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

BMC Genomics

Research Article

Claire Lemaitre¹  Christian Gautier²  Vincent Lacroix²  Marie-France Sagot²  Amélie S Véron³ 

[1] Université de Bordeaux, Centre de Bioinformatique et Génomique Fonctionnelle Bordeaux, F-33000, Bordeaux, France;Equipe SYMBIOSE, INRIA Rennes Bretagne Atlantique, Campus de Beaulieu, F-35042, Rennes, France;Université de Lyon, F-69000, Lyon, France;Laboratoire Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, F-69100, Villeurbanne, France;Equipe BAMBOO, INRIA Grenoble Rhône-Alpes, 655 avenue de l'Europe, F-38330, Montbonnot Saint-Martin, France;Université de Lyon, F-69000, Lyon, France;Laboratoire Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, F-69100, Villeurbanne, France;Equipe BAMBOO, INRIA Grenoble Rhône-Alpes, 655 avenue de l'Europe, F-38330, Montbonnot Saint-Martin, France;INSERM U1052, Cancerology Research Center of Lyon, Centre Léon Bérard, Lyon, France;

关键词: Segmental Duplication;    Gene Density;    Spatial Proximity;    Locus Pair;    Chromosome Territory;   

DOI  :  10.1186/1471-2164-12-303

 received in 2011-01-04, accepted in 2011-06-10,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundFolding 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.ResultsIn 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.ConclusionsThese 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.

【 授权许可】

CC BY   
© Véron et al; licensee BioMed Central Ltd. 2011