Publications

Relevant publications of the CIGR participants.

Dame Lab

Histones and histone variant families in prokaryotes. Schwab S, Hu Y, van Erp B, Cajili MKM, Hartmann MD, Hernandez Alvarez B, Alva V, Boyle AL, Dame RT. Nat Commun. 2024 Sep 11;15(1):7950. doi: 10.1038/s41467-024-52337-y.
Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. Hu Y, Schwab S, Deiss S, Escudeiro P, van Heesch T, Joiner JD, Vreede J, Hartmann MD, Lupas AN, Alvarez BH, Alva V, Dame RT. Nucleic Acids Res. 2024 Aug 12;52(14):8193-8204. doi: 10.1093/nar/gkae485.
The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli. Rashid FM, Crémazy FGE, Hofmann A, Forrest D, Grainger DC, Heermann DW, Dame RT. Nat Commun. 2023 Nov 17;14(1):7478. doi: 10.1038/s41467-023-43322-y.
Forrest D., Warman E.A., Erkelens A.M., Dame R.T., Grainger D.C. Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity. Nat Commun. 2022 Mar 3;13(1):1149. doi: 10.1038/s41467-022-28747-1.
Bdira F.B., Erkelens A.M., Qin L., Volkov A.N., Lippa A.M., Bowring N., Boyle A.L., Ubbink M., Dove S.L., Dame R.T. Novel anti-repression mechanism of H-NS proteins by a phage protein. Nucleic Acids Res. 2021 Oct 11;49(18):10770-10784. doi: 10.1093/nar/gkab793.
Henneman, B., Brouwer, T.B., Erkelens, A.M., Kuijntjes, G.J., van Emmerik, C., van der Valk, R.A., Timmer, M., Kirolos, N.C.S., van Ingen, H., van Noort, J. and Dame, R.T. Mechanical and structural properties of archaeal hypernucleosomes. Nucleic Acids Res. 2021 doi: 10.1093/nar/gkaa1196.
Qin, L., Bdira, F.B., Sterckx, Y.G.J., Volkov, A.N., Vreede, J., Giachin, G., van Schaik, P., Ubbink, M. and Dame, R.T. Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Res. 2020 48(4):2156-2172. doi: 10.1093/nar/gkz1226.
Henneman, B., van Emmerik, C.L., van Ingen, H. and Dame, R.T. Structure and function of archaeal histones. PLOS Gen. 2018 14(9):e1007582. doi: 10.1371/journal.pgen.1007582.
van der Valk, R.A, Vreede, J., Moolenaar, G.F., Hofmann, A., Goosen, N. and Dame, R.T. Environmentally driven conformational changes modulate the function of H-NS. eLife. 2017 6: 27369.

Mashaghi Lab

Barbara Scalvini and Alireza Mashaghi (2024)
Circuit Topology Analysis of Single-Cell HiC Data. In: Dame, R.T. (eds) Bacterial Chromatin. Methods in Molecular Biology, vol 2819. Humana, New York, NY. doi: 10.1007/978-1-0716-3930-6_2.
Barbara Scalvini, Helmut Schiessel, Anatoly Golovnev, Alireza Mashaghi, Circuit topology analysis of cellular genome reveals signature motifs, conformational heterogeneity and scaling. iScience 23(1), 103866 (2022). doi: 10.1016/j.isci.2022.103866.
Vahid Sheikhhassani, Barbara Scalvini, Julian Ng, Laurens W H J Heling, Yosri Ayache, Tom M J Evers, Eva Estébanez-Perpiñá, Iain J McEwan, Alireza Mashaghi, Topological dynamics of an intrinsically disordered N-terminal domain of the human androgen receptor. Protein Science 31(6):e4334 (2022). doi: 10.1002/pro.4334.
Maziar Heidari, Duane Moes, Otto Schullian, Barbara Scalvini, Alireza Mashaghi, A topology framework for macromolecular complexes and condensates. Nano Research 15, 9809–9817 (2022). doi: 10.1007/s12274-022-4355-x.
Heidari M., Schiessel H. and Mashaghi A. Circuit topology analysis of polymer folding reactions. ACS Central Science 2020, 2(7) P609-622. doi: 10.1021/acscentsci.0c00308.
Scalvini B, Sheikhhassani V., .Woodard J, Aupič J., Dame R.T., Jerala R. and Mashaghi A. Topology of folded molecular chains: from single biomolecules to engineered origami. Trends in Chemistry 2020, 2(7) P609-622. doi: 10.1016/j.trechm.2020.04.009.
Heidari M., Satarifard V. and Mashaghi A. Mapping a single-molecule folding process onto a topological space. Physical Chemistry Chemical Physics 2019, 21(36), 20338-20345. doi: 10.1039/C9CP03175H.
Satarifard V., Heidari M., Mashaghi S., Tans S.J., Ejtehadi M.R. and Mashaghi A. Topology of polymer chains under nanoscale confinement. Nanoscale 2017, 9, 12170 – 12177. doi: 10.1039/C7NR04220E.
Mashaghi A., Bezrukavnikov S., Minde D., Kityk R., Zachmann-Brand B., Mayer M., Kramer G., Bukau B. and Tans S.J. Functional plasticity in Hsp70 enabled by diverse modes of client binding. Nature 2016, 539(7629):448-451. doi: 10.1038/nature20137.

Van Noort Lab

Wong, Sook Yi and Soman, Aghil and Korolev, Nikolay and Surya, Wahyu and Chen, Qinming and Shum, Wayne and van Noort, John and Nordenskiold, Lars. The shelterin component TRF2 mediates columnar stacking of human telomeric chromatin. The EMBO journal 2024 43(1):87-111. doi: 10.1038/s44318-023-00002-3.
Severins, Ivo and Bastiaanssen, Carolien and Kim, Sung Hyun and Simons, Roy B and van Noort, John and Joo, Chirlmin. Single-molecule structural and kinetic studies across sequence space. Science 2024 385(6711):898-904. doi: 10.1126/science.adn5968.
Korolev N., Zinchenko A., Soman A., Chen Q., Wong S.Y., Berezhnoy N.V., Basak R., van der Maarel J.R.C., van Noort J., Nordenskiöld L. Reconstituted TAD-size chromatin fibers feature heterogeneous nucleosome clusters. Sci Rep. 2022 Sep 16;12(1):15558. doi: 10.1038/s41598-022-19471-3.
Soman A., Wong S.Y., Korolev N., Surya W., Lattmann S., Vogirala V.K., Chen Q., Berezhnoy N.V., van Noort J., Rhodes D., Nordenskiöld L. Columnar structure of human telomeric chromatin. Nature. 2022 Sep;609(7929):1048-1055. doi: 10.1038/s41586-022-05236-5. Epub 2022 Sep 14.
Severins I., Joo C., van Noort J. Exploring molecular biology in sequence space: The road to next-generation single-molecule biophysics Mol Cell. 2022 May 19;82(10):1788-1805. doi: 10.1016/j.molcel.2022.04.024. Epub 2022 May 12.
Kaczmarczyk, A., Allahverdi, A., Brouwer, T.B., Nordenskiöld, L., Dekker, N.H. and Van Noort, J. (2017). Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding. Journal of Biological Chemistry, 292(42), 17506–17513. doi: 10.1074/jbc.M117.791830.
Hermans, N., Huisman, J.J., Brouwer, T.B., Schächner, C., van Heusden, G.P.H., Griesenbeck, J. and van Noort, J. (2017). Toehold-enhanced LNA probes for selective pull down and single-molecule analysis of native chromatin. Scientific Reports, 7(1), 16721. doi: 10.1038/s41598-017-16864-7.