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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Record number 539038
Title Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana
Author(s) Aerts, Niels; Bruijn, Suzanne de; Mourik, Hilda van; Angenent, Gerco C.; Dijk, Aalt D.J. van
Source BMC Plant Biology 18 (2018)1. - ISSN 1471-2229
DOI https://doi.org/10.1186/s12870-018-1348-8
Department(s) PRI BIOS Applied Bioinformatics
PRI BIOS Plant Development Systems
Laboratory of Molecular Biology
EPS
Biometris (WU MAT)
Publication type Refereed Article in a scientific journal
Publication year 2018
Keyword(s) CArG-box - ChIP-seq - MADS-domain proteins - Sequence conservation - Transcription factor binding specificity
Abstract

Background: Correct flower formation requires highly specific temporal and spatial regulation of gene expression. In Arabidopsis thaliana the majority of the master regulators that determine flower organ identity belong to the MADS-domain transcription factor family. The canonical DNA binding motif for this transcription factor family is the CArG-box, which has the consensus CC(A/T)6GG. However, so far, a comprehensive analysis of MADS-domain binding patterns has not yet been performed. Results: Eight publicly available ChIP-seq datasets of MADS-domain proteins that regulate the floral transition and flower formation were analyzed. Surprisingly, the preferred DNA binding motif of each protein was a CArG-box with an NAA extension. Furthermore, motifs of other transcription factors were found in the vicinity of binding sites of MADS-domain transcription factors, suggesting that interaction of MADS-domain proteins with other transcription factors is important for target gene regulation. Finally, conservation of CArG-boxes between Arabidopsis ecotypes was assessed to obtain information about their evolutionary importance. CArG-boxes that fully matched the consensus were more conserved than other CArG-boxes, suggesting that the perfect CArG-box is evolutionary more important than other CArG-box variants. Conclusion: Our analysis provides detailed insight into MADS-domain protein binding patterns. The results underline the importance of an extended version of the CArG-box and provide a first view on evolutionary conservation of MADS-domain protein binding sites in Arabidopsis ecotypes.

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