of these enzymes have been isolated from rat, mouse and calf DNAs. The method revealed the existence in rat of several components having the properties of satellite DNAs. Mouse DNA was shown to contain a new satellite of buoyant density 1. 704. Therefore, this appears to be a powerfull method for the isolation of “hidden” satellite DNAs. Calf satellite DNAs ρ = 1.705 and ρ = 1.723 were those resistant to the action of the restriction enzymes whilst satellite DNAs ρ = 1.714 and ρ = 1.710 gave fragments of discrete lengths, suggesting internal repeat units of 1 500 and 5 000 base pairs respectively

Haplotypes obtained with 17-α1/17-α2 in the five DNA fragments (F1–F5) generated upon SacI digestion of GM10498 DNA prepared in agarose plugs

<p><b>Copyright information:</b></p><p>Taken from "Human centromeric alphoid domains are periodically homogenized so that they vary substantially between homologues. Mechanism and implications for centromere functioning"</p><p>Nucleic Acids Research 2006;34(6):1912-1924.</p><p>Published online 5 Apr 2006</p><p>PMCID:PMC1447651.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> Pulsed field gel electrophoresis (data not shown) allowed an estimation of the DNA fragment lengths as about 100, 200, 250, 450 kb, and more than 1 Mb, for F1 to F5, respectively

Unrelated sequences at the 5′ end of mouse LINE-1 repeated elements define two distinct sub-families

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