A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana.

Søren Lindemose, Michael Krogh Jensen, Jan Van de Velde, Charlotte O'Shea, Ken S. Heyndrickx, Christopher Workman, Klaas Vandepoele, Karen Skriver, Federico De Masi

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Abstract

Target gene identification for transcription factors is a prerequisite for the systems wide understanding of organismal behaviour. NAM-ATAF1/2-CUC2 (NAC) transcription factors are amongst the largest transcription factor families in plants, yet limited data exist from unbiased approaches to resolve the DNA-binding preferences of individual members. Here, we present a TF-target gene identification workflow based on the integration of novel protein binding microarray data with gene expression and multi-species promoter sequence conservation to identify the DNA-binding specificities and the gene regulatory networks of 12 NAC transcription factors. Our data offer specific single-base resolution fingerprints for most TFs studied and indicate that NAC DNA-binding specificities might be predicted from their DNA-binding domain's sequence. The developed methodology, including the application of complementary functional genomics filters, makes it possible to translate, for each TF, protein binding microarray data into a set of high-quality target genes. With this approach, we confirm NAC target genes reported from independent in vivo analyses. We emphasize that candidate target gene sets together with the workflow associated with functional modules offer a strong resource to unravel the regulatory potential of NAC genes and that this workflow could be used to study other families of transcription factors.
Original languageEnglish
JournalNucleic acids research
Volume42
Issue number12
Pages (from-to)7681-7693
Number of pages13
ISSN0305-1048
DOIs
Publication statusPublished - 2014

Keywords

  • Gene regulation, Chromatin and Epigenetics

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