Genome‐wide Hi‐C analysis reveals extensive hierarchical chromatin interactions in rice

Abstract

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 TADs (Topologically Associated Domains) 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 IHIs/KEEs (Interactive Heterochromatic Islands or KNOT ENGAGED ELEMENTs) could trap transposable elements (TEs) via the enrichment of silencing epigenetic marks. In parallel, the near-diagonal FIREs (Frequently Interacting Regions) 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.

Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis

“…Briefly, the aerial parts of 10-day-old seedlings were collected, cut into pieces, and crosslinked in 2% formaldehyde solution for 15 min and then glycine was added to quench the cross-linking reaction. After the nuclei were isolated, the chromatin was digested 57 . To isolate the interacting chromatin fragments, the cross-linked DNA fragments were end-labeled with biotin-14-dCTP and end joined 58 .…”

Tissue‐specific Hi‐C analyses of rice, foxtail millet and maize suggest non‐canonical function of plant chromatin domains

“…TAD‐like domains have been reported in several plant species including cotton, maize, tomato, sorghum, foxtail millet and rice (Liu et al ; Wang et al ; Dong et al , ). Whether plant domains have the same biological function as their mammalian counterparts, however, remains largely unknown.…”

DNA replication and chromosome positioning throughout the interphase in three dimensional space of plant nuclei

“…So called Hi-C method (Lieberman-Aiden et al , 2009) analyses contacts between DNA loci across the whole genome. The contact maps thus obtained enable the analysis of chromosome contact patterns, genome packing and 3D chromatin architecture (Dong et al , 2018; Kempfer and Pombo, 2019). It should be noted, however, that Hi-C identifies genome loci that are associated in 3D space, but it does not provide the information on their physical position in the nuclei.…”