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Researcher

Prof. dr C.L. (Claire) Wyman, PhD

Principal Investigator

  • Department
  • Molecular Genetics
  • Focus area
  • Molecular nanomachinery of DNA break repair

About

Introduction

About Claire Wyman

BMW-MolGen-CW

Claire Wyman received her PhD in Molecular Biology from The University of California at Berkeley in 1990 in the group of Dr. E. Blackburn, where she studied transposons and transposition events involved in the developmental genome rearrangements of Tetrahymena thermophila. Her postdoctoral work in the laboratory of Dr. H. Echols at the University of California at Berkeley focused on determining the structure of complex nucleoprotein assemblies of DNA replication primarily using electron microscopy. In collaboration with Dr. Carols Bustamante at the University of Oregon she appled the newly developed technique of Scanning Force Microscopy (SFM) to study DNA replication and transcription mechanisms. In 1996 she joined the Department of Cell Biology and Genetics at the Erasmus Medical Centre.  Here she set up the Centre for Scanning Force Microscopy of Biological Nanomachines to study the molecular machinery involved in DNA repair. This work has led to new understanding of several important functional assemblies of DNA repair machinery and their mechanism of action. In 2005 she was appointed Associate Professor in the Department of Radiation Oncology at the Erasmus MC and continues to apply novel microscopy and molecular manipulation techniques to advance our understanding of complex mechanisms of genome metabolism. In 2006 she received a VICI award from the Chemical Sciences division of NWO to expand this work in new directions. Since August 2008 she is Professor of Molecular Radiation Biology. 

She is academic director of Nanobiology, a new joint BSc program between Erasmus MC and TU Delft, started September 2012. 

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Field(s) of expertise

BMW-MolGen-CW-MRE11RAD50Molecular nanomachinery of DNA break repair

We aim to understand fundamental principles that determine complex biological processes. We currently focus on the process of double-strand DNA break repair in relation to genomic (in)stability, carcinogenesis and radio- and chemotherapy. We develop and apply new methods from single molecule imaging to live cell microscopy for quantitative analysis of detailed molecular function. Although our focus is fundamental knowledge, the mechanistic information we reveal are needed both to understand molecular causes that promote tumor formation, and to design of strategies specifically sensitizing rapidly dividing cells to anti-cancer treatments based on DSB induction.  

For more information on Research projects and projects for BEP/MEP students, scroll down:

GENERAL INTRODUCTION TO PROJECTS AND BEP/MEP POSSIBILITIES

BMW-MolGen-CW-joint-molecule-image

A major challenge in structural biology is to move beyond determining highly detailed but static uniform structure to learning how proteins work together in complex and dynamic assemblies that accomplish the work of living cells. Our multidisciplinary approach aims to determine how proteins work together achieving precision and control in Homologous Recombination (HR) DNA repair. We determine nanomachinery composition, architectural arrangement and how these are controlled in time and space.

The process we study is homologous recombination

This dramatic DNA rearrangements of this repair reaction are accomplished by coordinated action of several proteins, assembled into specific molecular nanomachinery at sites of DNA breaks, illustrated in this cartoon.   Proteins we are currently analyzing are shown: MRE11/RAD50/NBS1 (MRN) protein complex recognizes breaks and participates in end processing, RPA coats single stranded DNA, BRCA2 load RAD51 by replacing RPA on ssDNA, a RAD51 nucleoprotein filament catalyzes DNA homology search and strand exchange, RAD54 has roles in both homology search and stimulating filament disassembly to allow the repair processes to proceed to completion.

BMW-MolGen-CW-process-homologous-recombination

In vivo Biochemistry: how DNA repair proteins find their way to a break

Following the diffusive behavior of individual fluorescent proteins with advanced live cell imaging and analysis tools a completely new picture of protein activity comes into focus. These projects are in collaboration with A. Houtsmuller Optical Imaging Center and Erik Meijering Biomedical Imaging group Rotterdam . We determine the in vivo behavior of specific proteins and functional complexes in mammalian cell nuclei, how this changes in response to damage, and how this changes at sites of DNA breaks.

BMW-MolGen-CW-BRCA2

A striking characteristic of many proteins involved in HR, including MRN, RPA, BRCA2, RAD51, and RAD54, is their accumulation in high local concentration at the sites of DNA damage into structures termed foci. This observation raises questions about the physical processes and structural changes driving focus formation and dispersal that result in efficient DNA repair. The mechanisms promoting this accumulation are not well defined. To determine how proteins such as BRCA2 arrive at the needed nuclear location at the right time, we follow in vivo diffusive behavior directly using a combination single particle tracking, fluorescence correlation spectroscopy (FCS) and modeling. This work has already revealed surprises: (1) BRCA2 travels in the nucleus in multimeric clusters  and (2) all detectable nuclear RAD51 is traveling in the nucleus together with BRCA2 (ref= Reuter JCB 2014). Many questions remain concerning how specific BRCA2 domains and structural features determine and control the nuclear behavior we have observed contributing to efficient HR and ultimately cancer avoidance.

Nanobiology students>
Potential BEP/MEP projects involving cell biology, advanced optical imaging, image analysis challenges, data simulation and model testing. Contact Claire Wyman

What is in a DNA repair focus

We use super-resolution microscopy (collaboration with A. Houtsmuller Optical Imaging Center to define the organization of repair proteins that accumulate in high local concentration at break sites and relate this organization to function using variant and mutant proteins with known functional defects. 

BMW-MolGen-CW-Foci-at-super-resolution

The observation of DNA repair foci with even standard microscopy methods implies that many copies of many proteins accumulate in high local concentrations at sites where only one or a few are needed to preform specific DNA processing functions. Several open questions about the composition, organization, structure and function of these accumulations can be now addressed by super-resolution imaging. Determining the arrangement of HR proteins with nm resolution will allow us to answer many open questions about how the nanomachinery of homologous recombination is assembled, rearranged and controlled to achieve functional DNA transactions in the nucleus. 

Nanobiology students>
Potential BEP/MEP projects involving cell biology, fluorescent labeling methods, fluorescence nanoscopy, advanced optical imaging, and image analysis challenge. Contact Claire Wyman

Defining function of biological nanomachines by nm resolved structural/architectural transitions

Cellular proteins assemble into molecular nanomachines at sites of DNA breaks to preform the work of homologous recombination. These functional assemblies are characterized by often flexible and dynamic architectural arrangement of several proteins with relevant structural details in the nm length scale. We unravel key steps in homologous recombination at the molecular mechanistic level using state-of-the-art nanotechnology imaging tools applied to purified components. We currently focus on the core reaction of homologous recombination, DNA strand exchange, catalyzed by RAD51.  The dynamic assembly, rearrangement and disassembly of a RAD51 nucleoprotein filament on single-stranded (ss)DNA is controlled by the activity of proteins such as BRCA2, RAD54, the MRN complex, the RAD51 paralogs, and RPA. 

BMW-MolGen-CW-SFM-TIRF
The arrangement of these proteins in functional complexes and intermediates reveal how they work together and identify points of control. We have developed methods to combine SFM nm resolution topography and single-molecule sensitivity fluorescence to identify individual proteins in complex assemblies and greatly expand the information we can obtain (REF = sanchez PNAS 2013). 

BMW-MolGen-CW-SFM-Lab
Nanobiology students>
Potential BEP/MEP projects involving biochemistry, molecular biology, protein engineering, Scanning Force Microscopy single molecule imaging, combined single molecule fluorescence and scanning force microscopy, and image analysis challenges. Contact Claire Wyman

Education and career

Claire Wyman serves on many local and national science advisory committees including:

  • ErasmusMC MRACE, Member fellowship selection committee
  • FOM Physics of Life processes, Chair advisory committee
  • AMOLF institute, Member directors advice committee (Beleidsadviescommissie)
  • TKI Chemie (knowledge and innovation), Member Chemistry of Life Program Council

ACADEMIC EDUCATION AND DEGREES

Doctorate (PhD) in Molecular Biology, awarded 30/09/1990
University of California at Berkeley, USA
Department of Molecular Biology, Laboratory of Dr. Elizabeth H. Blackburn

Master of Science (MSc) in Immunology and Infectious Diseases, awarded 30/06/1984
The Johns Hopkins University, School of Hygiene and Public Health,
Baltimore Maryland, USA

Bachelor of Science (BS) in Natural Sciences/Public Health, awarded 05/06/1980
The Johns Hopkins University, Baltimore Maryland, USA

APPOINTMENTS

Current (UHD 2005-2008, HL 2008) Professor Molecular Radiobiology and
Medical Delta Professor since 2016
Department of Radiation Oncology, Erasmus MC – Cancer Institute and
Department of Molecular Genetics, Erasmus MC, Rotterdam

May 2001 through December 2004  Research Group Leader
Department of Radiation Oncology Erasmus MC – Cancer Institute and
Department of Cell Biology and Genetics Erasmus MC, Rotterdam

April 1996 through April 2001   Research Scientist
Department of Cell Biology and Genetics, Erasmus MC, Rotterdam

Publications

Publications

Hermans N, Laffeber C, Cristovão M, Artola-Borán M, Mardenborough Y, Ikpa P, Jaddoe A, Winterwerp HH, Wyman C, Jiricny J, Kanaar R, Friedhoff P, Lebbink JH. Dual daughter strand incision is processive and increases the efficiency of DNA mismatch repair.
Nucleic Acids Res. 2016 Aug 19;44(14):6770-86. doi: 10.1093/nar/gkw411.

Elbatsh AM, Haarhuis JH, Petela N, Chapard C, Fish A, Celie PH, Stadnik M, Ristic D, Wyman C, Medema RH, Nasmyth K, Rowland BD. Cohesin Releases DNA through Asymmetric ATPase-Driven Ring Opening. 
Mol Cell. 2016 Feb 18;61(4):575-88. doi: 10.1016/j.molcel.2016.01.025.

Carrasco B, Serrano E, Sánchez H, Wyman C, Alonso JC. Chromosomal transformation in Bacillus subtilis is a non-polar recombination reaction.  Nucleic Acids Res. 2016 Apr 7;44(6):2754-68. doi: 10.1093/nar/gkv1546.

H. Sánchez, C. Wyman.
SFMetrics: An analysis tool for scanning force microscopy images of biomolecules.
BMC Bioinformatics. 2015;16(1).
doi: 10.1186/s12859-015-0457-8.

E. Kinoshita, S. van Rossum-Fikkert, H. Sanchez, A. Kertokalio, C. Wyman.
Human RAD50 makes a functional DNA-binding complex.
Biochimie. 2015;113:47-53.
doi: 10.1016/j.biochi.2015.03.017

M. Bermúdez-López, I. Pociño-Merino, H. Sánchez, A. Bueno, C. Guasch, S. Almedawar,  S. Bru-Virgili, E. Garí, C. Wyman, D. Reverter, N. Colomina, J. Torres-Rosell.
ATPase-Dependent Control of the Mms21 SUMO Ligase during DNA Repair.
PLoS Biology. 2015;13(3).
doi: 10.1371/journal.pbio.1002089. 

N. Ameziane, P. May, A. Haitjema, H.J. van de Vrugt, S.E. van Rossum-Fikkert, D. Ristic, G.J. Williams, J. Balk, D. Rockx, H. Li, M.A. Rooimans, A.B. Oostra, E. Velleuer, R. Dietrich, O.B. Bleijerveld, A.F. Maarten, H. Meijers-Heijboer, H. Joenje, G. Glusman, J. Roach, L. Hood, D. Galas, C. Wyman, R. Balling, J. den Dunnen, J.P. de Winter, R. Kanaar, R. Gelinas, J.C. Dorsman.
A novel Fanconi anaemia subtype associated with a dominant-negative mutation in RAD51.
Nat Commun. 2015 Dec 18;6:8829. doi: 10.1038/ncomms9829.

Zelensky A, Kanaar R and Wyman C
Mediators of homologous DNA pairing
Cold Spring Harb. Perspect. Biol. 2014 doi: 10.1101/cshperspect.a016451

Xue X, Choi K, Bonner J, Chiba T, Kwon Y, Xu Y, Sanchez H, Wyman C, Niu H, Zhao X,  Sung P
Restriction of Replication Fork Regression Activities by a Conserved SMC Complex
Mol Cell 2014 available on line Oct.16, DOI: 10.1016/j.molcel.2014.09.013

Sanchez H, Reuter M, Yokokawa M, Takeyasu K, Wyman C
Taking it one step at a time in homologous recombination repair
DNA Repair (Amst). 2014 Aug;20:110-8

Reuter M, Zelensky A, Smal I, Meijering E, van Cappellen WA, de Gruiter HM, van Belle GJ, van Royen ME, Houtsmuller AB, Essers J, Kanaar R, Wyman C
BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells
J Cell Biol 2014 207, 599–613

Candelli A, Holthausen JT, Depken M, Brouwer I, Franker MM, Marchetti M, Heller I, Bernard S, Garcin EB, Modesti M, Wyman C, Wuite GJL, Peterman EJG
Visualization and quantification of nascent RAD51-filament formation at single-monomer resolution
Proc. Natl. Acad. Sci. USA 2014 111, p.15090-15095

Lee, J-H, M.R. Mand, R.Deshpande, E.Kinoshita, S-H. Yang, C. Wyman, and T. T. Paull (2013) ATM kinase activity is regulated by ATP-driven conformational changes in the MRN complex. J. Biol. Chem. 288, p. 12840-12851.

Zelensky, A., H. Sanchez,D.  Ristic, I. Vidic, S. van Rossum-Fikkert, J. Essers, C. Wyman, R. Kanaar (2013), Caffeine Suppresses Homologous Recombination Through Interference with RAD51-Mediated Joint Molecule Formation, Nucl. Acids Res. 41, p. 6475-6489.

Lee, M., J. Lipfert, H. Sanchez, C. Wyman, and N. H. Dekker (2013) Structural and Torsional Properties of the RAD51-dsDNA Nucleoprotein Filament. Nucl. Acids Res.  41, p. 7023-7030.

Balestrini, A., D. Ristic, I. Dionne, C. Wyman, R.J.  Wellinger and J. Petrini (2013) The Ku heterodimer and the metabolism of single-ended DNA double strand breaks, Cell Reports 3, p. 2033-2045.

Sanchez, H., A. Kertokalio, S. van Rossum-fikkert, R. Kanaar, C. Wyman (2013) TIRF-SFM imaging reveals different arrangements of human RAD54 with presynaptic and postsynaptic RAD51-DNA filaments, Proc. Natl. Acad. Sci. USA, 110, p. 11385-11390

Tham, K.C., N. Hermans, H.H. Winterwerp, M.M. Cox, C. Wyman, R. Kanaar, J.L. Lebbink (2013) Mismatch repair inhibits homeologous recombination via coordinated directional unwinding of trapped DNA structures, Mol. Cell, 51, p. 326-337.

 

Teaching activities

BMW-MolGen-CW-in-SFM-lab

Claire Wyman is the academic Director of the BSc Nanobiology a joint degree program with TU Delft partner department Bionanoscience.


I teach the two first year courses in Nanobiology:
NB1031 “Introduction to Studying in Nanobiology”
NB1052 “Journal Club: introduction to reading scientific literature”

I teach MSc courses, TUD course base and nanobiology programBMW-MolGen-CW-NB-BSc-graduation-cw-student

I regularly lecture in post-graduate courses on single molecule imaging (SFM, SFM-TIRF)  in biological sciences, nucleic acid structure, grant writing and presentation techniques.