Genome Biol. 2020 Apr 29. 21(1): 104
Lorenzo Concia,
Alaguraj Veluchamy,
Juan S Ramirez-Prado,
Azahara Martin-Ramirez,
Ying Huang,
Magali Perez,
Severine Domenichini,
Natalia Y Rodriguez Granados,
Soonkap Kim,
Thomas Blein,
Susan Duncan,
Clement Pichot,
Deborah Manza-Mianza,
Caroline Juery,
Etienne Paux,
Graham Moore,
Heribert Hirt,
Catherine Bergounioux,
Martin Crespi,
Magdy M Mahfouz,
Abdelhafid Bendahmane,
Chang Liu,
Anthony Hall,
Cécile Raynaud,
David Latrasse,
Moussa Benhamed.
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.
Keywords: DNA loops; Genome territories; Hi-C; Hi-ChIP; Transcription factories