Molecular Dynamics and Evolution of Centromeres in the Genus Equus

Abstract

The centromere is the chromosomal locus essential for proper chromosome segregation. While the centromeric function is well conserved and epigenetically specified, centromeric DNA sequences are typically composed of satellite DNA and represent the most rapidly evolving sequences in eukaryotic genomes. The presence of satellite sequences at centromeres hampered the comprehensive molecular analysis of these enigmatic loci. The discovery of functional centromeres completely devoid of satellite repetitions and fixed in some animal and plant species represented a turning point in centromere biology, definitively proving the epigenetic nature of the centromere. The first satellite-free centromere, fixed in a vertebrate species, was discovered in the horse. Later, an extraordinary number of satellite-free neocentromeres had been discovered in other species of the genus Equus, which remains the only mammalian genus with numerous satellite-free centromeres described thus far. These neocentromeres arose recently during evolution and are caught in a stage of incomplete maturation. Their presence made the equids a unique model for investigating, at molecular level, the minimal requirements for centromere seeding and evolution. This model system provided new insights on how centromeres are established and transmitted to the progeny and on the role of satellite DNA in different aspects of centromere biology.

Robertsonian Fusion and Centromere Repositioning Contributed to the Formation of Satellite-free Centromeres During the Evolution of Zebras

“…The first satellite-free centromere, fixed in a vertebrate species, was discovered by our group in one horse chromosome ( Wade et al 2009 ). Our discovery that equids are characterized by the existence of centromeres completely devoid of satellite DNA made these species an exceptional model system for dissecting the molecular architecture of mammalian centromeres as well as understanding the mechanisms driving centromere birth and maturation during evolution ( Wade et al 2009 ; Piras et al 2010 , 2022 ; Purgato et al 2015 ; Giulotto et al 2017 ; Nergadze et al 2018 ; Roberti et al 2019 ).…”

A Satellite-Free Centromere in Equus przewalskii Chromosome 10

“…These sequences represent the most rapidly evolving DNA sequences in eukaryotic genomes [ 6 ] and their presence has so far hampered comprehensive molecular analysis of these intriguing loci. In this context, our discovery that the species of the genus Equus are characterized by an extraordinarily high number of centromeres completely devoid of satellite DNA made these species a good model system for studying the epigenetic control and evolution of the centromere function [ 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ].…”

“…We then studied the chromosomal distribution of satellite sequences, namely 37cen and 2PI, in E. caballus (domestic horse), E. asinus (donkey), E. grevyi (Grevy’s zebra), and E. burchelli (Burchell’s zebra) which revealed a peculiar uncoupling between centromeric function and satellite repeats. In particular, several centromeres were found to be devoid of satellite DNA whereas blocks of satellite DNA were observed at some chromosomal termini, representing relics of ancestral inactivated centromeres [ 13 , 16 ].…”

“…Later on, using an anti-CENP-A antibody in ChIP experiments on chromatin extracted from primary fibroblast cell lines, we proved at the molecular level that several equid centromeres are completely devoid of satellite repeats [ 7 , 9 , 12 , 13 , 14 , 17 ]. While only one satellite-free centromere was found in the horse, on chromosome 11 (ECA11) [ 12 ], 16 were described in the donkey [ 7 ], 15 in the Burchell’s zebra, and 13 in the Grevy’s zebra [ 14 ].…”

“…Interestingly, it was observed that these CENP-A binding domains can slide within a genomic region of a few hundred kbs, probably limited by epigenetic boundaries. These domains were defined as epialleles and the phenomenon was called centromere sliding [ 7 , 9 , 13 , 14 ]. Studies on families composed of donkeys, horses, and their hybrid offspring (mule/hinny) revealed that the epialleles are inherited as Mendelian traits but their position can slide in one generation [ 7 ] while it is stable during propagation in cell culture, suggesting that the sliding can presumably take place during meiosis [ 7 ].…”