Wheat chromatin architecture is organized in genome territories and transcription factories

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.

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.

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.

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  • Name: Concia, Lorenzo, Type: Corresponding Author,
  • Name: Veluchamy, Alaguraj, Type: Author,
  • Name: Ramirez-Prado, Juan S., Type: Author,
  • Name: Martin-Ramirez, Azahara, Type: Author,
  • Name: Huang, Ying, Type: Author,
  • Name: Perez, Magali, Type: Author,
  • Name: Domenichini, Severine, Type: Author,
  • Name: Rodriguez Granados, Natalia Y., Type: Author,
  • Name: Kim, Soonkap, Type: Author,
  • Name: Blein, Thomas, Type: Author,
  • Name: Duncan, Susan, Type: Author,
  • Name: Pichot, Clement, Type: Author,
  • Name: Manza-Mianza, Deborah, Type: Author,
  • Name: Juery, Caroline, Type: Author,
  • Name: Paux, Etienne, Type: Author,
  • Name: Moore, Graham, Type: Author,
  • Name: Hirt, Heribert, Type: Author,
  • Name: Bergounioux, Catherine, Type: Author,
  • Name: Crespi, Martin, Type: Author,
  • Name: Mahfouz, Magdy M., Type: Author,
  • Name: Bendahmane, Abdelhafid, Type: Author,
  • Name: Liu, Chang, Type: Author,
  • Name: Hall, Anthony, Type: Author,
  • Name: Raynaud, Cécile, Type: Author,
  • Name: Latrasse, David, Type: Author,
  • Name: Benhamed, Moussa, Type: Author,
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Article Host Type publisher
Article Is Open Access true
Article License Type cc-by
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1186/s13059-020-01998-1
DFW Organisation EI
DFW Work Package 4
DOI 10.1186/s13059-020-01998-1
Date Last Updated 2020-11-30T16:02:00.776851
Evidence oa journal (via doaj)
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Journal Is Open Access true
Open Access Status gold
PDF URL https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-020-01998-1.pdf
Publisher URL https://doi.org/10.1186/s13059-020-01998-1