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Plant Development & (Epi)Genetics

Publications Paul Fransz and Maike Stam

Before joining the Plant Development and (Epi)Genetics group, assistant professors Fransz and Stam were part of the Nuclear Organisation Group (NOG) at SILS. Below are their publications with this group from 2009-2015.



Alves Aflitos, S., Sanchez-Perez, G., Ridder, D. de, Fransz, P., Schranz, M.E., Jong, H. de & Peters, S.A. (2015). Introgression browser: high-throughput whole-genome SNP visualization. Plant Journal, 82 (1), 174-182. doi: 10.1111/tpj.12800


Batzenschlager, M., Lermontova, I., Schubert, V., Fuchs, J., Berr, A., Koini, M.A., Houlné, G., Herzog, E., Rutten, T., Alioua, A., Fransz, P., Schmit, A.C. & Chabouté, M.E. (2015). Arabidopsis MZT1 homologs GIP1 and GIP2 are essential for centromere architecture. Proceedings of the National Academy of Sciences of the United States of America, 112 (28), 8656-8660. doi: 10.1073/pnas.1506351112


Bourbousse, C., Mestiri, I., Zabulon, G., Bourge, M., Formiggini, F., Koini, M.A., Brown, S.C., Fransz, P., Bowler, C. & Barneche, F. (2015). Light signaling controls nuclear architecture reorganization during seedling establishment. Proceedings of the National Academy of Sciences of the United States of America, 112 (21), E2836-E2844. doi: 10.1073/pnas.1503512112


Hovel, I., Pearson, N.A. & Stam, M. (2015). Cis-acting determinants of paramutation. Seminars in Cell & Developmental Biology, 44, 22-32. doi: 10.1016/j.semcdb.2015.08.012




Gent, J.I. van, Madzima, T.F., Bader, R., Kent, M.R., Zhang, X., Stam, M., McGinnis, K.M. & Dawe, R.K. (2014). Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation. The Plant Cell, 26 (12), 4903-4917. doi: 10.1105/tpc.114.130427


Lysak, M.A. & Fransz, P.F. (2014). From transposon to chromosome and polyploidy. An update on cytogenetics and genomics of Arabidopsis. Chromosome Research, 22 (2), 99-101. doi: 10.1007/s10577-014-9427-7




Belele, C.L., Sidorenko, L., Stam, M., Bader, R., Arteaga-Vazquez, M.A. & Chandler, V.L. (2013). Specific tandem repeats are sufficient for paramutation-induced trans-generational silencing. PLOS Genetics, 9 (10), e1003773. doi: 10.1371/journal.pgen.1003773


Book chapter

Zanten, M. van, Tessadori, F., Peeters, A.J.M. & Fransz, P. (2013). Environment-Induced Chromatin Reorganisation and Plant Acclimation. In G. Grafi & N. Ohad (Eds.), Epigenetic Memory and Control in Plants (Signaling and Communication in Plants, 18) (pp. 21-40). Heidelberg: Springer-Verlag.



3C Technologies in plants. Authors: Hövel I, Louwers M, Stam M. Methods. 2012 Nov;58(3):204-11 View PubMed


Shedding light on large-scale chromatin reorganization in Arabidopsis thaliana. Authors: van Zanten M, Tessadori F, Peeters AJ, Fransz P. Mol Plant. 2012 May;5(3):583-90 View PubMed


Signals of speciation within Arabidopsis thaliana in comparison with its relatives. Authors: Alcázar R, Pecinka A, Aarts MG, Fransz PF, Koornneef M. Curr Opin Plant Biol. 2012 Apr;15(2):205-11 

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Seed maturation in Arabidopsis thaliana is characterized by nuclear size reduction and increased chromatin condensation. Authors: van Zanten M, Koini MA, Geyer R, Liu Y, Brambilla V, Bartels D, Koornneef M, Fransz P, Soppe WJ. Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20219-24 View PubMed


Programmed cell death in the leaves of the Arabidopsis spontaneous necrotic spots (sns-D) mutant correlates with increased expression of the eukaryotic translation initiation factor eIF4B2. Authors: Gaussand GM, Jia Q, Van Der Graaff E, Lamers GE, Fransz PF, Hooykaas PJ and De Pater S. Front. Plant Sci. 2:9. doi: 10.3389/fpls.2011.00009


From nucleosome to chromosome: a dynamic organization of genetic information. Authors: Fransz P.F. and de Jong J.H. Plant J. 2011 Apr;66(1):4-17 View PubMed



Immunocytological analysis of chromatin in isolated nuclei. Authors: Pavlova, P., Tessadori, F., De Jong, H.J., Fransz P.F. Methods Mol Biol. 2010;655:413-32 View PubMed


Large-scale chromatin de-compaction induced by low light is not accompanied by nucleosomal displacement. Authors: van Zanten, M., Tessadori, F., Bossen, L., Peeters A.J.M., and Fransz P. Plant Signal Behav. 2010 Dec 1;5(12) View PubMed


The role of DNA methylation, nucleosome positioning and histone modifications in paramutation in maize. Authors: Haring M, Bader R, Louwers M, van Driel R, Stam M. Plant J. 2010 Apr 29 63, 366-378 View PubMed


Book chapter

Pavlova, P., Tessadori, F., Jong, H.J. de & Fransz, P. (2010). Immunocytological analysis of chromatin in isolated nuclei. In L. Hennig & C. Köhler (Eds.), Plant developmental biology: methods and protocols (Methods in molecular biology, 655) (pp. 413-432). New York: Humana Press.


Tissue- and expression level-specific chromatin looping at maize b1 epialleles

Authors: Louwers M, Bader R, Haring M, van Driel R, de Laat W and Stam M

Plant Cell. 2009 Mar;21(3):832-42

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Paramutation: A heritable change in gene expression by allelic interactions in trans

Author: Stam M

Mol Plant. 2009 Jul;2(4):578-88

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Paramutation: Heritable in Trans Effects

Authors: Stam, M, Louwers, M

In Handbook of Maize; Genetics and Genomics. Jeff Bennetzen and Sarah Hake (eds). Springer New York. pp 405-427


Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)

Authors: Louwers, M, Splinter, E. van Driel R, de Laat, W and Stam, M

Nat Protoc. 2009;4(8):1216-29

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Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana

Authors: Tessadori, F., van Zanten M., Pavlova P., Clifton R., Pontvianne F., Snoek L.B., Millenaar F.F., Schulkes R.K., van Driel R., Voesenek L.A.C.J., Spillane C., Pikaard C.S., Fransz P., Peeters A.J.M

PLoS Genet. 2009 Sep;5(9):e1000638

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Chromatin Domains and Function

Author: Fransz, P

In Functional Organization of the Plant Nucleus, Volume 14, I. Meier, ed. (Berlin/Heidelberg: Springer), pp. 131-155