Project

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Functional transitions of DNA structure

English title Functional transitions of DNA structure
Applicant Stasiak Andrzej
Number 116275
Funding scheme Project funding (Div. I-III)
Research institution Laboratoire d'Analyse Ultrastructurale Centre de Microscopie Electronique Université de Lausanne
Institution of higher education University of Lausanne - LA
Main discipline Molecular Biology
Start/End 01.04.2007 - 31.10.2011
Approved amount 260'000.00
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Keywords (5)

DNA topology; DNA topoisomerases; DNA recombination; protein-DNA interactions; transcription factors

Lay Summary (English)

Lead
Lay summary
In the first part of the project will try to explain very intriguing observation that type-2 DNA topoisomerases while allowing passages between DNA segments controls these passages in such a way that DNA knotting is rather removed than introduced. DNA topoisomerases interact only locally with long and therefore very flexible circular DNA molecules with overall dimensions much bigger than dimensions of the enzyme, how then the enzyme can “tell” whether a given intersegmental passage will knot or unknot the DNA. Several different groups over the years proposed a range of models to explain this observation but all these models predicted less efficient unknotting than this observed experimentally. More recently a new type of mechanism was proposed where a simple selection of certain geometries of segment juxtapositions could guide topoisomerases in efficient unknotting. We plan to perform to test this model by numerical simulations using a freely jointed chain model and complement simulations by electron microscopy study of type-2 DNA topoisomerases that are blocked at the stage of passage.The second part will be a continuation of our long-term project directed to understand the mechanism of DNA homologous recombination and DNA repair. The leading points of this project will address a role of human Rad54 protein in homologous recombination. In particular we will study by electron microscopy what is the mechanism by which Rad54 protein drives branch migration of Holliday junctions. We will investigate whether Rad54 forms multimeric rings enclosing the DNA and whether the architecture of the complex resembles this known for the RuvARuvB complexes formed with Holliday junctions. Separately the interactions of FANCD2 and FANCM proteins with DNA will be studied to shed light on the role of these proteins in DNA repair in order to explain the underlying mechanism of Fanconi anaemia, an inherited genetic disease that causes severe, life-threatening aplastic anaemia.The third part will be directed to investigate changes of DNA structure and shape connected to binding of transcription factors to pol II and pol III promoters of eukaryotic snRNA genes. Various transcription factors such as TATA box binding protein (TBP), snRNA activating protein complex (SNAPc), a general transcription factor for pol II (TFIIB), TFIIB-related factor Brf2 will be bound, either as individual proteins or forming functional complexes involving several transcription factors, to DNA containing pol II and pol II promoters. Electron microscopy will be then used to study the overall architecture of the formed complexes. We will measure the extent of DNA bending and unwinding caused by formation of these complexes. In particular we will address the question whether these promoters that do not have TATA boxes are bent in a similar way as these that contain them. Biochemical tests will complement EM observations.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Cooperative kinking at distant sites in mechanically stressed DNA.
Lionberger Troy A, Demurtas Davide, Witz Guillaume, Dorier Julien, Lillian Todd, Meyhöfer Edgar, Stasiak Andrzej (2011), Cooperative kinking at distant sites in mechanically stressed DNA., in Nucleic acids research, 39(22), 9820-9832.
DNA knots and DNA supercoiling
Witz G, Dietler G, Stasiak A (2011), DNA knots and DNA supercoiling, in CELL CYCLE, 10(9), 1339-1340.
Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases
Witz G, Dietler G, Stasiak A (2011), Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases, in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108(9), 3608-3611.
The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture
Dorier J, Stasiak A (2010), The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture, in NUCLEIC ACIDS RESEARCH, 38(21), 7410-7421.
Cooperation of breast cancer proteins PALB2 and piccolo BRCA2 in stimulating homologous recombination
Buisson R, Dion-Cote AM, Coulombe Y, Launay H, Cai H, Stasiak AZ, Stasiak A, Xia B, Masson JY (2010), Cooperation of breast cancer proteins PALB2 and piccolo BRCA2 in stimulating homologous recombination, in NATURE STRUCTURAL & MOLECULAR BIOLOGY, 17(10), 1247-1247.
Symmetry-breaking in cumulative measures of shapes of polymer models (vol 133, 154113, 2010)
Millett KC, Rawdon EJ, Tran VT, Stasiak A (2010), Symmetry-breaking in cumulative measures of shapes of polymer models (vol 133, 154113, 2010), in JOURNAL OF CHEMICAL PHYSICS, 133(16), 154113-154113.
Design of Potent Inhibitors of Human RAD51 Recombinase Based on BRC Motifs of BRCA2 Protein: Modeling and Experimental Validation of a Chimera Peptide
Nomme J, Renodon-Corniere A, Asanomi Y, Sakaguchi K, Stasiak AZ, Stasiak A, Norden B, Tran V, Takahashi M (2010), Design of Potent Inhibitors of Human RAD51 Recombinase Based on BRC Motifs of BRCA2 Protein: Modeling and Experimental Validation of a Chimera Peptide, in JOURNAL OF MEDICINAL CHEMISTRY, 53(15), 5782-5791.
DNA supercoiling and its role in DNA decatenation and unknotting
Witz G, Stasiak A (2010), DNA supercoiling and its role in DNA decatenation and unknotting, in NUCLEIC ACIDS RESEARCH, 38(7), 2119-2133.
A Histone-Fold Complex and FANCM Form a Conserved DNA-Remodeling Complex to Maintain Genome Stability
Yan ZJ, Delannoy M, Ling C, Daee D, Osman F, Muniandy PA, Shen X, Oostra AB, Du HS, Steltenpool J, Lin T, Schuster B, Decaillet C, Stasiak A, Stasiak AZ, Stone S, Hoatlin ME, Schindler D, Woodcock CL, Joenje H, Sen R, de Winter JP, Li L, Seidman MM, Whitby MC (2010), A Histone-Fold Complex and FANCM Form a Conserved DNA-Remodeling Complex to Maintain Genome Stability, in MOLECULAR CELL, 37(6), 865-878.
ParA2, a Vibrio cholerae chromosome partitioning protein, forms left-handed helical filaments on DNA
Hui MP, Galkin VE, Yu X, Stasiak AZ, Stasiak A, Waldor MK, Egelman EH (2010), ParA2, a Vibrio cholerae chromosome partitioning protein, forms left-handed helical filaments on DNA, in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107(10), 4590-4595.
DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting
Marenduzzo D, Orlandini E, Stasiak A, De Sumners W, Tubiana L, Micheletti C (2009), DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting, in Proceedings of the National Academy of Sciences of the United States of America, 106(52), 22269-22274.
Topological origins of chromosomal territories
Dorier J, Stasiak A (2009), Topological origins of chromosomal territories, in NUCLEIC ACIDS RESEARCH, 37(19), 6316-6322.
Interplay of DNA supercoiling and catenation during the segregation of sister duplexes
Martinez-Robles ML, Witz G, Hernandez P, Schvartzman JB, Stasiak A, Krimer DB (2009), Interplay of DNA supercoiling and catenation during the segregation of sister duplexes, in NUCLEIC ACIDS RESEARCH, 37(15), 5126-5137.
MRE11-RAD50-NBS1 is a critical regulator of FANCD2 stability and function during DNA double-strand break repair
Roques C, Coulombe Y, Delannoy M, Vignard J, Grossi S, Brodeur I, Rodrigue A, Gautier J, Stasiak AZ, Stasiak A, Constantinou A, Masson JY (2009), MRE11-RAD50-NBS1 is a critical regulator of FANCD2 stability and function during DNA double-strand break repair, in EMBO JOURNAL, 28(16), 2400-2413.
Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
Demurtas D, Amzallag A, Rawdon EJ, Maddocks JH, Dubochet J, Stasiak A (2009), Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles, in NUCLEIC ACIDS RESEARCH, 37(9), 2882-2893.
A PARTIAL ORDERING OF KNOTS AND LINKS THROUGH DIAGRAMMATIC UNKNOTTING
Diao YA, Ernst C, Stasiak A (2009), A PARTIAL ORDERING OF KNOTS AND LINKS THROUGH DIAGRAMMATIC UNKNOTTING, in JOURNAL OF KNOT THEORY AND ITS RAMIFICATIONS, 18(4), 505-522.
Effect of knotting on polymer shapes and their enveloping ellipsoids
Millett KC, Plunkett P, Piatek M, Rawdon EJ, Stasiak A (2009), Effect of knotting on polymer shapes and their enveloping ellipsoids, in JOURNAL OF CHEMICAL PHYSICS, 130(16), 165104-165104.
Mechanism of homologous recombination from the RecA-ssDNA/dsDNA complexes: Commentary
Stasiak A. Z., Stasiak A (2008), Mechanism of homologous recombination from the RecA-ssDNA/dsDNA complexes: Commentary, in Chemtracts, 20(10), 399-405.
Effect of Knotting on the Shape of Polymers
Rawdon EJ, Kern JC, Piatek M, Plunkett P, Stasiak A, Millett KC (2008), Effect of Knotting on the Shape of Polymers, in MACROMOLECULES, 41(21), 8281-8287.
DNA supercoiling inhibits DNA knotting
Burnier Y, Dorier J, Stasiak A (2008), DNA supercoiling inhibits DNA knotting, in NUCLEIC ACIDS RESEARCH, 36(15), 4956-4963.
Functional and structural basis for a bacteriophage homolog of human RAD52
Ploquin M, Bransi A, Paquet ER, Stasiak AZ, Stasiak A, Yu X, Cieslinska AM, Egelman EH, Moineau S, Masson JY (2008), Functional and structural basis for a bacteriophage homolog of human RAD52, in CURRENT BIOLOGY, 18(15), 1142-1146.
3D visualization software to analyze topological outcomes of topoisomerase reactions
Darcy IK, Scharein RG, Stasiak A (2008), 3D visualization software to analyze topological outcomes of topoisomerase reactions, in NUCLEIC ACIDS RESEARCH, 36(11), 3515-3521.
Scaling behavior and equilibrium lengths of knotted polymers
Rawdon E, Dobay A, Kern JC, Millett KC, Piatek M, Plunkett P, Stasiak A (2008), Scaling behavior and equilibrium lengths of knotted polymers, in MACROMOLECULES, 41(12), 4444-4451.
A glycine-arginine domain in control of the human MRE11 DNA repair protein
Dery U, Coulombe Y, Rodrigue A, Stasiak A, Richard S, Masson JY (2008), A glycine-arginine domain in control of the human MRE11 DNA repair protein, in MOLECULAR AND CELLULAR BIOLOGY, 28(9), 3058-3069.
The Fanconi anemia protein FANCM can promote branch migration of Holliday junctions and replication forks
Gari K, Decaillet C, Stasiak AZ, Stasiak A, Constantinou A (2008), The Fanconi anemia protein FANCM can promote branch migration of Holliday junctions and replication forks, in MOLECULAR CELL, 29(1), 141-148.
Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases
Burnier Y, Weber C, Flammini A, Stasiak A (2007), Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases, in Nucleic Acids Research, 35(15), 5223-5231.
Structural motifs of biomolecules
Banavar JR, Trinh XH, Maddocks JH, Maritan A, Poletto C, Stasiak A, Trovato A (2007), Structural motifs of biomolecules, in Proceedings of the National Academy of Sciences of the United States of America, 104(44), 17283-17286.

Scientific events



Self-organised

Title Date Place
Conference: Statistical Physics and Topology of Polymers with Ramifications to structure and function of DNA and Proteins 02.08.2010 Yukawa Institute for Theoretical Physics, Kyoto University, Japan.
CIG Symposium 2009 : DNA Repair and Human Health. 10.06.2009 CIG, Lausanne University, Switzerland.
Conference: Knots and other entanglements in Biopolymers. 15.09.2008 International Centre for Theoretical Physics, Trieste, Italy.
Conference: Knots and soft matter physics 26.08.2008 Yukawa Institute for Theoretical Physics, Kyoto University, Japan.
The Mathematics of Knotting and Linking in Polymer Physics and Molecular Biology 20.05.2007 Banff International Research Station for Mathematical Innovation and Discovery, Banff, Canada

Associated projects

Number Title Start Funding scheme
138367 Functional transitions of DNA structure. A: Organization of nuclear architecture:Understanding the correlation between the transcriptional status and spatial proximity within human chromosomes B:Mechanism of branch migration of homologous pairing pro 01.08.2012 Project funding (Div. I-III)
103962 Functional transitions of DNA structure 01.04.2004 Project funding (Div. I-III)

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