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| Chromosome Structure and Function
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Analysis of cell-cycle dependent post-translational histone modifications
Histone phosphorylation has been linked to chromosome condensation/segregation, activation of transcription, apoptosis and DNA damage repair. In plants, the cell cycle dependent phosphorylation of histone H3 has been described; it is hyperphosphorylated at serines 10/28 and at threonines 3/11 during both mitosis and meiosis in patterns that are specifically coordinated in both space and time. Although this post-translational modification is highly conserved, data show that the chromosomal distribution of individual modifications can differ between groups of eukaryotes. Initial results indicate that members of the plant Aurora kinase family have the capacity to control cell cycle regulated histone H3 phosphorylation. The analysis of other potential H3 kinases and its interaction partners is in progress.
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Model: In plants the cell cycle dependent phosphorylation at H3T11/3 may serve as a signal for other proteins involved in chromosome condensation, while H3S10/28ph is involved sister chromatid cohesion at the pericentromeres of metaphase chromosomes during mitosis and meiosis II. Aurora-like kinase phosphorylates H3 at S10/28. |
Analysis of the function and evolution of B chromosomes
B chromosomes are dispensable components of the genomes of numerous plant and animal species. They do not pair with any of the standard A chromosomes at meiosis, by definition, and have irregular modes of inheritance. Bs are generally assumed to be genetically inactive, because no major genes with specific phenotypic effects, necessary for normal development, are known to occur on these chromosomes. The origin of B chromosomes remains obscure but it is likely that those of different organisms arose in different ways. It is has been argued that Bs could be derived from A chromosomes or from sex chromosomes. Since, B chromosomes of maize and B. dichromosomatica contain sequences that originate from different A chromosomes, B chromosomes could also represent an amalgamation of sequences coming from several A chromosomes.
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One species with an extraordinary plasticity of the genome is an Australian member of the Asteraceae Brachycome dichromosomatica (synonym Brachyscome dichromosomatica). B. dichromosomatica is an annual outbreeder with only two pairs of A chromosomes that occurs in four karyotypically distinct cytodemes. In addition to supernumerary A chromosome fragments different types of B chromosomes may be found within a single plant. These are the somatically stable large B chromosomes and the somatically unstable dot-like micro B chromosomes. Image shows a mitotic cell of B. dichromosomatica (2n = 4 chromosomes + 2 standard B chromosomes and 2 iso-micro B chromosomes) after fluorescence in situ hybridisation (FISH) performed with a micro B specific probe (in yellow) and a standard B centromere-specific probe (in blue). |
iii) Analysis of mechanisms involved in inter- and intraspecifc hybridisation.
Heterosis is a genetic phenomenon sometimes observed when two inbred strains are crossed. This phenomenon was defined by Shull (1911) as ‘the superiority of heterozygous genotypes with respect to one or more characters in comparison with the corresponding homozygous’ parental lines. Such 'hybrid vigour' is often manifested in increased size and growth rate of the organisms. Although the application of heterosis to the breeding and development of crop hybrids (eg. maize, wheat) has made an enormous contribution to 20th century agriculture, the genetic basis for this phenomenon remains conjectural. We analyse the relationship between heterosis and changes in chromatin composition at the global genome and single gene level in plants. Epigenetic modifications of DNA and histones will be compared between inbred lines and hybrids of Arabidopsis thaliana.
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| 2011 |
AGUECI, F., T. RUTTEN, D. DEMIDOV & A. HOUBEN
| Arabidopsis AtNek2 kinase is essential and associates with microtubules. Plant Molecular Biology Reporter, in press. |
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| 2011 |
AREFIAN, E., J. KIANI, M. SOLEIMANI, S.A. SHARIATI, S.H. AGHAEE-BAKHTIARI, A. ATASHI, Y. GHEISARI, N. AHMADBEIGI, A.M. BANAEI-MOGHADDAM, M. NADERI, N. NAMVARASL, L. GOOD & O.R. FARIDANI
| Analysis of microRNA signatures using size-coded ligation-mediated PCR. Nucleic Acids Research. 2011 doi:10.1093/nar/gkr214 |
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| 2011 |
BANAEI, M.A., F. ROUDIER, M. SEIFERT, C. BéRARD, M.-L. MARTIN MAGNIETTE, R. KARIMI, A. HOUBEN, V. COLOT, M.F. METTE
| Additive inheritance of histone modifications in Arabidopsis thaliana intraspecific hybrids. Plant Journal 67: 691-700. |
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| 2011 |
BANDOPADHYAY, R., S. RUSTGI, R.K. CHAUDHURI, P. KHURANA, J.P. KHURANA, A.K. TYAGI, H.S. BALYAN, A. HOUBEN & P.K. GUPTA
| Use of methylation filtration and C(0)t fractionation for analysis of genome composition and comparative genomics in bread wheat. J Genet Genomics 38: 315-325. |
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| 2011 |
HECKMANN, S., I. LERMONTOVA, B. BERCKMANS, L. DE VEYLDER, H. BÄUMLEIN & I. SCHUBERT
| The E2F transcrition factor family regulates CENH3 expression in Arabidopsis thaliana. Plant Journal, DOI: 10.1111/j.1365-313X.2011.04715.x. |
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| 2011 |
HECKMANN, S., E. SCHROEDER-REITER, K. KUMKE, L. MA, K. NAGAKI, M. M. MURATA, G. WANNER & A. HOUBEN
| Holocentric chromosomes of Luzula elegans are characterized by a longitudinal centromere groove, chromosome bending and a terminal nucleolus organizer region. Cytogenetics Genome Research, in press. |
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| 2011 |
HOUBEN, A., K. KUMKE, K. NAGAKI & G. HAUSE
| CENH3 distribution and differential chromatin modifications during pollen development in rye (Secale cereale L). Chromosome Research 19: 471-480. |
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| 2011 |
HOUBEN, A., S. NASUDA, & T.R. ENDO
| Plant B chromosomes. Methods Mol Biol 701: 97-111. |
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| 2011 |
HOUBEN, A., M. SANEI & R. PICKERING
| Barley doubled-haploid production by uniparental chromosome elimination. Plant Cell Tissue and Organ Culture 3: 321-327. |
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| 2011 |
KARIMI, R., M.A. BANAEI, V. SCHUBERT, T. RUTTEN, J. FUCHS, D. DEMIDOV, F. BLATTNER, & A. HOUBEN
| AtHaspin phosphorylates histone H3 at threonine 3 during mitosis and contributes to embryonic patterning in Arabidopsis. Plant Journal , in press. |
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| 2011 |
MARQUES, A., J. FUCHS, L. MA, S. HECKMANN, M. GUERRA & A. HOUBEN
| Characterization of eu- and heterochromatin of Citrus with a focus on the condensation behaviour of 45S rDNA chromatin. Cytogenetics and Genome Research 134: 72-82. |
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| 2011 |
PEDERSEN, D.S., F. COPPENS, L. MA, M. ANTOSCH, B. MARKTL, T. MERKLE, G.T.S. BEEMSTER, A. HOUBEN & K.D. GRASSER
| The plant-specific family of DNA-binding proteins containing three HMG-box domains interacts with mitotic and meiotic chromosomes. New Phytologist, in press. |
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| 2011 |
SANEI, M., R. PICKERING, K. KUMKE, S. NASUDA & A. HOUBEN
| Loss of CENH3 from centromeres preceds uniparental chromosome elimination in interspecific barley hybrids. PNAS USA, in press. |
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| 2011 |
SCHUBERT, V., A. MEISTER, H. TSUJIMOTO, T. ENDO & A. HOUBEN
| Similar rye A and B chromosome organization in meristematic and differentiated interphase nuclei. Chromosome Research, in press. |
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| 2011 |
TEO, C.H., L. MA, E. KAPUSI, G. HENSEL, J. KUMLEHN, I. SCHUBERT, A. HOUBEN & M.F. METTE
| Induction of telomere-mediated chromosomal truncation and stability of truncated chromosomes in Arabidopsis thaliana. Plant Jounal, in press.
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| 2010 |
BANAEI MOGHADDAM, A.M., J. FUCHS, T. CZAUDERNA, A. HOUBEN & F.M. METTE
| Intraspecific hybrids of Arabidopsis thaliana revealed no gross alterations in endopolyploidy, DNA methylation, histone modifications and transcript levels. Theor. Appl. Genet. 120: 215-226. |
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| 2010 |
HOUBEN, A., M. SANEI & R. PICKERING
| Barley doubled-haploid production by uniparental chromosome elimination, PCTOC. Journal of Plant Biotechnology, in press. |
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| 2010 |
KACZMARCZYK, A., A. HOUBEN, E.R.J. KELLER & F.M. METTE
| The influence of cryoconservation on the cytosine methylation state of potato genomic DNA. Cryoletters 31: 380-391. |
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| 2010 |
KOTSERUBA, V., K. PISTRICK, F.R. BLATTNER, K. KUMKE, O. WEISS, T. RUTTEN, J. FUCHS, T. ENDO, S. NASUDA, A. GHUKASYAN & A. HOUBEN
| The evolution of the hexaploid grass Zingeria kochii (Mez) Tzvel. (2n = 12) was accompanied by complex hybridization and uniparental loss of ribosomal DNA. Molecular Phylogenetics and Evolution 56: 146-155. |
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| 2010 |
LOLAS, I.B., K. HIMANEN, J. GRØNLUND, T.C. LYNGAARD, A. HOUBEN, M. MELZER, M. VAN LIJSEBETTENS & K.D. GRASSER
| The transcript elongation factor FACT affects Arabidopsis vegetative and reproductive development and genetically interacts with HUB1/2. Plant J. 61: 686–697. |
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| 2010 |
MA, L., T.H. GIANG, G.T.H. VU, V. SCHUBERT, K. WATANABE, N. STEIN, A. HOUBEN & I. SCHUBERT
| Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH. Chromosome Res. 18(7): 841-850. |
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| 2010 |
MARQUES, A., J. FUCHS, L. MA, S. HECKMANN, M. GUERRA & A. HOUBEN
| Characterization of eu- and heterochromatin of Citrus with a focus on the condensation behaviour of 45S rDNA chromatin. Cytogenetics and Genome Research, in press. |
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| 2010 |
NELISSEN, H., D. FLEURY, S. DE GROEVE, L. BRUNO, T. YAMAGUCHI, E. PRINSEN, G. CNOPS, P. NEYT, B. BITONTI, M. DE BLOCK, E. WITTERS, G. DE JAEGER, H. TSUKAYA, A. HOUBEN & M. VAN LIJSEBETTENS
| The Arabidopsis Elongator complex represses stress response and promotes growth through hormone signaling. PNAS USA 107: 1678-1683. |
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| 2010 |
SANEI, M., R. PICKERING, J. FUCHS, A.M. BANAEI MOGHADDAM, A. DZIURLIKOWSKA & A. HOUBEN
| Interspecific hybrids of Hordeum marinum ssp. marinum x H. bulbosum are mitotically stable and reveal no gross alterations in chromatin properties. Cytogenet. Genome Res. 129: 110-116. |
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| 2009 |
CARCHILAN, M., K KUMKE, S MIKOLAJEWSKI & A. HOUBEN
| Rye B chromosomes are weakly transcribed and might alter the transcriptional activity of A chromosome sequences. Chromosoma 118: 607-616. |
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| 2009 |
DEMIDOV, D., H. HESSE, A. TEWES, T. RUTTEN, J. FUCHS, R. KARIMI, S. LEIN, A. FISCHER, G. REUTER & A. HOUBEN
| Aurora1 phosphorylation activity on histone H3 and its cross talk with other post-translational histone modifications in Arabidopsis. Plant Journal 59: 221-230. |
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| 2009 |
DHAR, M.K., J. FUCHS & A. HOUBEN
| Distribution of eu- and heterochromatin of Plantago ovata. Genome 125: 235-240. |
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| 2009 |
HOUBEN, A.
| Chromosome microdissection and utilization of microisolated DNA. In: Plant Cytogenetics, Vol. 1: Genome Structure and Chromosome Function, Eds.: Bass, H. and Birchler, J.A., Springer-Verlag New York, USA, in press. |
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| 2009 |
HOUBEN, A.
| Chromosome strucuture and function. Preface. Cytogenet. Genome Res. 124: 191-192. |
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| 2009 |
HOUBEN, A. & M. CARCHILAN
| Plant B chromosomes – What makes them different? In: Plant Cytogenetics, Vol. 1: Genome Structure and Chromosome Function, Eds.: Bass, H. and Birchler, J.A., Springer-Verlag New York, USA, in press. |
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| 2009 |
HOUBEN, A. & R. PICKERING
| Applying Cytogenetics and Genomics to Wide Hybridisations in the Genus Hordeum. In: Genetics and Genomics of Triticeae, edited: C. Feuillet, J. Muehlbauer, Springer-Verlag New York, USA, pp. 137-162. |
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| 2009 |
SEIFERT, M., A. BANAEI, J. KEILWAGEN, M.F. METTE, A. HOUBEN, F. ROUDIER, V. COLOT, I. GROSSE & M. STRICKERT
| Array-based Genome Comparison of Arabidopsis Ecotypes Using Hidden Markov Models, Proceedings of Biosignals 2009, Second International Conference on Bio-inspired Systems and Signal Processing, ISBN: 978-989-8111-65-4, p. 3-11. |
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| 2009 |
WICKER, T., S. TAUDIEN, A. HOUBEN, B. KELLER, A. GRANER, M. PLATZER & N. STEIN
| A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size equilibrium in wheat and barley. Plant Journal 59: 712-722. |
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| 2008 |
CAPERTA, A., M. ROSA, M. DELGADO, R. KARIMI, D. DEMIDOV, W. VIEGAS & A. HOUBEN
| Distribution patterns of phosphorylated Thr 3 and Thr 32 of histone H3 in mitosis and meiosis of plants. Cytogenet. Genome Res.112: 73-79. |
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| 2008 |
COHEN, S., A. HOUBEN & D. SEGAL
| Existence of extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plant genomes. Plant Journal 53: 1027-1034. |
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| 2008 |
HOUBEN, A., R.K. DAWE, J. JIANG & I. SCHUBERT
| Engineered Plant Minichromosomes - A Bottom-Up Success? Plant Cell 20: 8-10. |
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| 2008 |
JONES, R.N., W. VIEGAS & A. HOUBEN
| A Century of B A Century of B Chromosomes in plants – so what? Annals of Botany 101: 767-775. |
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| 2008 |
KUMKE, K., R.N. JONES & A. HOUBEN
| B chromosomes of Puschkinia libanotica are characterized by a reduced level of euchromatic histone H3 methylation marks. Cytogenet Genome Res. 121: 266-270. |
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| 2008 |
LILDBALLE, D.L., D.S. PEDERSEN, R. KALAMAJKA, J. EMMERSEN, A. HOUBEN & K.D. GRASSER
| The expression level of the chromatin-associated HMGB1 protein influences growth, stress tolerance and transcriptome in Arabidopsis. Journal of Molecular Biology 384: 9-21. |
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| 2007 |
CARCHILAN, M., M. MARGARIDA DELGADO, T. TERESA RIBEIRO, P. COSTA-NUNES, A. CAPERTA, L. MORAIS-CECILIO, R.N. JONES, W. VIEGAS & A. HOUBEN
| Transcriptionally active heterochromatin in rye B chromosomes. Plant Cell 19: 1738-1749. |
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| 2007 |
GERNAND, D., H. GOLCZYK, T. RUTTEN, T. ILNICKI, A. HOUBEN & A.J. JOACHIMIAK
| Tissue culture triggers chromosome alterations, amplification and transposition of repeat sequences in Allium fistulosum. Genome 50: 435-442. |
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| 2007 |
HOUBEN, A., D. DEMIDOV, A.D. CAPERTA, R. KARIMI, F. AGUECI & L. VLASENKO
| Phosphorylation of histone H3 in plants – a dynamic affair. Biochimica et Biophysica Acta 1769: 308-315. |
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| 2007 |
HOUBEN, A., E. SCHROEDER-REITER, K. NAGAKI, S. NASUDA, G. WANNER, M. MURATA & T. ENDO
| CENH3 interacts with the centromeric retrotransposon cereba and GC-rich satellites and locates to centromeric substructures in barley. Chromosoma 116: 275-283. |
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| 2007 |
HOUBEN, A. & I. SCHUBERT
| Engineered plant minichromosomes - a resurrection of B chromosomes? Plant Cell 19: 2323-2327. |
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| 2007 |
HOUBEN, A. & I. SCHUBERT
| The cytogenetics and genomics of crop plants. Chromosome Research 15: 1-2. |
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| 2007 |
JONES, R.N., W. VIEGAS & A. HOUBEN
| A Century of B Chromosomes in plants - so what? Annaly of Botany. Annals of Botany, in press. |
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| 2007 |
MARSCHNER, S., K. KUMKE & A. HOUBEN
| B chromosomes of B. dichromosomatica show a reduced level of euchromatic histone H3 methylation marks. Chromosome Research 15: 215-222. |
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| 2007 |
MARSCHNER, S., A. MEISTER, F.R. BLATTNER & A. HOUBEN
| Evolution and function of B chromosomal 45S rDNA sequences in Brachycome dichromosomatica. Genome 50: 638-644. |
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| 2007 |
SCHUBERT, V., Y.M. KIM, A. BERR, J. FUCHS, A. MEISTER, S. MARSCHNER & I. SCHUBERT
| Random homologous pairing and incomplete sister chromatid alignment are common in angiosperm interphase nuclei. MGG 278: 167-176 |
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| 2007 |
TIKHENKO, N., T. RUTTEN, A. VOYLOKOV & A. HOUBEN
| Analysis of hybrid lethality in F1 wheat-rye hybrid embryos. Euphytica 159: 367-375. |
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| 2006 |
CAPERTA, A.D., M. DELGADO, F. RESSUREIÇÃO, A. MEISTER, N. JONES, W. VIEGAS & A. HOUBEN
| Polyploidization of rye cells induced by colchicine is concentration dependent and associated with the formation of new tubulin containing structures. Protoplasma 227: 147-153. |
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| 2006 |
FIELD, B.L., A. HOUBEN, J.N. TIMMIS & C.R. LEACH
| Internal transcribed spacer sequence analyses indicate cytoevolutionary patterns within Brachycome (Asteraceae). Plant Systematics and Evolution 129: 39-51. |
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| 2006 |
FUCHS, J., D. DEMIDOV, A. HOUBEN & I. SCHUBERT
| Chromosomal histone modification patterns – from conservation to diversity. Trends in Plant Science 11: 199-208. |
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| 2006 |
GERNAND, D., T. RUTTEN, R. PICKERING & A. HOUBEN
| Elimination of chromosomes in Hordeum vulgare x H. bulbosum crosses at mitosis and interphase involves micronucleus formation and progressive heterochromatinization. Cytogenetics Genome Research 114: 169-174. |
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| 2006 |
HOUBEN, A., S.J. ORFORD & J.N. TIMMIS
| In situ hybridization to plant tissues and chromosomes. Methods Mol. Biol. 326: 203-218. |
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| 2006 |
LAUNHOLT, D., T. MERKLE, A. HOUBEN, A. SCHULZ & K.D. GRASSER
| Chromatin-associated HMGA and HMGB proteins use different signals for nuclear targeting and display a highly dynamic localization within the cell nucleus. Plant Cell 18: 2904-2918. |
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| 2006 |
LEACH, R.C., I.S. DUNDAS & A. HOUBEN
| Construction of comparative genetic maps of two 4BS.4BL-5RL translocations in bread wheat Triticum aestivum L. Genome 49: 729-734. |
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| 2006 |
MÜLLER, F., A. HOUBEN, P.E. BARKER, Y. XIAO, J.A. KÄS & M. MELZER
| Quantum dots – a versatile tool in plant science? Journal of Nanobiotechnology 4, 5. |
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| 2006 |
SCHROEDER-REITER, E., A. HOUBEN, J. GRAU & G. WANNER
| Characterization of a peg-like terminal NOR structure with light microscopy and high resolution scanning electron microscopy. Chromosoma 115: 50-59. |
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| 2005 |
DEMIDOV, D., D. VAN DAMME, D. GEELEN, F.R. BLATTNER & A. HOUBEN
| Identification and dynamics of two classes of Aurora-like kinases in Arabidopsis and other plants. Plant Cell 17: 836-848. |
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| 2005 |
GERNAND, D., T. RUTTEN, A. VARSHNEY, M. RUBTSOVA, S. PRODANOVIC, C. BRÜß, J. KUMLEHN, F. MATZK & A. HOUBEN
| Uniparental chromosome elimination at mitosis and interphase in wide crosses involves micronucleus formation, progressive heterochromatinization and DNA fragmentation. Plant Cell 17: 2431-2438. |
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| 2005 |
HOUBEN, A., D. DEMIDOV, T. RUTTEN & K.H. SCHEIDTMANN
| Novel phosphorylation of histone H3 at threonine 11 that temporally correlates with condensation of mitotic and meiotic chromosomes in plant cells. Cytogenetic and Genome Research 109:148-155. |
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| 2005 |
KOTSERUBA, V., K. PISTRICK, D. GERNAND, A. MEISTER, A. GHUKASYAN, I. GABRIELYAN & A. HOUBEN
| Characterisation of the low-chromosome number grass Colpodium versicolor (Stev.) Schmalh. (2n = 4) by molecular cytogenetics. Caryologia 58: 241-245. |
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| 2005 |
LEACH, C.R., A. HOUBEN, B. FIELD, K. PISTRICK, D. DEMIDOV & J.N. TIMMIS
| Molecular evidence for transcription of B chromosome ribosomal RNA genes in Crepis capillaris. Genetics 171: 269-278. |
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| 2005 |
NASUDA, S., S. HUDAKOVA, I. SCHUBERT, A. HOUBEN & T.R. ENDO
| Stable barley chromosomes without centromeres repeats - the first fully functional neocentromeres in plants? Proc. Natl. Acad. Sci. USA 103: 9842-9847. |
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| 2004 |
DUROUX, M., A. HOUBEN, K. RUZICKA, J. FRIML & K. GRASSER
| The chromatin-remodelling complex FACT associates with actively transcribed regions of the Arabidopsis genome. Plant J. 40: 660-671. |
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| 2004 |
LEACH, C.R., A. HOUBEN & J.N. TIMMIS
| The B chromosomes in Brachycome. Cytogenetic and Genome 106: 199-209. |
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| 2004 |
PICKERING, R.A., S. HUDAKOVA, A. HOUBEN, P.A. JOHNSTON & R.C. BUTLER
| Reduced metaphase I associations between the short arms of homoeologous chromosomes in a Hordeum vulgare L. x H. bulbosum L. diploid hybrid influences the frequency of recombinant progeny. Theor. Appl. Genet. 109: 911-916. |
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