ArticleBMC genomics2011
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 43 citations in OpenAlex.
- SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes.Bioinformatics (Oxford, England) · 2022Article
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- Large-scale mammalian genome rearrangements coincide with chromatin interactions.Bioinformatics (Oxford, England) · 2019Article
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- Patterns of microchromosome organization remain highly conserved throughout avian evolution.Chromosoma · 2019Article
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- A general framework for genome rearrangement with biological constraints.Algorithms for molecular biology : AMB · 2019Article
- Gene Repositioning Is Under Constraints After Evolutionary Conserved Gene Neighborhood Separate.Frontiers in genetics · 2019Article
- Finding local genome rearrangements.Algorithms for molecular biology : AMB · 2018Article
- Genome Architecture and Evolution of a Unichromosomal Asexual Nematode.Current biology : CB · 2017Article
- Organization and function of the 3D genome.Nature reviews. Genetics · 2016Review
- Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process.Biology · 2016Review
- Three Dimensional Organization of Genome Might Have Guided the Dynamics of Gene Order Evolution in Eukaryotes.Genome biology and evolution · 2016Article
- History of chromosome rearrangements reflects the spatial organization of yeast chromosomes.Journal of bioinformatics and computational biology · 2016Article
- Models and algorithms for genome rearrangement with positional constraints.Algorithms for molecular biology : AMB · 2016Article
- Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome.Nucleic acids research · 2014Article
- Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7.BMC genomics · 2014Article
- Genomic positions of co-expressed genes: echoes of chromosome organisation in gene expression data.BMC research notes · 2013Article
- The footprint of metabolism in the organization of mammalian genomes.BMC genomics · 2012Article
- EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.Evolutionary bioinformatics online · 2012Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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