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

(2014) NUCLEIC ACIDS RESEARCH. 42(12). p.7681-7693
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
MICROARRAY DATA, PROTEIN, FACTOR FAMILY, ABIOTIC STRESS RESPONSES, GENE, SPECIFICITY, SENESCENCE, SEQUENCE, PROMOTER, DOMAIN

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Citation

Please use this url to cite or link to this publication:

Chicago
Lindemose, Søren, Michael K Jensen, Jan Van de Velde, Charlotte O’Shea, Ken Heyndrickx, Christopher T Workman, Klaas Vandepoele, Karen Skriver, and Federico De Masi. 2014. “A DNA-binding-site Landscape and Regulatory Network Analysis for NAC Transcription Factors in Arabidopsis Thaliana.” Nucleic Acids Research 42 (12): 7681–7693.
APA
Lindemose, S., Jensen, M. K., Van de Velde, J., O’Shea, C., Heyndrickx, K., Workman, C. T., Vandepoele, K., et al. (2014). A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana. NUCLEIC ACIDS RESEARCH, 42(12), 7681–7693.
Vancouver
1.
Lindemose S, Jensen MK, Van de Velde J, O’Shea C, Heyndrickx K, Workman CT, et al. A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana. NUCLEIC ACIDS RESEARCH. 2014;42(12):7681–93.
MLA
Lindemose, Søren, Michael K Jensen, Jan Van de Velde, et al. “A DNA-binding-site Landscape and Regulatory Network Analysis for NAC Transcription Factors in Arabidopsis Thaliana.” NUCLEIC ACIDS RESEARCH 42.12 (2014): 7681–7693. Print.
@article{5709583,
  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.},
  author       = {Lindemose, S{\o}ren and Jensen, Michael K and Van de Velde, Jan and O'Shea, Charlotte and Heyndrickx, Ken and Workman, Christopher T and Vandepoele, Klaas and Skriver, Karen and De Masi, Federico},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {MICROARRAY DATA,PROTEIN,FACTOR FAMILY,ABIOTIC STRESS RESPONSES,GENE,SPECIFICITY,SENESCENCE,SEQUENCE,PROMOTER,DOMAIN},
  language     = {eng},
  number       = {12},
  pages        = {7681--7693},
  title        = {A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1093/nar/gku502},
  volume       = {42},
  year         = {2014},
}

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