Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis

Abstract

The non-random three-dimensional organization of genomes is critical for many cellular processes. Recently, analyses of genome-wide chromatin packing in the model dicot plant Arabidopsis thaliana have been reported1,2,3,4. At a kilobase scale, the A. thaliana chromatin interaction network is highly correlated with a range of genomic and epigenomic features1,2,3,4. Surprisingly, topologically associated domains (TADs), which appear to be a prevalent structural feature of genome packing in many animal species, are not prominent in the A. thaliana genome1,2,4,5,6. Using a genome-wide chromatin conformation capture approach, Hi-C (ref. 7), we report high-resolution chromatin packing patterns of another model plant, rice. We unveil new structural features of chromatin organization at both chromosomal and local levels compared to A. thaliana, with thousands of distinct TADs that cover about a quarter of the rice genome. The rice TAD boundaries are associated with euchromatic epigenetic marks and active gene expression, and enriched with a sequence motif that can be recognized by plant-specific TCP proteins. In addition, we report chromosome decondensation in rice seedlings undergoing cold stress, despite local chromatin packing patterns remaining largely unchanged. The substantial variation found already in a comparison of two plant species suggests that chromatin organization in plants might be more diverse than in multicellular animals.

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Fig. 1: Chromosome packing in rice seedlings.
Fig. 2: Identification of rice TADs.
Fig. 3: Features at TAD boundaries.
Fig. 4: Chromatin packing patterns in cold-stressed plants.

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Acknowledgements

We thank C. Lanz and K. Fritschi for assistance with sequencing. We thank X. Gao and Y. He for their assistance in microscopy. We thank members of the Liu and Weigel laboratories for critical review and comments on the manuscript. This work was supported by Marie Curie Fellowship PIIF-GA-2012-327608 (C.L.), Deutsche Forschungsgemeinschaft LI 2862/1 (C.L.), a grant from the DFG Collaborative Research Center SFB1101 (D.W.) and the Max Planck Society (D.W.).

Author information

C.L. and D.W. conceived and designed the experiments. Y.C. and J.W. performed FISH experiments. CL performed the Hi-C and RNA-seq experiments. C.L. and D.W. analysed and interpreted the data and wrote the paper.

Correspondence to Chang Liu or Detlef Weigel.

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Supplementary Information

Supplementary Figures 1–11, Supplementary Tables 3 and 5, Supplementary References.

Supplementary Table 1

Statistics of Hi-C reads.

Supplementary Table 2

TADs identified in the rice genome.

Supplementary Table 4

RNA-seq analyses.

Supplementary Table 6

DI and HMM-state of rice chromatin.

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