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Genome‐wide Hi‐C analysis reveals extensive hierarchical chromatin interactions in rice
Author(s) -
Dong Qianli,
Li Ning,
Li Xiaochong,
Yuan Zan,
Xie Dejian,
Wang Xiaofei,
Li Jianing,
Yu Yanan,
Wang Jinbin,
Ding Baoxu,
Zhang Zhibin,
Li Changping,
Bian Yao,
Zhang Ai,
Wu Ying,
Liu Bao,
Gong Lei
Publication year - 2018
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13925
Subject(s) - chromatin , biology , epigenetics , genetics , gene , genome , chromosome conformation capture , transposable element , gene expression , arabidopsis thaliana , oryza sativa , computational biology , mutant , enhancer
Summary The non‐random spatial packing of chromosomes in the nucleus plays a critical role in orchestrating gene expression and genome function. Here, we present a Hi‐C analysis of the chromatin interaction patterns in rice ( Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter‐chromosomal associations. Moderate compartment delimitation and extensive TAD s ( T opologically A ssociated D omain s ) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome. We found subtle features including chromatin loops, gene loops, and off‐/near‐diagonal intensive interaction regions. Gene chromatin loops associated with H3K27me3 could be positively involved in gene expression. In addition to insulated enhancing effects for neighbor gene expression, the identified rice gene loops could bi‐directionally (+/−) affect the expression of looped genes themselves. Finally, web‐interleaved off‐diagonal IHI s/ KEE s ( I nteractive H eterochromatic I sland s or K NOT E NGAGED E LEMENT s ) could trap transposable elements ( TE s) via the enrichment of silencing epigenetic marks. In parallel, the near‐diagonal FIRE s ( F requently I nteracting Re gion s ) could positively affect the expression of involved genes. Our results suggest that the chromatin packing pattern in rice is generally similar to that in Arabidopsis thaliana but with clear differences at specific structural levels. We conclude that genomic composition, epigenetic modification, and transcriptional activity could act in combination to shape global and local chromatin packing in rice. Our results confirm recent observations in rice and A . thaliana but also provide additional insights into the patterns and features of chromatin organization in higher plants.