Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast

Nature Genetics volume 49, pages 1553–1557 (2017)Cite this article

Subjects

Abstract

The eukaryotic genome consists of DNA molecules far longer than the cells that contain them. They reach their greatest compaction during chromosome condensation in mitosis. This process is aided by condensin, a structural maintenance of chromosomes (SMC) family member1,2. The spatial organization of mitotic chromosomes and how condensin shapes chromatin architecture are not yet fully understood. Here we use chromosome conformation capture (Hi-C)3,4 to study mitotic chromosome condensation in the fission yeast Schizosaccharomyces pombe5,6,7. This showed that the interphase landscape characterized by small chromatin domains is replaced by fewer but larger domains in mitosis. Condensin achieves this by setting up longer-range, intrachromosomal DNA interactions, which compact and individualize chromosomes. At the same time, local chromatin contacts are constrained by condensin, with profound implications for local chromatin function during mitosis. Our results highlight condensin as a major determinant that changes the chromatin landscape as cells prepare their genomes for cell division.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Hi-C identifies genome-wide contact changes during chromosome condensation.
Figure 2: Mitotic conformational changes depend on the condensin complex.
Figure 3: Condensin replaces local contacts with longer-range interactions in mitosis.
Figure 4: Condensin-dependent chromatin domain expansion in mitosis.
Figure 5: Condensin confines local chromatin motility.

Accession codes

Primary accessions

Gene Expression Omnibus

References

  1. Hirano, T. Condensin-based chromosome organization from bacteria to vertebrates. Cell 164, 847–857 (2016).

    Article  CAS  Google Scholar 

  2. Uhlmann, F. SMC complexes: from DNA to chromosomes. Nat. Rev. Mol. Cell Biol. 17, 399–412 (2016).

    Article  CAS  Google Scholar 

  3. Belton, J.M. et al. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 58, 268–276 (2012).

    Article  CAS  Google Scholar 

  4. Dekker, J., Marti-Renom, M.A. & Mirny, L.A. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 14, 390–403 (2013).

    Article  CAS  Google Scholar 

  5. Saka, Y. et al. Fission yeast cut3 and cut14, members of a ubiquitous protein family, are required for chromosome condensation and segregation in mitosis. EMBO J. 13, 4938–4952 (1994).

    Article  CAS  Google Scholar 

  6. Sutani, T. et al. Fission yeast condensin complex: essential roles of non-SMC subunits for condensation and Cdc2 phosphorylation of Cut3/SMC4. Genes Dev. 13, 2271–2283 (1999).

    Article  CAS  Google Scholar 

  7. Hiraoka, Y., Toda, T. & Yanagida, M. The NDA3 gene of fission yeast encodes β-tubulin: a cold-sensitive nda3 mutation reversibly blocks spindle formation and chromosome movement in mitosis. Cell 39, 349–358 (1984).

    Article  CAS  Google Scholar 

  8. Flemming, W. Zellsubstanz, Kern und Zelltheilung (F.C.W. Vogel, 1882).

  9. Mizuguchi, T. et al. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature 516, 432–435 (2014).

    Article  CAS  Google Scholar 

  10. Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).

    Article  CAS  Google Scholar 

  11. Naumova, N. et al. Organization of the mitotic chromosome. Science 342, 948–953 (2013).

    Article  CAS  Google Scholar 

  12. Funabiki, H., Hagan, I., Uzawa, S. & Yanagida, M. Cell cycle–dependent specific positioning and clustering of centromeres and telomeres in fission yeast. J. Cell Biol. 121, 961–976 (1993).

    Article  CAS  Google Scholar 

  13. Petrova, B. et al. Quantitative analysis of chromosome condensation in fission yeast. Mol. Cell. Biol. 33, 984–998 (2013).

    Article  CAS  Google Scholar 

  14. Tanizawa, H. et al. Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res. 38, 8164–8177 (2010).

    Article  CAS  Google Scholar 

  15. Nagasaka, K., Hossain, M.J., Roberti, M.J., Ellenberg, J. & Hirota, T. Sister chromatid resolution is an intrinsic part of chromosome organization in prophase. Nat. Cell Biol. 18, 692–699 (2016).

    Article  CAS  Google Scholar 

  16. Kanke, M. et al. Auxin-inducible protein depletion system in fission yeast. BMC Cell Biol. 12, 8 (2011).

    Article  CAS  Google Scholar 

  17. Petersen, J. & Hagan, I.M.S. S. pombe aurora kinase/survivin is required for chromosome condensation and the spindle checkpoint attachment response. Curr. Biol. 13, 590–597 (2003).

    Article  CAS  Google Scholar 

  18. Hauf, S. et al. Aurora controls sister kinetochore mono-orientation and homolog bi-orientation in meiosis-I. EMBO J. 26, 4475–4486 (2007).

    Article  CAS  Google Scholar 

  19. Tada, K., Susumu, H., Sakuno, T. & Watanabe, Y. Condensin association with histone H2A shapes mitotic chromosomes. Nature 474, 477–483 (2011).

    Article  CAS  Google Scholar 

  20. Nakazawa, N., Mehrotra, R., Ebe, M. & Yanagida, M. Condensin phosphorylated by the Aurora-B-like kinase Ark1 is continuously required until telophase in a mode distinct from Top2. J. Cell Sci. 124, 1795–1807 (2011).

    Article  CAS  Google Scholar 

  21. Oliveira, R.A., Coelho, P.A. & Sunkel, C.E. The condensin I subunit Barren/CAP-H is essential for the structural integrity of centromeric heterochromatin during mitosis. Mol. Cell. Biol. 25, 8971–8984 (2005).

    Article  CAS  Google Scholar 

  22. Ribeiro, S.A. et al. Condensin regulates the stiffness of vertebrate centromeres. Mol. Biol. Cell 20, 2371–2380 (2009).

    Article  CAS  Google Scholar 

  23. Gerlich, D., Hirota, T., Koch, B., Peters, J.M. & Ellenberg, J. Condensin I stabilizes chromosomes mechanically through a dynamic interaction in live cells. Curr. Biol. 16, 333–344 (2006).

    Article  CAS  Google Scholar 

  24. Dixon, J.R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).

    Article  CAS  Google Scholar 

  25. Crane, E. et al. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature 523, 240–244 (2015).

    Article  CAS  Google Scholar 

  26. Sofueva, S. et al. Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J. 32, 3119–3129 (2013).

    Article  CAS  Google Scholar 

  27. Kim, K.-D., Tanizawa, H., Iwasaki, O. & Noma, K. Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast. Nat. Genet. 48, 1242–1252 (2016).

    Article  CAS  Google Scholar 

  28. Shin, H. et al. TopDom: an efficient and deterministic method for identifying topological domains in genomes. Nucleic Acids Res. 44, e70 (2016).

    Article  Google Scholar 

  29. Cheng, T.M. et al. A simple biophysical model emulates budding yeast chromosome condensation. eLife 4, e05565 (2015).

    Article  Google Scholar 

  30. Fudenberg, G. et al. Formation of chromosomal domains by loop extrusion. Cell Reports 15, 2038–2049 (2016).

    Article  CAS  Google Scholar 

  31. Ganier, O. et al. Synergic reprogramming of mammalian cells by combined exposure to mitotic Xenopus egg extracts and transcription factors. Proc. Natl. Acad. Sci. USA 108, 17331–17336 (2011).

    Article  CAS  Google Scholar 

  32. Li, Y.C., Cheng, T.H. & Gartenberg, M.R. Establishment of transcriptional silencing in the absence of DNA replication. Science 291, 650–653 (2001).

    Article  CAS  Google Scholar 

  33. Martins-Taylor, K., Dula, M.L. & Holmes, S.G. Heterochromatin spreading at yeast telomeres occurs in M phase. Genetics 168, 65–75 (2004).

    Article  CAS  Google Scholar 

  34. Shintomi, K., Takahashi, T.S. & Hirano, T. Reconstitution of mitotic chromatids with a minimum set of purified factors. Nat. Cell Biol. 17, 1014–1023 (2015).

    Article  CAS  Google Scholar 

  35. Bähler, J. et al. Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe. Yeast 14, 943–951 (1998).

    Article  Google Scholar 

  36. Moreno, S., Klar, A. & Nurse, P. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 194, 795–823 (1991).

    Article  CAS  Google Scholar 

  37. Nishimura, K., Fukagawa, T., Takisawa, H., Kakimoto, T. & Kanemaki, M. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat. Methods 6, 917–922 (2009).

    Article  CAS  Google Scholar 

  38. Basi, G., Schmid, E. & Maundrell, K. TATA box mutations in the Schizosaccharomyces pombe nmt1 promoter affect transcription efficiency but not the transcription start point or thiamine repressibility. Gene 123, 131–136 (1993).

    Article  CAS  Google Scholar 

  39. Kakui, Y. et al. Module-based construction of plasmids for chromosomal integration of the fission yeast Schizosaccharomyces pombe. Open Biol. 5, 150054 (2015).

    Article  Google Scholar 

  40. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article  CAS  Google Scholar 

  41. Abella, J.V. et al. Isoform diversity in the Arp2/3 complex determines actin filament dynamics. Nat. Cell Biol. 18, 76–86 (2016).

    Article  CAS  Google Scholar 

  42. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article  CAS  Google Scholar 

  43. Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999–1003 (2012).

    Article  CAS  Google Scholar 

  44. Hu, M. et al. HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics 28, 3131–3133 (2012).

    Article  CAS  Google Scholar 

  45. Zhu, L.J. et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP–seq and ChIP–chip data. BMC Bioinformatics 11, 237 (2010).

    Article  Google Scholar 

  46. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).

    Article  Google Scholar 

Download references

Acknowledgements

We would like to thank J. Abella and M. Way for their help with high-speed microscopy, A. Stewart for bioinformatic support, C. Haering (EMBL, Heidelberg) for Slp1 shutoff and chromosomal loci–tagged strains and H. Masukata (Osaka University) for the Skp1–Tir1 strain and AID plasmids, and P. Bates, E. Wershof, B. Khatri, Y. Murayama, T. Toda and our laboratory members for discussions and critical reading of the manuscript. This work was supported by the European Research Council and the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001198), the UK Medical Research Council (FC001198) and the Wellcome Trust (FC001198). Y.K. was supported by the Japanese Society for the Promotion of Science (JSPS Overseas Research Fellowships).

Author information

Authors and Affiliations

  1. Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK

    Yasutaka Kakui & Frank Uhlmann

  2. Bioinformatics Core, The Francis Crick Institute, London, UK

    Adam Rabinowitz

  3. Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK

    David J Barry

Authors
  1. Yasutaka Kakui
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Adam Rabinowitz
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. David J Barry
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Frank Uhlmann
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.K. and F.U. conceived the study, Y.K. performed the experiments, Y.K., A.R. and D.J.B. analyzed the data, and Y.K. and F.U. wrote the manuscript with input from A.R.

Corresponding author

Correspondence to Frank Uhlmann.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Confirmation of mitotic arrest and condensin depletion.

(a) Chromosome morphology in mitotically arrested wild-type cells (WT; left) and following condensin depletion (cut14SO; right). DNA was stained with DAPI and visualized together with microtubules (GFP-Atb2) to confirm mitotic arrest. Dotted squares indicate the areas of the magnified images on the right. Scale bar, 1 μm. (b) Depletion of the condensin subunits Cut14 or Cnd3 in the presence of thiamine to repress gene transcription and auxin (NAA) to promote protein degradation via an auxin-inducible degron (aid)16, was confirmed by western blotting. Tat1 (α-tubulin) served as a loading control. (c) Schematic of the positions on chromosome I, where LacO repeats (green) and TetO repeats (red) were inserted and visualized by LacI-GFP and TetR-tdTomato repressor fusion proteins, respectively13. (d) Examples of images to visualize LacO and TetO localization in mitotically arrested wild-type cells and following condensin depletion. Nuclear DNA was counterstained with DAPI. Dotted squares indicate areas corresponding to the individual color images on the right. Scale bar, 1 μm. (e) Box plots of the LacO–TetO distance distributions (n ≥ 155 cells for each condition). The box shows the 25th, 50th and 75th percentiles of distance between two dots. Whiskers indicate 1.58 times the interquantile distance divided by the square roots of total cell number. Distances more than 1.5 times the 75th percentile or less than 1.5 times the 25th percentile are shown as outliers. (f) Chromosome morphology in interphase, mitosis and mitosis following chemical inhibition of Ark1/Aurora B kinase (+1NM-PP1). A Cnd3-GFP fusion visualizes condensin, DNA was stained with DAPI. Magnified individual color images of the highlighted squares are shown at the bottom. Scale bar, 1 μm.

Supplementary Figure 2 Quality control of the Hi-C data sets.

(a) Distribution of read counts within each 2-kb bin. The blue dotted line demarcates bins containing less than 500 reads that were discounted from the analysis. The red dashed line indicates the median read count. Distributions of one replicate of wild-type cells in interphase (WT Interphase Replicate 1) and in mitosis (WT Mitosis Replicate 1) are shown. (b) log2 directionality plots, with the identified boundary positions indicated (red lines), along the chromosome I left arm of the same samples shown in a. (c) Clustering of Euclidean distances between the interaction directionality plots of all the samples included in this study. (d) Smoothed mean normalized log2 directionalities at the identified boundaries. Gray areas show the 95% confidential interval. (e) Average normalized log2 insulation scores around boundaries determined by log2 directionality are shown as a function of insulation distance in interphase (left) and mitosis (right).

Supplementary Figure 3 Schematic Hi-C map, illustrating chromosomal interactions.

(a) The different types of chromosomal interactions studied in our Hi-C analyses are illustrated. Interactions within a chromosome arm (Intra-arm) are shown in red; those between the two arms of one chromosome (Inter-arm) are shown in dark blue. Interactions between different chromosomes (Inter-chr) are represented in light blue. Inter-centromeric and inter-telomeric interactions (Inter-cen and Inter-tel) are highlighted in yellow and green, respectively. (b) Schematic Hi-C map, highlighting the areas corresponding to each of the interactions shown in a, identified by the use of the same color. Note that rDNA repeats are found at the ends of chromosome III. Because of their repetitive nature, we could not analyze chromosome interactions close to the ends of chromosome III.

Supplementary Figure 4 The effect of cnd3SO and mitotic Ark1 inhibition on contact probability changes between interphase and mitosis.

(a,b) Hi-C difference maps from experiments comparing interphase to mitosis following depletion of the condensin subunit Cnd3 (cnd3SO) or mitotic Ark1 inhibition (+1NM-PP1). (c) Distribution of normalized contact probabilities between chromosomes (Inter-chr), within chromosome arms (Intra-arm) or between the two arms of the same chromosome (Inter-arm). (d) Median contact probabilities in interphase and mitosis as a function of genomic distance along the chromosome II right arm are shown, corresponding to the above comparisons.

Supplementary Figure 5 Moving intra-arm median interacting distances along chromosome II.

As in Figure 3g, the moving intra-arm median interacting distances along chromosome II (solid lines) are shown together with shaded areas representing the 25th and 75th percentiles in each indicated condition. In contrast to the iteratively normalized matrices used in Figure 3g, interacting distances were calculated from HiCNorm-normalized matrices (a) or from raw count matrices (b).

Supplementary Figure 6 Chromatin domain boundaries following Cnd3 depletion or mitotic Ark1 inhibition.

(a,b) Hi-C contact probability maps along a section of chromosome I are shown under the indicated conditions. Domain boundaries are indicated (black triangles). (c) Effect of Cnd3 depletion or mitotic Ark1 inhibition on domain size distribution.

Supplementary Figure 7 Numbers and overlap of boundary positions in interphase and mitosis.

(a) Numbers and overlap of boundary positions in interphase and mitosis. Boundary positions were determined using either log2 directionality or the TopDom algorithm. (b) Correlation between boundaries determined by log2 directionality and by the TopDom algorithm in each of the indicated conditions.

Supplementary Figure 8 Boundaries overlap with condensin peaks.

(a–c) Correlation between condensin peaks in mitosis and boundary positions in mitosis (a), in interphase (b) and in mitosis following depletion of condensin (c).

Supplementary Figure 9 Chromatin motility in interphase and mitosis.

(a) Schematic of the locations where LacO (green) or TetO (red) repeats were inserted in chromosomes I and II, respectively. (b) A typical image of a cell harboring LacO and TetO repeats bound by LacI-GFP and TetR-tdTomato, respectively. (c) Mean square displacement (MSD) of the TetO locus in wild-type interphase and mitosis. Mean ± s.e.m. is shown (n = 22 interphase, n = 26 mitosis).

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–9 and Supplementary Tables 2 and 3. (PDF 1974 kb)

Life Sciences Reporting Summary (PDF 159 kb)

Supplementary Table 1

Condensin ChIP peaks along fission yeast chromosomes I–III. (XLSX 80 kb)

Supplementary Table 4

Hi-C library sequencing metrics. (XLSX 47 kb)

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kakui, Y., Rabinowitz, A., Barry, D. et al. Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast. Nat Genet 49, 1553–1557 (2017). https://doi.org/10.1038/ng.3938

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.3938

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research