Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    AIL and HDG proteins act antagonistically to control cell proliferation
    Horstman, A. ; Fukuoka, H. ; Muino Acuna, J.M. ; Nitsch, L.M.C. ; Guo, Changhao ; Passarinho, P.A. ; Sanchez Perez, G.F. ; Immink, R.G.H. ; Angenent, G.C. ; Boutilier, K.A. - \ 2015
    Development 142 (2015). - ISSN 0950-1991 - p. 454 - 464.
    arabidopsis-thaliana - transcription factors - plant transformation - ectopic expression - quantitative pcr - chip-seq - differentiation - genes - plethora - growth
    AINTEGUMENTA-LIKE (AIL) transcription factors are key regulators of cell proliferation and meristem identity. Although AIL functions have been well described, the direct signalling components of this pathway are largely unknown.We show that BABY BOOM(BBM) and other AIL proteins physically interact with multiple members of the L1-expressed HOMEODOMAIN GLABROUS (HDG) transcription factor family, including HDG1, HDG11 and HDG12. Overexpression of HDG1, HDG11 and HDG12 restricts growth due to root and shoot meristem arrest, which is associated with reduced expression of genes involved in meristem development and cell proliferation pathways, whereas downregulation of multiple HDG genes promotes cell overproliferation. These results suggest a role for HDG proteins in promoting cell differentiation. We also reveal a transcriptional network in which BBM andHDG1regulate several common target genes, and whereBBM/AIL and HDG regulate the expression of each other. Taken together, these results suggest opposite roles for AIL and HDG proteins, with AILs promoting cell proliferation and HDGs stimulating cell differentiation, and that these functions are mediated at both the protein-protein interaction and transcriptional level.
    Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factorsin flower development
    Pajoro, A. ; Madrigal, P. ; Muiño, J.M. ; Tomas Matus, J. ; Jin, J. ; Mecchia, M.A. ; Debernardi, J.M. ; Palatnik, J.F. ; Balazadeh, S. ; Arif, M. ; Ó’Maoiléidigh, D.S. ; Wellmer, F. ; Krajewski, P. ; Riechmann, J.L. ; Angenent, G.C. - \ 2014
    Genome Biology 15 (2014)3. - ISSN 1474-7596
    floral organ identity - arabidopsis-thaliana - chip-seq - genomic regions - molecular-basis - target genes - zinc-finger - expression - protein - dna
    Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.
    Single-tube linear DNA amplification for genome-wide studies using a few thousand cells
    Shankaranarayanan, P. ; Mendoza-Parra, M.A. ; Gool, W. van; Trindade, L.M. ; Gronemeyer, H. - \ 2012
    Nature protocols 7 (2012)2. - ISSN 1754-2189 - p. 328 - 339.
    t7 rna-polymerase - chip-seq - displacement amplification - limited numbers - chromatin - methylation - challenges - principles - samples - domain
    Linear amplification of DNA (LinDA) by T7 polymerase is a versatile and robust method for generating sufficient amounts of DNA for genome-wide studies with minute amounts of cells. LinDA can be coupled to a great number of global profiling technologies. Indeed, chromatin immunoprecipitation coupled to massive parallel sequencing (ChIP-seq) has been achieved for transcription factors and epigenetic modification of chromatin histones with 1,000 to 5,000 cells. LinDA largely simplifies reChIP-seq experiments to monitor co-binding at chromatin target sites. The single-tube design of LinDA is ideal for handling ultrasmall amounts of DNA (
    Mutational Robustness of Gene Regulatory Networks
    Dijk, A.D.J. van; Mourik, S. van; Ham, R.C.H.J. van - \ 2012
    PLoS ONE 7 (2012)1. - ISSN 1932-6203 - 9 p.
    transcription factor-binding - chip-seq - expression - evolution - evolvability - noise - yeast - autoregulation - dimerization - mechanisms
    Mutational robustness of gene regulatory networks refers to their ability to generate constant biological output upon mutations that change network structure. Such networks contain regulatory interactions (transcription factor – target gene interactions) but often also protein-protein interactions between transcription factors. Using computational modeling, we study factors that influence robustness and we infer several network properties governing it. These include the type of mutation, i.e. whether a regulatory interaction or a protein-protein interaction is mutated, and in the case of mutation of a regulatory interaction, the sign of the interaction (activating vs. repressive). In addition, we analyze the effect of combinations of mutations and we compare networks containing monomeric with those containing dimeric transcription factors. Our results are consistent with available data on biological networks, for example based on evolutionary conservation of network features. As a novel and remarkable property, we predict that networks are more robust against mutations in monomer than in dimer transcription factors, a prediction for which analysis of conservation of DNA binding residues in monomeric vs. dimeric transcription factors provides indirect evidence
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