Abstract
Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA exhibits complex DNA folds such as local hairpins. Upon binding to a specific sequence within centromeric regions, the DNA-binding protein CENP-B compacts centromeres by forming pronounced DNA loops between the repeats, which favor inter-chromosomal centromere compaction and clustering. This DNA-loop-mediated organization of centromeric chromatin participates in maintaining centromere position and integrity upon microtubule pulling during mitosis. Our findings emphasize the importance of DNA topology in centromeric regulation and stability.
| Original language | English |
|---|---|
| Article number | e8 |
| Pages (from-to) | 1751-1767 |
| Number of pages | 16 |
| Journal | Molecular cell |
| Volume | 82 |
| Issue number | 9 |
| Early online date | 22 Mar 2022 |
| DOIs | |
| Publication status | Published - 5 May 2022 |
Bibliographical note
Funding Information:The authors would like to thank Erwin J.G. Peterman and Andreas Biebricher (VU University, NL), L. Mirny (MIT, US), and from I. Curie: C. Bartocci, Aurelien Dauphin, R. Gamba, S. Hoffmann, A. Scelfo, S. Herve, and all other Fachinetti team members for helpful suggestions. We would also like to thank A. Straight (Stanford, US) for helpful suggestions, A. Houdusse (I. Curie, FR) for technical suggestions and the usage of biophysics equipment, R. Fujita and H. Kurumizaka (U. Tokyo), C. Francastel (Paris Diderot, FR), and H. Masumoto (Kazusa DNA Research Institut, Japan) for providing reagents, J. Cabanas-Danes, J. Boggers, A. Mukhortava, and all the Lumicks team for helpful suggestions, providing reagents and the hospitality. We also thank the flow cytometry platform, the cell and tissue imaging facility (PICT-IBiSA, member of the French National Research Infrastructure France-BioImaging ANR10-INBS-04), the antibody facility platform, and the sequencing platform at Institut Curie. D.F. receives salary support from the CNRS. D.F. has received support for this project by Labex « CellnScale», the Institut Curie, the ATIP-Avenir 2015 program, the program «Investissements d'Avenir» launched by the French Government and implemented by ANR with the references ANR-10-LABX-0038 and ANR-10-IDEX-0001-02 PSL, the Emergence grant 2018 from the city of Paris and Fondation ARC pour la Recherche sur Le Cancer PGA1 RF20190208583. C.C. is supported by the Institut Curie EuReCa PhD Programme, Marie Skłodowska-Curie Actions, 847718. C.D. acknowledges supported by the ERC Advanced Grant LoopingDNA (no. 883684) and the Netherlands Organization for Scientific Research (NWO/OCW), as part of the NanoFront and BaSyC programs. A.J. acknowledges support by the Swiss National Science Foundation (grant no. P300P2_177768). G.W. has received funding for this project from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. [883240]) and support by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the BaSyC program. H.W. would like to thank the Deutsche Forschungsgemeinschaft for financial support (WI 5434/1-1). A.-S.M. is part of the UMR 144-Cell and Tissue Imaging Facility (PICT-IBiSA). F.C. conceived and performed the in vitro protein purification, interaction assay, and the optical tweezers experiment; A.J. conceived, performed, and analyzed the AFM experiments, and A.J. and W.Y. performed the nanopore analysis, both under the supervision of C.D.; H.W. analyzed and performed some of the optical tweezers experiment under the supervision of G.W.; C.K. performed SEC-MALS experiment; S.G. performed EMSA assay and L.V. the MST and protein purification; T.W. M.D. and C.C. performed the experiment in cells; A.-S.M. designed macro for imaging analysis, and L.V. and F.C. analyzed data; D.F. directed the research and conceived the experimental design; D.F. C.D. and G.W. provide financial support. D.F. F.C. A.J. and H.W. made figures and wrote the manuscript. All authors contributed to manuscript editing. The authors declare no competing interests.
Funding Information:
D.F. receives salary support from the CNRS . D.F. has received support for this project by Labex « CellnScale» , the Institut Curie , the ATIP-Avenir 2015 program, the program «Investissements d’Avenir» launched by the French Government and implemented by ANR with the references ANR-10-LABX-0038 and ANR-10-IDEX-0001-02 PSL , the Emergence grant 2018 from the city of Paris and Fondation ARC pour la Recherche sur Le Cancer PGA1 RF20190208583 . C.C. is supported by the Institut Curie EuReCa PhD Programme, Marie Skłodowska-Curie Actions , 847718 . C.D. acknowledges supported by the ERC Advanced Grant LoopingDNA (no. 883684 ) and the Netherlands Organization for Scientific Research (NWO/OCW), as part of the NanoFront and BaSyC programs. A.J. acknowledges support by the Swiss National Science Foundation (grant no. P300P2_177768 ). G.W. has received funding for this project from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. [ 883240 ]) and support by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the BaSyC program. H.W. would like to thank the Deutsche Forschungsgemeinschaft for financial support ( WI 5434/1-1 ). A.-S.M. is part of the UMR 144-Cell and Tissue Imaging Facility (PICT-IBiSA).
Publisher Copyright:
© 2022 Elsevier Inc.
Keywords
- AFM microscopy
- CENP
- centromere
- chromosomes
- DNA breaks
- DNA compaction
- DNA topology
- genome stability
- optical tweezers
- secondary structures