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Promoter motif analysis

SX Shichao Xin
YH Yuwei Hua
JL Ji Li
XD Xuemei Dai
XY Xianfeng Yang
JU Jinu Udayabhanu
HH Huasun Huang
TH Tiandai Huang
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To identify the potential cis-regulatory elements and transcription factors involved in latex molecular weight regulation, we studied the promoters of those upregulated genes in IPP-generating pathways in latex samples from 30-year-old trees of RRIM600. The 1000 bp sequences upstream of the transcription start site of these genes were extracted for motif discovery. The MEME suite was used in classic mode to identify enriched motifs [36], with the following parameters: maximum number of motifs = 12, minimum motif width = 6, maximum motif width = 14 and background model set to 1st order. Using the TomTom tool from the MEME suite with default parameters, the top three statistically significant (low E-value) motifs for each gene set were searched against the Arabidopsis DAP motif database to identify potential transcription factors (TFs) capable of recognizing those enriched motifs. The expression levels of these TF genes in four latex samples were further analyzed.

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