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Wheat chromatin architecture is organized in genome territories and transcription factories
Genome Biology ( IF 10.1 ) Pub Date : 2020-04-29 , DOI: 10.1186/s13059-020-01998-1 Lorenzo Concia 1 , Alaguraj Veluchamy 2 , Juan S Ramirez-Prado 1 , Azahara Martin-Ramirez 3 , Ying Huang 1 , Magali Perez 1 , Severine Domenichini 1 , Natalia Y Rodriguez Granados 1 , Soonkap Kim 2 , Thomas Blein 1 , Susan Duncan 4 , Clement Pichot 1 , Deborah Manza-Mianza 1 , Caroline Juery 5 , Etienne Paux 5 , Graham Moore 3 , Heribert Hirt 1, 2 , Catherine Bergounioux 1 , Martin Crespi 1 , Magdy M Mahfouz 2 , Abdelhafid Bendahmane 1 , Chang Liu 6 , Anthony Hall 4 , Cécile Raynaud 1 , David Latrasse 1 , Moussa Benhamed 1, 7
Genome Biology ( IF 10.1 ) Pub Date : 2020-04-29 , DOI: 10.1186/s13059-020-01998-1 Lorenzo Concia 1 , Alaguraj Veluchamy 2 , Juan S Ramirez-Prado 1 , Azahara Martin-Ramirez 3 , Ying Huang 1 , Magali Perez 1 , Severine Domenichini 1 , Natalia Y Rodriguez Granados 1 , Soonkap Kim 2 , Thomas Blein 1 , Susan Duncan 4 , Clement Pichot 1 , Deborah Manza-Mianza 1 , Caroline Juery 5 , Etienne Paux 5 , Graham Moore 3 , Heribert Hirt 1, 2 , Catherine Bergounioux 1 , Martin Crespi 1 , Magdy M Mahfouz 2 , Abdelhafid Bendahmane 1 , Chang Liu 6 , Anthony Hall 4 , Cécile Raynaud 1 , David Latrasse 1 , Moussa Benhamed 1, 7
Affiliation
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.
更新日期：2020-04-29
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