Abstract
The centromere directs the segregation of chromosomes during mitosis and meiosis. It is a distinct genetic locus whose identity is established through epigenetic mechanisms that depend on the deposition of centromere-specific centromere protein A (CENP-A) nucleosomes. This important chromatin domain has so far escaped comprehensive molecular analysis due to its typical association with highly repetitive satellite DNA. In previous work, we discovered that the centromere of horse chromosome 11 is completely devoid of satellite DNA; this peculiar feature makes it a unique model to dissect the molecular architecture of mammalian centromeres. Here, we exploited this native satellite-free centromere to determine the precise localization of its functional domains in five individuals: We hybridized DNA purified from chromatin immunoprecipitated with an anti CENP-A antibody to a high resolution array (ChIP-on-chip) of the region containing the primary constriction of horse chromosome 11. Strikingly, each individual exhibited a different arrangement of CENP-A binding domains. We then analysed the organization of each domain using a single nucleotide polymorphism (SNP)-based approach and single molecule analysis on chromatin fibres. Examination of the ten instances of chromosome 11 in the five individuals revealed seven distinct ‘positional alleles’, each one extending for about 80–160 kb, were found across a region of about 500 kb. Our results demonstrate that CENP-A binding domains are autonomous relative to the underlying DNA sequence and are characterized by positional instability causing the sliding of centromere position. We propose that this dynamic behaviour may be common in mammalian centromeres and may determine the establishment of epigenetic alleles.Electronic supplementary materialThe online version of this article (doi:10.1007/s00412-014-0493-6) contains supplementary material, which is available to authorized users.
Highlights
Centromeres are genetic loci whose identity depends not on the sequence of DNA on which they are formed but on a specific nucleosome configuration containing the centromerespecific histone H3, centromere protein A (CENP-A) (Sullivan 2001; Black and Cleveland 2011)
The results presented here reveal a remarkable plasticity of the satellite-less centromere of horse chromosome 11
In this analysis of ten horse chromosomes 11, at least seven distinct CENP-A binding domains, each one extending for about 80– 160 kb, were found across a region of about 500 kb. These results demonstrate that, in a native mammalian centromere, the positioning of CENP-A binding domains is unrelated to the sequence of the DNA the centromere is associated with and that centromere position can be flexible across a relatively
Summary
Centromeres are genetic loci whose identity depends not on the sequence of DNA on which they are formed but on a specific nucleosome configuration containing the centromerespecific histone H3, centromere protein A (CENP-A) (Sullivan 2001; Black and Cleveland 2011). Centromere-associated DNA varies widely in different species and even within a karyotype, but the core protein composition, based on the presence of CENP-A nucleosomes, is a universal feature of eukaryotic chromosomes (Malik and Henikoff 2009). Both CENP-A and its deposition machinery, comprising a distinct pathway for chromatin assembly, are highly conserved during evolution (Maddox et al 2012; Kato et al 2013). How this chromatin architecture is related to its underlying DNA is still poorly understood. Taking advantage of the presence of two alpha satellite subfamilies at the centromere of human chromosome 17, Chromosoma (2015) 124:277–287
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