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Two-step regulation of centromere distribution by condensin II and the nuclear envelope proteins

Nature Plants volume 8, pages 940–953 (2022)Cite this article

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Abstract

The arrangement of centromeres within the nucleus differs among species and cell types. However, neither the mechanisms determining centromere distribution nor its biological significance are currently well understood. In this study, we demonstrate the importance of centromere distribution for the maintenance of genome integrity through the cytogenic and molecular analysis of mutants defective in centromere distribution. We propose a two-step regulatory mechanism that shapes the non-Rabl-like centromere distribution in Arabidopsis thaliana through condensin II and the linker of the nucleoskeleton and cytoskeleton (LINC) complex. Condensin II is enriched at centromeres and, in cooperation with the LINC complex, induces the scattering of centromeres around the nuclear periphery during late anaphase/telophase. After entering interphase, the positions of the scattered centromeres are then stabilized by nuclear lamina proteins of the CROWDED NUCLEI (CRWN) family. We also found that, despite their strong impact on centromere distribution, condensin II and CRWN proteins have little effect on chromatin organization involved in the control of gene expression, indicating a robustness of chromatin organization regardless of the type of centromere distribution.

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Fig. 1: Condensin II is enriched at centromeres from late G2 to early G1 phase.
Fig. 2: Condensin II is required to form the scattered distribution of centromeres.
Fig. 3: LINC complexes are involved in the formation of scattered centromere distribution in cooperation with condensin II.
Fig. 4: CRWNs stabilize centromere position during interphase.
Fig. 5: CII–LINC and CRWNs contribute independently to the regulation of centromere distribution.
Fig. 6: Comparison of chromatin organization between the wild type and mutants affecting condensin II and CRWNs.
Fig. 7: Mutants showing abnormal centromere distribution show perturbation in genome stability.

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Data availability

The microarray data (GEO ID: GSE179466) are available on the GEO website (https://www.ncbi.nlm.nih.gov/geo/). The Hi-C (DRA013016), RNA-seq (DRA014243), BS-seq (DRA014250) data are available on the DDBJ website (https://www.ddbj.nig.ac.jp/index-e.html). We used a modified version of Araport11 downloaded from https://plants.ensembl.org for RNA-seq data analysis and a TAIR10 genome downloaded from https://www.arabidopsis.org/index.jsp for Hi-C and BS-seq data analysis. Source data are provided with this paper.

Code availability

R scripts for Hi-C, BS-seq analysis (https://doi.org/10.5281/zenodo.6631550) and RNA-seq analysis (https://doi.org/10.5281/zenodo.6637416) are available on Zenodo.

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Acknowledgements

We thank S. Mibu, Y. Asako (Tokyo University of Science, Japan) and Y. Inui (University of Tokyo, Japan) for substantial technical assistance. This research was supported by grants from Takeda Science Foundation and Tokyo University of Science Grant for International Joint Research to T. Sakamoto, grant from Chube Ito Foundation and MXT/JSPS KAKENHI (21K06247) to Y.S., grants from MXT/JSPS KAKENHI (26291067, 15H05955, 15H05962, 15K21750, 19H03259, 20H05911, 20H03297 and 22H00415) and JST CREST (grant number JPMJCR20S6) to S.M., as well as the University of Zurich and a grant from the European Research Council (ERC AdG number 243996) to U.G.

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Author notes

  1. Yuki Sakamoto

    Present address: Department of Biological Sciences, Osaka University, Toyonaka, Japan

  2. Nanami Ito

    Present address: Department of Integrated Biosciences, The University of Tokyo, Kashiwa, Japan

  3. Takumi Higaki

    Present address: International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, Japan

  4. Seiichiro Hasezawa

    Present address: Graduate School of Science and Engineering, Hosei University, Tokyo, Japan

  5. These authors contributed equally: Takuya Sakamoto, Yuki Sakamoto.

Authors and Affiliations

  1. Department of Applied Biological Science, Tokyo University of Science, Noda, Japan

    Takuya Sakamoto, Yuki Sakamoto, Tomoe Yamashita, Nanami Ito, Yuka Oko, Tomoya Sugiyama & Sachihiro Matsunaga

  2. Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland

    Stefan Grob & Ueli Grossniklaus

  3. Department of Integrated Biosciences, The University of Tokyo, Kashiwa, Japan

    Daniel Slane, Seiichiro Hasezawa & Sachihiro Matsunaga

  4. Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan

    Takumi Higaki

  5. Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan

    Maho Tanaka, Akihiro Matsui & Motoaki Seki

  6. College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan

    Takamasa Suzuki

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Contributions

T. Sakamoto, Y.S. and S.M. designed the experiments. T. Sakamoto, Y.S., S.G. and S.M. wrote the manuscript. T. Sakamoto, Y.S., T.Y., N.I., Y.O., T. Sugiyama and T.H. performed the experiments and analysed the data. T. Suzuki performed the sequencing. D.S. analysed the RNA-seq data. S.G. analysed the Hi-C and BS-seq data. M.T. performed the microarray experiments, and A.M. analysed the microarray data. S.H., M.S., U.G. and S.M. supervised the study. T. Sakamoto, U.G. and S.M. raised funding. All authors contributed through discussions and reviewed the manuscript.

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Correspondence to Takuya Sakamoto or Sachihiro Matsunaga.

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Supplementary Data 1

Microarray data for Col-0, cap-h2-2 and crwn1/4 grown under normal conditions.

Supplementary Data 2

RNA-seq data for Col-0, cap-h2-2, crwn1/4, and cap-h2-2 crwn1/4 treated with zeocin for 0, 3 and 48 h.

Supplementary Data 3

Enriched GO terms in the DEGs of cap-h2-2 crwn1/4 treated with zeocin.

Supplementary Data 4

Statistical source data for supplementary figures.

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Sakamoto, T., Sakamoto, Y., Grob, S. et al. Two-step regulation of centromere distribution by condensin II and the nuclear envelope proteins. Nat. Plants 8, 940–953 (2022). https://doi.org/10.1038/s41477-022-01200-3

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