Wheat chromatin architecture is organized in genome territories and transcription factories

被引:103
作者
Concia, Lorenzo [1 ]
Veluchamy, Alaguraj [2 ]
Ramirez-Prado, Juan S. [1 ]
Martin-Ramirez, Azahara [3 ]
Huang, Ying [1 ]
Perez, Magali [1 ]
Domenichini, Severine [1 ]
Rodriguez Granados, Natalia Y. [1 ]
Kim, Soonkap [2 ]
Blein, Thomas [1 ]
Duncan, Susan [4 ]
Pichot, Clement [1 ]
Manza-Mianza, Deborah [1 ]
Juery, Caroline [5 ]
Paux, Etienne [5 ]
Moore, Graham [3 ]
Hirt, Heribert [1 ,2 ]
Bergounioux, Catherine [1 ]
Crespi, Martin [1 ]
Mahfouz, Magdy M. [2 ]
Bendahmane, Abdelhafid [1 ]
Liu, Chang [6 ]
Hall, Anthony [4 ]
Raynaud, Cecile [1 ]
Latrasse, David [1 ]
Benhamed, Moussa [1 ,7 ]
机构
[1] INRA, CNRS, IPS2, UMR 9213 UMR1403, Orsay, France
[2] King Abdullah Univ Sci & Technol, Div Biol & Environm Sci & Engn, Thuwal 239556900, Saudi Arabia
[3] John Innes Ctr, Norwich Res Pk, Norwich NR4 7UH, England
[4] Earlham Inst, Norwich Res Pk, Norwich NR4 7UG, England
[5] INRA, UMR1095 Genet Divers & Ecophysiol Cereals, 5 Chemin Beaulieu, F-63039 Clermont Ferrand, France
[6] Univ Tubingen, Ctr Plant Mol Biol ZMBP, ZMBP, Morgenstelle 32, D-72076 Tubingen, Germany
[7] IUF, Paris, France
基金
英国生物技术与生命科学研究理事会;
关键词
Hi-C; Hi-ChIP; DNA loops; Transcription factories; Genome territories; NONCODING TRANSCRIPTION; FUNCTIONAL-ORGANIZATION; GENE-EXPRESSION; POLYPLOID WHEAT; TRITICUM; SEQUENCE; DOMAINS; LOCUS; PRINCIPLES; DIVERSITY;
D O I
10.1186/s13059-020-01998-1
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
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.
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页数:20
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