Author:
Concia Lorenzo,Veluchamy Alaguraj,Ramirez-Prado Juan S.,Martin-Ramirez Azahara,Huang Ying,Perez Magali,Domenichini Severine,Rodriguez Granados Natalia Y.,Kim Soonkap,Blein Thomas,Duncan Susan,Pichot Clement,Manza-Mianza Deborah,Juery Caroline,Paux Etienne,Moore Graham,Hirt Heribert,Bergounioux Catherine,Crespi Martin,Mahfouz Magdy M.,Bendahmane Abdelhafid,Liu Chang,Hall Anthony,Raynaud Cécile,Latrasse David,Benhamed Moussa
Abstract
Abstract
Background
Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in the nucleus to establish functional structures.
Results
We examine the hexaploid wheat nuclear architecture by integrating RNA-seq, ChIP-seq, ATAC-seq, Hi-C, and Hi-ChIP data. Our results highlight the presence of three levels of large-scale spatial organization: the arrangement into genome territories, the diametrical separation between facultative and constitutive heterochromatin, and the organization of RNA polymerase II around transcription factories. We demonstrate the micro-compartmentalization of transcriptionally active genes determined by physical interactions between genes with specific euchromatic histone modifications. Both intra- and interchromosomal RNA polymerase-associated contacts involve multiple genes displaying similar expression levels.
Conclusions
Our results provide new insights into the physical chromosome organization of a polyploid genome, as well as on the relationship between epigenetic marks and chromosome conformation to determine a 3D spatial organization of gene expression, a key factor governing gene transcription in polyploids.
Funder
Agence Nationale de la Recherche
Institut Universitaire de France
Publisher
Springer Science and Business Media LLC
Cited by
96 articles.
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