Publications (2000-2008)

2008

• Bruggeman, F. J., I. Oancea, et al. (2008). "Exploring the behavior of small eukaryotic gene networks." J Theor Biol 252(3): 482-487.
  
• Bohn, M., D. W. Heermann, et al. (2007). "Random loop model for long polymers." Phys Rev E Stat Nonlin Soft Matter Phys 76(5 Pt 1): 051805Tessadori, F., Chupeau, M.C., Chupeau, Y., Knip, M., Germann, S., Driel, R. van, Fransz, P.F. & Gaudin, V. (2007). Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells. J Cell Sci, 120(7), 1200-1208.
  Fransz, P. 2008, Chromatin domains and function, in Plant Cell Monographs, Functional Organization of the Plant Nucleus, ed. I. Meier (in press).
  Kanger, J. S., V. Subramaniam, et al. (2008). "Intracellular manipulation of chromatin using magnetic nanoparticles." Chromosome Res 16(3): 511-22.
  Stam, M, Louwers, M. (2008) Paramutation: Heritable in Trans Effects. In maize handbook. In Press.

2007
de Vries, A. H., B. E. Krenn, et al. (2007). "Direct observation of nanomechanical properties of chromatin in living cells." Nano Lett 7(5): 1424-7.
Fakan, S. and R. van Driel (2007). "The perichromatin region: a functional compartment in the nucleus that determines large-scale chromatin folding." Semin Cell Dev Biol 18(5): 676-81.
Gierman, H. J., M. H. Indemans, et al. (2007). "Domain-wide regulation of gene expression in the human genome." Genome Res 17(9): 1286-95.Tessadori, F., Schulkes, R.K., Driel, R. van & Fransz, P.F. (2007). Light-regulated large-scale reorganization of chromatin during the floral transition in Arabidopsis. Plant J., 50(5), 848-857.
Gladilin, E., S. Goetze, et al. (2007). "Stochastical analysis of finite point sampling of 3D chromatin fiber in interphase cell nuclei." Proc. of BIRD: 104-118.
Goetze, S., J. Mateos-Langerak, et al. (2007). "The three-dimensional structure of human interphase chromosomes is related to the transcriptome map." Mol Cell Biol 27(12): 4475-87
Goetze, S., J. Mateos-Langerak, et al. (2007). "Three-dimensional genome organization in interphase and its relation to genome function." Semin Cell Dev Biol 18(5): 707-14.
Haring M, Offermann S, Danker T, Horst I, Peterhaensel C, Stam M. (2007) Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization. Plant Methods, 3, 11.
Lindhout B.I., Fransz P., Tessadori F., Meckel T., Hooykaas P.J., van der Zaal B.J. (2007). Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins. Nucl. Ac. Res. 35, e107
Luijsterburg, M. S., J. Goedhart, et al. (2007). "Dynamic in vivo interaction of DDB2 E3 ubiquitin ligase with UV-damaged DNA is independent of damage-recognition protein XPC." J Cell Sci 120(Pt 15): 2706-16.
Mateos-Langerak, J., M. C. Brink, et al. (2007). "Pericentromeric heterochromatin domains are maintained without accumulation of HP1." Mol Biol Cell 18(4): 1464-71.
Mateos-Langerak, J., S. Goetze, et al. (2007). "Nuclear architecture: is it important for genome function and can we prove it?" J. Cell. Biochem.
Oacea, I., R. Van Driel, et al. (2007). "Exploring the behavior of small eukaryotic gene clusters." J. Theor. Biol. in preparation.
Post, L. J., M. Roos, et al. (2007). "A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data." Bioinformatics 23(22): 3080-7.
van Driel, R. (2007). "Chromatin is wonderful stuff." Semin Cell Dev Biol.
Van Royen, ME, Cunha, SM, Brink, MC, Mattern, KA, Nigg, AL, Dubbink, HJ, Verschure, PJ, Trapman, J., Houtsmuller, AB (2007): Compartmentalization of androgen receptor protein-protein interactions in living cells. J. Cell Biol. 177:63-72.
Yang, S., S. Goetze, et al. (2007). "Variability of the large-scale structure of interphase chromatin fiber based based on statistical shape theory."

2006
Brink MC, Y der Velden, W de Leeuw, J Mateos-Langerak, AS Belmont, R Van Driel, Verschure PJ (2006): Truncated HP-1 lacking a functional chromodomain induces heterochromatinization upon in vivo targeting. Histochem. Cell Biol. 125:53-61.
De Leeuw, W, Verschure PJ, van Liere R (2006): Visualization and analysis of large data collections: a case study applied to confocal microscopy data. IEEE Trans Vis Comput Graph. 12(5):1251-8.
Fransz P., R. ten Hoopen  and F. Tessadori (2006) Composition and formation of heterochromatin in Arabidopsis thaliana. Chromosome Research 14, 71-82.
Gladilin, E., S. Goetze, et al. (2006). "Topological analysis of 3D cell nuclei using finite element template-based spherical mapping." Proceedings SPIE 6144: 1557-1566.
Lysak M., Fransz P., Schubert I. (2006) Cytogenetic Analyses of Arabidopsis. Methods Mol Biol. 323, p173-186.
Mylne J.S., Barrett L., Tessadori F., Mesnage S, Johnson L., Bernatavichute Y, Jacobsen S., Fransz P. and Dean C. (2006) LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1 is required for epigenetic silencing of FLC. Proc. Nat. Acad. Sci. 103, 5012-5017.
Verschure PJ, Visser AE, MG Rots (2006): Step out of the groove: epigenetic gene control systems and engineered transcription factors. Adv Genet. 56:163-204.
Verschure PJ (2006): Chromosome organization and gene control: It is difficult to see the picture when you are inside the frame. J. Cell. Biochem. 99(1):23-34.
Visser AE, PJ Verschure, WM Gommans, HJ Haisma, MG Rots (2006): Step into the groove: engineered transcription factors as modulators of gene expression. Adv Genet. 56:131-61.
Zotter, A., M. S. Luijsterburg, et al. (2006). "Recruitment of the nucleotide excision repair endonuclease XPG to sites of UV-induced dna damage depends on functional TFIIH." Mol Cell Biol 26(23): 8868-79.

2005
de Vries, A. H., B. E. Krenn, et al. (2005). "Micro magnetic tweezers for nanomanipulation inside live cells." Biophys J 88(3): 2137-44.
Cremazy, F. G., E. M. Manders, et al. (2005). "Imaging in situ protein-DNA interactions in the cell nucleus using FRET-FLIM." Exp Cell Res 309(2): 390-6.
Louwers, M., Haring, M. and Stam, M. (2005) When alleles meet: Paramutation. In P. Meyer, ed, Plant Epigenetics. Blackwell Publishing Ltd, Oxford, UK, 134-173.
Libault M., Tessadori F., Germann S., Snijder B., Fransz P., Gaudin V. (2005) The Arabidopsis LHP1 protein is a component of euchromatin. Planta 222, 910-25.
Politi, A., M. J. Mone, et al. (2005). "Mathematical Modeling of Nucleotide Excision Repair Reveals Efficiency of Sequential Assembly Strategies." Mol Cell 19(5): 679-690.
Stam M., Mittelsten Scheid O. (2005) Paramutation: an encounter leaving a lasting impression. TIPS 10, 283-290.
Verschure, P. J., I. van der Kraan, et al. (2005). "In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation." Mol Cell Biol 25(11): 4552-64.

2004
Baroux C, Fransz P, and Grossniklaus U. (2004) Nuclear fusions contribute to polyploidization of the gigantic nuclei in the chalazal endosperm of Arabidopsis. Planta 220, 38-46.
Fakan, S. and R. Van Driel (2004). "Where do we go in the nucleus?" Biol Cell 96(8): 553-554.
De Vries, A. H. B., S. J. Kanger, et al. (2004). "Patterned electroplating of micrometer scale magnetic structures on glass substrates." J. Microelectromechanical systems 13(3): 391-395.
Van Driel R. and P. Fransz (2004) Nuclear architecture and genome functioning in plants and animals: what can we learn from both? Exp. Cell Res. 296, 86-90.
Fransz P. (2004) The interphase nucleus. In: Encyclopedia of Plant and Crop Science. (R.M. Goodman ed.), Marcel Dekker, New York, Basel, p.568-571.
Mone, M. J., T. Bernas, et al. (2004). "In vivo dynamics of chromatin-associated complex formation in mammalian nucleotide excision repair." Proc Natl Acad Sci U S A 101(45): 15933-7.
Chandler V.L., Stam M. (2004) Chromatin conversations: mechanisms and implications of paramutation. Nat Rev Genet. 5, 532-44.
Tessadori F, Van Driel R, Fransz P. (2004) Cytogenetics as a tool to study gene regulation. Trends Plant Sci. 9, 147-153.
Visser, A. E., Van Driel, R. and Verschure, P.J. (2004). Functional organization of chromosomes in the interphase nucleus. Visions of the nucleus. P. Hemmerich, Diekmann, S. Stevenson Ranch, CA, USA, American Scientific Publishers.
Verschure PJ (2004): Positioning the genome within the nucleus. Biol. Cell 96: 569-577.

2003
CMarko D, Verschure PJ, Otte AP, Van Driel R, Fakan F (2003): Polycomb group gene silencing proteins are concentrated in the perichromatin compartment of the mammalian nucleus. J. Cell Science 116: 335-343.
Van Driel R., Fransz P.F. and Verschure P.J. (2003) The eukaryotic genome: a system regulated at different hierarchical levels. J Cell Sci. 116, 4067-4075.
Vleghels I, Hontelez J, Ribeiro A, Fransz P, Bisseling T, Franssen H. (2003) Expression of ENOD40 during tomato plant development. Planta 218, 42-49.
Fransz P., Soppe W. and Schubert I. (2003) Heterochromatin in interphase nuclei of Arabidopsis. Chrom. Res. Chrom. Res. 11, 227-240.
Greil, F., I. Van Der Kraan, et al. (2003). "Distinct HP1 and Su(var)3-9) complexes bind to sets of developmentally co-expressed genes depending on chromosomal location." Genes and Development 17: 2825-38.
Koornneef M., Fransz P. and De Jong J.H. (2003) Cytogenetic tools for Arabidopsis thaliana. Chrom. Res. Chrom. Res. 11, 183-194.
Politz, J., R. van Driel, et al. (2003). "From linear genome sequence to three-dimensional organization of the cell nucleus." Genome Biol 4(3): 310.
Probst A.V , Mittelsten Scheid O., Fransz P.F. and Paszkowski J. (2003) Transcriptional reactivation can modify or maintain properties and organization of heterochromatin. Plant J. 33, 743–749
Verschure PJ, Van der Kraan I, Manders EMM, Houtsmuller AB, Van Driel R (2003): Chromatin domains in the mammalian cell nucleus are accessible for large macromolecules. EMBO Rep. 4: 861-866.

2002
Chandler, V.L., Stam, M. and Sidorenko, L.V. (2002) Long distance cis and trans interactions mediate paramutation. In: Advances in Genetics, Vol. 46. J.C. Dunlap and C.-ting Wu. Academic Press, San Diego, USA, pp. 215-234.
Fransz P.F. and De Jong J.H. (2002) Chromatin dynamics in plants. Curr. Opin. Plant Biol. 5, 560-567.
Fransz P. , De Jong J.H., Lysak M., Ruffini Castiglione M. and Schubert I. (2002) Interphase chromosomes in Arabidopsis are organised as well-defined chromocenters from which euchromatin loops emanate. Proc. Natl. Acad. Sci. 99, 14584 – 14589.
Soppe W.J.J., Jasencakova Z., Houben A., Kakutani T., Meister A., Huang H.S., Jacobsen S.E., Schubert I. and Fransz P.F. (2002) DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis EMBO J. 21, 6549-6559.
Stam, M., Belele, C., Ramakrishna, W., Dorweiler, J., Bennetzen, J. and Chandler, V.L. (2002) The regulatory regions required for B’ paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162, 917-930.
Van Driel, R. (2002). Method for the detection of mammalian carcinomas. Netherlands.
Verschure, P. J., I. Van Der Kraan, et al. (2002). "Large-scale chromatin organization and the localization of proteins involved in gene expression in human cells." J Histochem Cytochem 50(10): 1303-12.

2001
Haupt W., Fischer T.C.,  Winderl S., Fransz P. and Torres-Ruiz R.A. (2001)  The CENTROMERE1 (CEN1) region of Arabidopsis thaliana: architecture and chromatin and its impact on gene expression, recombination and size estimation of centromeres. Plant J. 27, 285-297.
Kulikova O., Gualtieri G., Geurts R., Kim D.-J, Cook D., Huguet T., de Jong J.H., Fransz P.F. and Bisseling T. (2001) Integration of the FISH-pachytene and genetic maps of Medicago truncatula Plant J. 27, 49-58.
Lysak M. A., Fransz  P.F, Ali H.B.M.  and Schubert I. (2001) Chromosome painting in Arabidopsis thaliana. The Plant Journal 28, 689-697.
Mone MJ, Volker M, Nikaido O, Mullenders LHF, Van Zeeland AA, Verschure PJ, Manders EMM and Van Driel R (2001): Local induced DNA damage in cell nuclei results in local transcription inhibition. EMBO Rep. 21: 1013-1017.
Passarinho P.A., van Hengel A.J., Fransz P.F. and de Vries S.C. (2001) Expression of the Arabidopsis thaliana AtEP3/AtchitIV endochitinase gene. Planta 212, 556-567.
Schubert I, Fransz P.F., Fuchs J. and de Jong J.H. (2001) Chromosome painting in plants.Methods in Cell Science23: 57–69.
Stam, M., Belele, C., Dorweiler, J and Chandler, V.L. (2002) Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes and Development 16, 1906-1918.
Van Driel, R. (2001). "Kun je Leven uitrekenen?" Kanker 25(2): 22-22.
Volker, M., M. J. Mone, et al. (2001). "Sequential assembly of the nucleotide excision repair factors in vivo." Mol Cell 8(1): 213-24.

2000
CMarko D, Verschure PJ, Rothblum LI, Hernandez-Verdun D, Amalric F, Van Driel R, Fakan S (2000): Ultrastructural analysis of nucleolar transcription in the cells microinjected with 5-bromo-UTP. Histochem. Cell Biol. 113:181-187.
De Leeuw, W., R. Van Liere, et al. (2000). "Visualization of Time Dependent Confocal Microscopy Data." Proceedings IEEE Visualization 2000: 473-476.
De Jong J.H., X.-B. Zhong, P.F. Fransz, J. Wennekes-van Eden, E. Jacobsen and P. Zabel (2000) High resolution FISH reveals the molecular and chromosomal organisation of repetitive sequences of individual tomato chromosomes. In: Chromosomes today. Vol 13, E. Olmo and C.A. Redi (eds), Birkhäuser Verlag, Basel-Boston-Berlin.
Fransz P., Armstrong S., De Jong J.H., Parnell L., Van Drunen C.M., Dean C., Zabel P., Bisseling T. and Jones G. (2000) Integrated Cytogenetic Map of Chromosome Arm 4S of A. thaliana: Structural Organization of Heterochromatic Knob and Centromere Region. Cell 100, 367-376.
Stam, M., de Bruin, R., Van Blokland, R., Van der Hoorn, R.A.L., Mol, J.N.M. and Kooter, J. (2000) Distinct features of post-transcriptional gene silencing by antisense transgenes in single copy and inverted T-DNA repeat loci. Plant J. 21, 27-42.
Steimer A., Amedeo P., Fransz P., Afsar K., Mittelsten Scheid O. and Paszkowski J. (2000) Endogenous targets of transcriptional gene silencing in Arabidopsis thaliana. Plant Cell 12, 1165-1178.
van der Vlag, J., J. L. den Blaauwen, et al. (2000). "Transcriptional repression mediated by polycomb group proteins and other chromatin-associated repressors is selectively blocked by insulators." Journal of Biological Chemistry 275(1): 697-704.
Tabata S, Kaneko T, et al. (2000) Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature 408, 823-826.
Vergunst A.C, L.E.T Jansen, P.F. Fransz, J.H. de Jong and P.J.J. Hooykaas (2000) Cre/lox-mediated recombination in Arabidopsis: evidence for transmission of a translocation and a deletion event. Chromosoma 109, 287-297.