Publications

Relevant publications of the CIGR participants.

Dame Lab

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, 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.

The Schaaf Lab

Keizer V.I.P., Coppola S., Houtsmuller A.B., Geverts B., van Royen M.E., Schmidt T. and Schaaf M.J.M. Repetitive switching between DNA-binding modes enables target finding by the glucocorticoid receptor. J Cell Sci. 2019 Feb 25;132(5):jcs217455. doi: 10.1242/jcs.217455.
Carattino A., Keizer V.I.P., Schaaf M.J.M. and Orrit M. Background Suppression in Imaging Gold Nanorods through Detection of Anti-Stokes Emission. Biophys J. 2016 Dec 6;111(11):2492-2499. doi: 10.1016/j.bpj.2016.10.035.
Harkes R., Keizer V.I., Schaaf M.J. and Schmidt T. Depth-of-Focus Correction in Single-Molecule Data Allows Analysis of 3D Diffusion of the Glucocorticoid Receptor in the Nucleus. PLoS One. 2015 Nov 10;10(11):e0141080. doi: 10.1371/journal.pone.0141080. eCollection 2015.
Groeneweg F.L., van Royen M.E., Fenz S., Keizer V.I., Geverts B., Prins J., de Kloet E.R., Houtsmuller A.B., Schmidt T.S. and Schaaf M.J. Quantitation of glucocorticoid receptor DNA-binding dynamics by single-molecule microscopy and FRAP. PLoS One. 2014 Mar 14;9(3):e90532. doi: 10.1371/journal.pone.0090532. eCollection 2014.
Van Royen M.E., van Cappellen W.A., Geverts B., Schmidt T., Houtsmuller A.B. and Schaaf M.J. Androgen receptor complexes probe DNA for recognition sequences by short random interactions. J Cell Sci. 2014 Apr 1;127(Pt 7):1406-16. doi: 10.1242/jcs.135228. Epub 2014 Jan 30.

Van Noort Lab

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.