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  • Template-based structure prediction and classification of transcription factors in Arabidopsis thaliana

    Author(s)
    Lu, Tao
    Yang, Yuedong
    Yao, Bo
    Liu, Song
    Zhou, Yaoqi
    Zhang, Chi
    Griffith University Author(s)
    Zhou, Yaoqi
    Yang, Yuedong
    Year published
    2012
    Metadata
    Show full item record
    Abstract
    Transcription factors (TFs) play important roles in plants. However, there is no systematic study of their structures and functions of most TFs in plants. Here, we performed template-based structure prediction for all TFs in Arabidopsis thaliana, with their full-length sequences as well as C-terminal and N-terminal regions. A total of 2918 model structures were obtained with a high confidence score. We find that TF families employ only a smaller number of templates for DNA-binding domains (DBD) but a diverse number of templates for transcription regulatory domains (TRD). Although TF families are classified according to DBD, ...
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    Transcription factors (TFs) play important roles in plants. However, there is no systematic study of their structures and functions of most TFs in plants. Here, we performed template-based structure prediction for all TFs in Arabidopsis thaliana, with their full-length sequences as well as C-terminal and N-terminal regions. A total of 2918 model structures were obtained with a high confidence score. We find that TF families employ only a smaller number of templates for DNA-binding domains (DBD) but a diverse number of templates for transcription regulatory domains (TRD). Although TF families are classified according to DBD, their sizes have a significant correlation with the number of unique non-DNA-binding templates employed in the family (Pearson correlation coefficient of 0.74). That is, the size of TF family is related to its functional diversity. Network analysis reveals new connections between TF families based on shared TRD or DBD templates; 81% TF families share DBD and 67% share TRD templates. Two large fully connected family clusters in this network are observed along with 69 island families. In addition, 25 genes with unknown functions are found to be DNA-binding and/or TF factors according to predicted structures. This work provides a global view of the classification of TFs based on their DBD or TRD templates, and hence, a deeper understanding of DNA-binding and regulatory functions from structural perspective.
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    Journal Title
    Protein Science
    Volume
    21
    Issue
    6
    DOI
    https://doi.org/10.1002/pro.2066
    Subject
    Biochemistry and cell biology
    Theory of computation
    Other information and computing sciences
    Publication URI
    http://hdl.handle.net/10072/90014
    Collection
    • Journal articles

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