Biased gene retention during diploidization in Brassica linked to three-dimensional genome organization

Nature Plants
Ting XieXiao-Ming Wu

Abstract

The non-random three-dimensional (3D) organization of the genome in the nucleus is critical to gene regulation and genome function. Using high-throughput chromatin conformation capture, we generated chromatin interaction maps for Brassica rapa and Brassica oleracea at a high resolution and characterized the conservation and divergence of chromatin organization in these two species. Large-scale chromatin structures, including A/B compartments and topologically associating domains, are notably conserved between B. rapa and B. oleracea, yet their KNOT structures are highly divergent. We found that genes retained in less fractionated subgenomes exhibited stronger interaction strengths, and diploidization-resistant duplicates retained in pairs or triplets are more likely to be colocalized in both B. rapa and B. oleracea. These observations suggest that spatial constraint in duplicated genes is correlated to their biased retention in the diploidization process. In addition, we found strong similarities in the epigenetic modification and Gene Ontology terms of colocalized paralogues, which were largely conserved across B. rapa and B. oleracea, indicating functional constraints on their 3D positioning in the nucleus. This study present...Continue Reading

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Citations

Jul 9, 2020·Journal of Experimental Botany·Ying HuangJuan Sebastian Ramirez-Prado
Oct 8, 2020·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Weizhi OuyangXingwang Li
Nov 19, 2020·Trends in Genetics : TIG·Ittai E Eres, Yoav Gilad
Feb 10, 2021·The New Phytologist·Liuling PeiMaojun Wang
Apr 7, 2021·Nature Plants·Péter SzövényiFay-Wei Li
Apr 1, 2021·The Plant Journal : for Cell and Molecular Biology·Marleny Garcia-LozanoUmesh K Reddy

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Methods Mentioned

BETA
Hi-C
PCA
ChIP
immunoprecipitation
pull down
PCR
DNA-Seq
ChIP-seq
BS-seq
RNA-seq

Software Mentioned

StringTie
HiTAD
browser
HiCExplorer
deepTools2
HISAT2
runHiC
Bowtie2
Bismark
Genome

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