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Telomere binding protein TRB1 is associated with promoters of translation machinery genes in vivo

Abstract

Recently we characterised TRB1, a protein from a single-myb-histone family, as a structural and functional component of telomeres in Arabidopsis thaliana. TRB proteins, besides their ability to bind specifically to telomeric DNA using their N-terminally positioned myb-like domain of the same type as in human shelterin proteins TRF1 or TRF2, also possess a histone-like domain which is involved in protein–protein interactions e.g., with POT1b. Here we set out to investigate the genome-wide localization pattern of TRB1 to reveal its preferential sites of binding to chromatin in vivo and its potential functional roles in the genome-wide context. Our results demonstrate that TRB1 is preferentially associated with promoter regions of genes involved in ribosome biogenesis, in addition to its roles at telomeres. This preference coincides with the frequent occurrence of telobox motifs in the upstream regions of genes in this category, but it is not restricted to the presence of a telobox. We conclude that TRB1 shows a specific genome-wide distribution pattern which suggests its role in regulation of genes involved in biogenesis of the translational machinery, in addition to its preferential telomeric localization.

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Acknowledgments

We thank Vladimir Benes from the European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Heidelberg, Germany, for valuable comments and recommendations on our ChIP procedure. We also thank Ronald Hancock, Hôtel-Dieu de Québec for critical reading of the manuscript. Access to computing and storage facilities owned by parties and projects contributing to the National Grid Infrastructure MetaCentrum, provided under the programme “Projects of Large Infrastructure for Research, Development, and Innovations” (LM2010005), is greatly appreciated. This research was supported by the Czech Science Foundation (13-06943S) and by project CEITEC (CZ.1.05/1.1.00/02.0068) of the European Regional Development Fund.

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Correspondence to Jiří Fajkus.

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Schrumpfová, P.P., Vychodilová, I., Hapala, J. et al. Telomere binding protein TRB1 is associated with promoters of translation machinery genes in vivo. Plant Mol Biol 90, 189–206 (2016). https://doi.org/10.1007/s11103-015-0409-8

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  • DOI: https://doi.org/10.1007/s11103-015-0409-8

Keywords

  • Telomere repeat binding (TRB)
  • ChIP-seq
  • Arabidopsis thaliana
  • Ribosome
  • snoRNA
  • Translation machinery