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Genomic properties of chromosomal bands are linked to evolutionary rearrangements and new centromere formation in primates

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Abstract

Chromosomal rearrangements in humans are largely related to pathological conditions, and phenotypic effects are also linked to alterations in the expression profile following nuclear relocation of genes between functionally different compartments, generally occupying the periphery or the inner part of the cell nuclei. On the other hand, during evolution, chromosomal rearrangements may occur apparently without damaging phenotypic effects and are visible in currently phylogenetically related species. To increase our insight into chromosomal reorganisation in the cell nucleus, we analysed 18 chromosomal regions endowed with different genomic properties in cell lines derived from eight primate species covering the entire evolutionary tree. We show that homologous loci, in spite of their evolutionary relocation along the chromosomes, generally remain localised to the same functional compartment of the cell nuclei. We conclude that evolutionarily successful chromosomal rearrangements are those that leave the nuclear position of the regions involved unchanged. On the contrary, in pathological situations, the effect typically observed is on gene structure alteration or gene nuclear reposition. Moreover, our data indicate that new centromere formation could potentially occur everywhere in the chromosomes, but only those emerging in very GC-poor/gene-poor regions, generally located in the nuclear periphery, have a high probability of being retained through evolution. This suggests that, in the cell nucleus of related species, evolutionary chromosomal reshufflings or new centromere formation does not alter the functionality of the regions involved or the interactions between different loci, thus preserving the expression pattern of orthologous genes.

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Abbreviations

3C:

Chromosome conformation capture

4C:

Chromosome conformation capture-on-chip

5C:

Chromosome conformation capture carbon copy

AC:

Ancestral centromere

BAC:

Bacterial artificial chromosome

Cae :

Cercopithecus aethiops

Cja :

Callithrix jacchus

Cmo :

Callicebus moloch

DAPI:

4′,6-Diamidino-2-phenylindole

ENC:

Evolutionary new centromere

FISH:

Fluorescence in situ hybridisation

Ggo :

Gorilla gorilla

HCN:

Human constitutional new centromeres

Hi-C:

High-throughput chromosome capture

Hsa :

Homo sapiens

LAD:

Lamina associated domain

Lca :

Lemur catta

Mmu :

Macaca mulatta

PHA:

Phytohaemagglutinin

Ptr :

Pan troglodytes

RNL:

Radial nuclear location

SSC:

Saline sodium citrate buffer

TAD:

Topologically associated domain

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Acknowledgements

The authors wish to thank the anonymous reviewers for constructive comments. This work was supported by P.R.A. to SS and F.I.R. to VF from the University of Catania.

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Authors and Affiliations

  1. Department of Biological, Geological and Environmental Sciences, Section of Animal Biology “M. La Greca”, University of Catania, Via Androne, 81, 95124, Catania, Italy

    Concetta Federico, Anna Maria Pappalardo, Venera Ferrito & Salvatore Saccone

  2. Centre for Cell and Chromosome Biology, Division of Biosciences, Brunel University, Uxbridge, West London, UK

    Sabrina Tosi

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  1. Concetta Federico
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  2. Anna Maria Pappalardo
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  3. Venera Ferrito
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  4. Sabrina Tosi
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  5. Salvatore Saccone
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Correspondence to Concetta Federico.

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Responsible Editor: Rachel O’Neill

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Federico, C., Pappalardo, A.M., Ferrito, V. et al. Genomic properties of chromosomal bands are linked to evolutionary rearrangements and new centromere formation in primates. Chromosome Res 25, 261–276 (2017). https://doi.org/10.1007/s10577-017-9560-1

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  • DOI: https://doi.org/10.1007/s10577-017-9560-1

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