Universiteit Leiden

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Chromatin organization & dynamics (Dr. Remus Dame)

Full list of publications

Full list of research articles and book chapters of the Chromatin group.

51) R.A. van der Valk, J. Vreede, G.F. Moolenaar, A. Hoffman, N. Goosen and R.T. Dame
Environmentally driven conformational changes modulate the function of H-NS.
Submitted.

50) T.P. Hoekstra, M. Depken, S.N. Lin, J. Cabanas-Danes, P. Gross, R.T. Dame, E.J.G. Peterman and G.J.L. Wuite
Stochastic switching between processive exonucleolysis and replication by T7 DNA polymerase ensures high fidelity.
Submitted.

49) R.A. van der Valk, N. Laurens and R.T. Dame
Tethered Particle Motion analysis of the DNA binding properties of architectural proteins.
Submitted.

48) D.J.W. Brocken, M. Tark-Dame and R.T. Dame
dCas9: a versatile tool for epigenome editing.
In press.

47) 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 and R.T. Dame
Sso10a: a new member of archaeal chromatin proteins that exhibits diverse architectural properties.
Scientific Reports. 6:29422, 2016.

46) R.T. Dame and M. Tark-Dame
Bacterial chromatin: converging views at different scales
Current Opinion in Cell Biology. 40, 60-65, 2016.

45) B. Henneman and R.T. Dame
Archaeal histones: dynamic and versatile genome architects.
AIMS Microbiology. 1(1), 72-81, 2015.

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

43) K. Chintakayala, L.E. Sellars, S.S. Singh, R. Shahapure, I. Westerlaken, A. Meyer, R.T. Dame and D.C. Grainger.
DNA recognition by Escherichia coli CbpA protein requires a conserved arginine-minor-groove interaction.
Nucleic Acids Research. 43(4), 2282-2292, 2015.

42) R.A. van der Valk, J. Vreede, F. Crémazy and R.T. Dame
Genomic looping: a key principle of chromatin organization
Journal of Molecular Microbiology and Biotechnology. 24, 344-359,  2014.

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

40) R. Shahapure, R.P.C. Driessen, M.F. Haurat, S.V. Albers and  R.T. Dame
The archaellum: a rotating type IV pilus
Molecular Microbiology. 91(4), 716-723, 2014

39) R.P.C. Driessen and  R.T. Dame
Structure and dynamics of the crenarchaeal nucleoid
Biochemical Society Transactions. 41(1), 321-325, 2013

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

37) K. Chintakayala, S.S. Singh, R. Shahapure,  R.T. Dame and D.C. Grainger
Molecular basis for reorganisation of the Escherichia coli nucleoid in response to starvation.
PLOS Genetics. 9 (1), 2013

36) 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
* joint last authors

35) R.T. Dame, O. Espeli, D.C. Grainger and P.A. Wiggins
Multidisciplinary perspectives on bacterial genome organization and dynamics.
Molecular Microbiology. 86(5), 1023-30, 2012

34) E.R. Westra, B. Nilges, P.B.G. van Erp, J. van der Oost, R.T. Dame and S.J.J. Brouns
Cascade-mediated binding and bending of negatively supercoiled DNA.
RNA biology. 9(9), 1-5, 2012

33) K. Tavita, K. Mikkel, M. Tark-Dame, H. Jerabek, R. Teras, J. Sidorenko, R. Tegova, A. Tover, R.T. Dame and M. Kivisaar
Homologous recombination in bacteria is facilitated by starvation and affected by local genome accessibility.
Mutation Research. 737, 12-24, 2012

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

31) E.R. Westra, P.B.G. van Erp, S.P. Wong, T. Künne, C. Seegers, S. Bollen, M.M. Jore, E. Semenova, K. Severinov, W.M. de Vos, R.T. Dame, R. de Vries, S.J.J. Brouns, J. van der Oost
CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3
Molecular Cell. 46(5), 595-605, 2012

30) Z.F. Liu*, F. Galli, W.J. Waterreus, E. Meulenbroek, X. Zhou, G. Lamers, R. Olsthoorn, N.S. Pannu, T. Oosterkamp, R.T. Dame* and J.P. Abrahams*
Single walled carbon nanotubes as a scaffold to obtain physiological DNA concentrations.
ChemPhysChem. 13(6), 1569-1575, 2012
* joint corresponding authors

29) R.T. Dame, M. Tark-Dame and H. Schiessel
A physical approach to segregation and folding of the Caulobacter crescentus genome.
Molecular Microbiology. 82(6), 1311-1315, 2011

28) K. Sznee, J.P. Dekker, R.T. Dame, H. Van Roon, G.J.L. Wuite and R.N. Frese Jumping mode atomic force microscopy of native grana membranes from spinach.
Journal of Biological Chemistry. 286(45), 39164-39171, 2011

27) R.T. Dame, O.J. Kalmykowa and D.C. Grainger
Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in Gram negative bacteria.
PLoS Genetics 7, e1002123, 2011.

26) R.P. Driessen and R.T. Dame
Nucleoid-associated proteins in Crenarchaea.
Biochem. Soc. Trans. 39, 116-121, 2011.

25) R.T. Dame and C.J. Dorman (Eds.)
Bacterial Chromatin
Springer Publishing. 2010.

24) R.T. Dame
Ultrastructure and organization of bacterial chromosomes.
In: Bacterial Chromatin, Dame & Dorman Eds., Springer Publishing. 3-11, 2010

23) P.A. Wiggins, R.T. Dame, M.C. Noom and G.J.L. Wuite
Protein-mediated molecular bridging: a key mechanism in biopolymer organization.
Biophys. J. 97(7), 1997-2003, 2009
Featured article on the Biophys J site

22) R.T. Dame and J. van Mameren
Optical tweezers: empowering biology with the force of light.
Biophotonics. 5, 34-37, 2009

21) M.S. Luijsterburg, M.F. White, R. van Driel and R.T. Dame
The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes.
Crit. Rev. Biochem. Mol. Biol. 43, 393-418, 2008

20) R.T. Dame
Single-molecule micromanipulation studies of DNA and architectural proteins.
Biochem. Soc. Trans. 36, 732-37, 2008

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

18) M.C. Noom, R.T. Dame and G.J.L. Wuite
Het bacterieel chromosoom ontrafeld met een viervoudig optisch pincet.
Ned. Tijdschr. v. Natuurkunde, 46-48, 2007

17) R.T. Dame, M.C. Noom and G.J.L. Wuite.
Bacterial chromatin organization by H-NS protein unraveled using dual DNA manipulation.
Nature 444, 387-90, 2006
See also exclusive review in BioEssays 29, 212-216, 2007
See also conference report in Nature Chemical Biology 3, 193-197, 2007

See also Faculty of 1000 Biology

16) M.S. Luijsterburg, M.C. Noom, G.J.L. Wuite and R.T. Dame
The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective.
J. Struct. Biol. 165(2), 262-72, 2006

15) S.R. Leliveld, R.T. Dame, G.J.L. Wuite, L. Stitz and C. Korth
The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions.
J. Biol. Chem. 281(6), 3268-75, 2006

14) R.T. Dame, J. van Mameren, M.S. Luijsterburg, M.E. Mysiak, G. Pazdzior, P.C. van der Vliet, C. Wyman and G.J.L. Wuite
Simulation based estimation of protein-induced DNA bending by scanning force microscopy.
Nucl. Acids Res. 33(7), e68, 2005.

13) R.T. Dame
The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin.
Mol. Microbiol. 56(4), 858-70, 2005.

12) R.T. Dame, M.S. Luijsterburg, E. Krin, P.N. Bertin, R. Wagner and G.J.L. Wuite
DNA bridging: a property shared among H-NS like proteins.
J. Bacteriol. 187, 1845-48, 2005.

11) J. van Noort, S. Verbrugge, N. Goosen, C. Dekker and R.T. Dame
Dual architectural roles of HU: formation of flexible hinges and rigid filaments.
Proc. Natl. Acad. Sci. USA 101(18), 6969-74, 2004.

10) S.R. Leliveld, R.T. Dame, J.L. Rohn, M.H. Noteborn and J.P. Abrahams
Apoptin's functional N- and C-termini independently bind DNA.
FEBS Lett. 557, 155-58, 2004.

9) R.T. Dame and G.J.L. Wuite
On the role of H-NS in the organization of bacterial chromatin. From bulk to single molecules and back…
Biophys. J. 85, 4146-48, 2003.

8) R.T. Dame, C. Wyman and N. Goosen
Insights into the regulation of transcription by scanning force microscopy.
J. Microsc. 244-53, 2003.

7) S.R. Leliveld, R.T. Dame, M.A. Mommaas, H.K. Koerten, C. Wyman, A.A. Danen-van Oorschot, J.L. Rohn, M.H. Noteborn and J.P. Abrahams
Apoptin protein multimers form distinct higher-order nucleoprotein complexes with DNA.
Nucl. Acids Res. 31(16), 4805-13, 2003.

6) R.T. Dame, C. Wyman and N. Goosen
Analysis of transcription and its regulation by scanning force microscopy.
In: Science, technology and education of microscopy. Mendez-Vilas ed., 588-96, 2002.

5) R.T. Dame and N. Goosen:
HU promoting or counteracting DNA compaction?
FEBS Lett., 529(2-3),151-6, 2002.
See also Faculty of 1000 Biology

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

3) R.T. Dame, C. Wyman and N. Goosen
Structural basis for preferential binding of H-NS to curved DNA.
Biochimie 83(2), 231-4, 2001.

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

1) G. Zuccheri, R.T. Dame, M. Aquila, I. Muzzalupo and B. Samori'
Conformational fluctuations of supercoiled DNA molecules observed in real time with the scanning force microscope.
Appl. Phys. A 66, 585-9, 1998.

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