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Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

BACKGROUND: Folding and intermingling of chromosomes has the potential of bringing close to each other loci that are very distant genomically or even on different chromosomes. On the other hand, genomic rearrangements also play a major role in the reorganisation of loci proximities. Whether the same...

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Autores principales: Véron, Amélie S, Lemaitre, Claire, Gautier, Christian, Lacroix, Vincent, Sagot, Marie-France
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3132170/
https://www.ncbi.nlm.nih.gov/pubmed/21663614
http://dx.doi.org/10.1186/1471-2164-12-303
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author Véron, Amélie S
Lemaitre, Claire
Gautier, Christian
Lacroix, Vincent
Sagot, Marie-France
author_facet Véron, Amélie S
Lemaitre, Claire
Gautier, Christian
Lacroix, Vincent
Sagot, Marie-France
author_sort Véron, Amélie S
collection PubMed
description BACKGROUND: Folding and intermingling of chromosomes has the potential of bringing close to each other loci that are very distant genomically or even on different chromosomes. On the other hand, genomic rearrangements also play a major role in the reorganisation of loci proximities. Whether the same loci are involved in both mechanisms has been studied in the case of somatic rearrangements, but never from an evolutionary standpoint. RESULTS: In this paper, we analysed the correlation between two datasets: (i) whole-genome chromatin contact data obtained in human cells using the Hi-C protocol; and (ii) a set of breakpoint regions resulting from evolutionary rearrangements which occurred since the split of the human and mouse lineages. Surprisingly, we found that two loci distant in the human genome but adjacent in the mouse genome are significantly more often observed in close proximity in the human nucleus than expected. Importantly, we show that this result holds for loci located on the same chromosome regardless of the genomic distance separating them, and the signal is stronger in gene-rich and open-chromatin regions. CONCLUSIONS: These findings strongly suggest that part of the 3D organisation of chromosomes may be conserved across very large evolutionary distances. To characterise this phenomenon, we propose to use the notion of spatial synteny which generalises the notion of genomic synteny to the 3D case.
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spelling pubmed-31321702011-07-09 Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny Véron, Amélie S Lemaitre, Claire Gautier, Christian Lacroix, Vincent Sagot, Marie-France BMC Genomics Research Article BACKGROUND: Folding and intermingling of chromosomes has the potential of bringing close to each other loci that are very distant genomically or even on different chromosomes. On the other hand, genomic rearrangements also play a major role in the reorganisation of loci proximities. Whether the same loci are involved in both mechanisms has been studied in the case of somatic rearrangements, but never from an evolutionary standpoint. RESULTS: In this paper, we analysed the correlation between two datasets: (i) whole-genome chromatin contact data obtained in human cells using the Hi-C protocol; and (ii) a set of breakpoint regions resulting from evolutionary rearrangements which occurred since the split of the human and mouse lineages. Surprisingly, we found that two loci distant in the human genome but adjacent in the mouse genome are significantly more often observed in close proximity in the human nucleus than expected. Importantly, we show that this result holds for loci located on the same chromosome regardless of the genomic distance separating them, and the signal is stronger in gene-rich and open-chromatin regions. CONCLUSIONS: These findings strongly suggest that part of the 3D organisation of chromosomes may be conserved across very large evolutionary distances. To characterise this phenomenon, we propose to use the notion of spatial synteny which generalises the notion of genomic synteny to the 3D case. BioMed Central 2011-06-10 /pmc/articles/PMC3132170/ /pubmed/21663614 http://dx.doi.org/10.1186/1471-2164-12-303 Text en Copyright ©2011 Véron et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Véron, Amélie S
Lemaitre, Claire
Gautier, Christian
Lacroix, Vincent
Sagot, Marie-France
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny
title Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny
title_full Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny
title_fullStr Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny
title_full_unstemmed Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny
title_short Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny
title_sort close 3d proximity of evolutionary breakpoints argues for the notion of spatial synteny
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3132170/
https://www.ncbi.nlm.nih.gov/pubmed/21663614
http://dx.doi.org/10.1186/1471-2164-12-303
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