Analysis of plant TATA and TATA-less promoters by using sequence and structure features
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This work was supported by a grant from The National Natural Science Foundation of China(30560039)

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    Abstract:

    Analysis of regular elements in promoter region is the base for elucidating the mechanism of gene transcription initiation. The TATA and the TATA-less promoters of plant RNA polymeraseⅡ gene are chosen from the PlanPromDB. The GC bias,position structure conservation,nucleotide content and conservative motifs of sequences,position distribution of TATA box and conservation of correlation position are analyzed. Many specific regulars for the two types of promoters are found. These features can offer some help for revealing the transcription regulation of plant gene. A new prediction algorithm based on position-correlation weight matrix (PCWM) is proposed. The better discrimination results for two sort plant promoters are obtained by using score function. It is confirmed that the performance of position-correlation weight matrix (PCWM) is superior to single-base position weight matrix (PWM).

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ZUO Yong-Chun, LI Qian-Zhong. Analysis of plant TATA and TATA-less promoters by using sequence and structure features[J]. Progress in Biochemistry and Biophysics,2009,36(7):863-871

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History
  • Received:October 23,2008
  • Revised:December 03,2008
  • Accepted:
  • Online: February 23,2009
  • Published: July 20,2009