bims-plasge Biomed News
on Plastid genes
Issue of 2020‒05‒03
one paper selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences


  1. Genome Biol. 2020 Apr 29. 21(1): 104
    Concia L, Veluchamy A, Ramirez-Prado JS, Martin-Ramirez A, Huang Y, Perez M, Domenichini S, Rodriguez Granados NY, Kim S, Blein T, Duncan S, Pichot C, Manza-Mianza D, Juery C, Paux E, Moore G, Hirt H, Bergounioux C, Crespi M, Mahfouz MM, Bendahmane A, Liu C, Hall A, Raynaud C, Latrasse D, Benhamed M.
      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
    DOI:  https://doi.org/10.1186/s13059-020-01998-1