Key research articles, reviews and books of the Chromatin group.

Bacteria

REVIEWS

P. Ge, F.-Z. M. Rashid & R.T. Dame
The role of nucleoid-associated proteins in mediating responses to environmental changes.
Curr Opin Microbiol. 87:102628, 2025.

S. Schwab & R.T. Dame
Identification, characterization and classification of prokaryotic nucleoid-associated proteins
Molecular Microbiology 123 (3):206-217, 2025.

R.T. Dame, F.Z. Rashid & D.C. Grainger
Chromosome organization in bacteria: mechanistic insights into genome structure and function.
Nature Reviews Genetics. 21(4):227-242, 2020.

RESEARCH

Y. Hu, S. Schwab, S. Deiss, P. Escudeiro, T. van Heesch, J.D. Joiner, J. Vreede, M.D. Hartmann, A.N. Lupas, B. Hernandez Alvarez, V. Alva & R.T. Dame
Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending.
Nucleic Acids Research. 52(14): 8193-8204, 2024

F-Z. M. Rashid, F.G.E. Crémazy, A. Hofmann, D.W. Heermann & R.T. Dame
The interplay between local three-dimensional chromatin organisation and transcription of proVWX in Escherichia coli.
Nature Communications. 14(1):7478, 2023.

A.M. Erkelens, L. Qin, B. van Erp, A. Miguel-Arribas, D. Abia, H. Keek, D. Markus, M.K. Cajili, S. Schwab, W.J.J. Meijer & R.T. Dame
The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues.
Nucleic Acids Research. 50(21):12166-12185, 2022.

D. Forrest, E.A. Warman, A.M. Erkelens, R.T. Dame & D.C Grainger
Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity.
Nature Communications. 13(1): 1149, 2022.

F. Ben Bdira, L. Qin, A. Volkov, A.M. Lippa, A.M. Erkelens, N. Bowring, M. Ubbink, S.L. Dove & R.T. Dame 
Novel antirepression mechanism of H-NS proteins by a phage protein.
Nucleic Acids Research. 49:18, 10770-10784, 2021.

L. Qin, F. Ben Bdira, Y. Sterckx, A. Volkov, J. Vreede, G. Giachin, P. van Schaik, M. Ubbink & R.T. Dame 
Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins.
Nucleic Acids Research. 48(4): 2156-2172, 2020.

B.A. Boudreau, D.R. Hron, L. Qin, R.A. van der Valk, M.V. Kotlajich, R.T. Dame & R. Landick
StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments.
Nucleic Acids Research.  46(11):5525-5546, 2018.

R.A. van der Valk, J. Vreede, G.F. Moolenaar, A. Hofmann, N. Goosen & R.T. Dame
Environmentally driven conformational changes modulate the function of H-NS.
eLife. 6:27369, 2017.

J. Vreede & R.T. Dame
Structure and dynamics of the H-NS dimerization domain.
Biophysical Journal. 103(1), 89-98, 2012.

pre 2010:

M.C. Noom, W.W. Navarre, T. Oshima, G.J.L. Wuite & R.T. Dame
H-NS promotes looped domain formation in the bacterial chromosome. 
Current Biology 17(21), R913-914, 2007.

R.T. Dame, M.C. Noom & G.J.L. Wuite
Bacterial chromatin organization by H-NS protein unraveled using dual DNA manipulation.
Nature 444, 387-390, 2006.

J. van Noort, S. Verbrugge, N. Goosen, C. Dekker & R.T. Dame
Dual architectural roles of HU: formation of flexible hinges and rigid filaments.
Proceedings of the National Academy of Sciences USA 101(18), 6969-74, 2004.

R.T. Dame, C. Wyman, R. Wurm, R. Wagner & N. Goosen
Structural basis for H-NS mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1.
Journal of Biological Chemistry 277(3), 2146-2150, 2002.

R.T. Dame, C. Wyman & N. Goosen
H-NS mediated compaction of DNA visualized by atomic force microscopy.
Nucleic Acids Research 28(18), 3504-10, 2000.

 

Archaea

REVIEWS

S. Schwab, Y. Hu, B. Hernandez Alvarez, V. Alva & R.T. Dame
Histone-mediated chromatin organization in prokaryotes.
Trends in Biochemical Sciences. S0968-0004(25)00133-1, 2025.

B. Henneman, C.L. van Emmerik, H. van Ingen & R.T. Dame
Structure and function of archaeal histones.
PLOS Genetics. 14(9):e1007582, 2018.

R.P.C. Driessen, E. Peeters, F. Werner & R.T. Dame
The interplay between nucleoid organization and transcription in archaeal genomes.
Nature Reviews Microbiology. 13(6), 333-341, 2015.

RESEARCH

S. Schwab, Y. Hu, B. van Erp, M.K.M. Cajili, M.D. Hartmann, B. Hernandez Alvarez, V. Alva, A.L. Boyle & R.T. Dame
Novel histones and histone variant families in prokaryotes.
Nature Communications. 15:7950, 2024.

S. Ofer, F. Blombach, A.M. Erkelens, D. Barker, Z. Soloviev, S. Schwab, K. Smollett, D. Matelska, T. Fouqueau, N. van der Vis, N.A. Kent, K. Thalassinos, R.T. Dame & F. Werner
DNA-bridging by an archaeal histone variant via a unique tetramerisation interface. 
Communications Biology. 6:698, 2023.

B. Henneman, T.B. Brouwer, A. M. Erkelens, G.-J. Kuijntjes, C. van Emmerik, R.A. van der Valk, M. Timmer, N.C.S. Kirolos, H. van Ingen, J. van Noort & R.T. Dame
Mechanical and structural properties of archaeal hypernucleosomes.
Nucleic Acids Research. 49(8): 4338-4349, 2021.

R.P.C. Driessen, S.N. Lin, W.J. Waterreus, A.L.H van der Meulen, R.A. van der Valk, G.F. Moolenaar, N. Laurens, G.J.L. Wuite, N.S. Pannu, N. Goosen & R.T. Dame
Sso10a: a new member of archaeal chromatin proteins that exhibits diverse architectural properties.
Scientific Reports. 6:29422, 2016.

R.P.C. Driessen, G. Sitters, N. Laurens, G.F. Moolenaar, G.J.L. Wuite, N. Goosen & R.T. Dame
Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins.
Biochemistry. 53(41), 6430-6438, 2014.

R.P.C. Driessen, H. Meng, G. Suresh, R. Shahapure, G. Lanzani, U.D. Priyakumar, M.F. White, H. Schiessel, J. van Noort & R.T. Dame
Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends 
Nucleic Acids Research. 41(1), 196-205, 2013.

N. Laurens, R.P.C. Driessen, I. Heller, D. Vorselen, M.C. Noom, F.J.H. Hol, M.F. White, R.T. Dame & G.J.L. Wuite
Alba shapes the archaeal genome using a delicate balance of bridging and stiffening the DNA
Nature Communications. 3 (1328), 2012.