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Identification and Characterization of Promoters in Silkworm Based on Gene Expression Data

Author: YinZhiMing
Tutor: XiaQingYou
School: Southwestern University
Course: Biochemistry and Molecular Biology
Keywords: Bombyx mori promoter prediction testis specific promoter TFBS
CLC: Q75
Type: Master's thesis
Year: 2011
Downloads: 21
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Abstract


Promoters are important elements in gene transcriptional control, which accomplish the reasonable differentiation and development of the organism by regulate the transcription of the mRNA. The research on the structure and function of promoters is important for the work on gene expression pattern and regulation network. How to identify a promoter quickly and exactly has becoming one of the crucial topics in functional genomics era for its considerable biological functions.Based on the silkworm genome sequences, full-length cDNA sequences and expression data of the silkworm larval 3 days 5 instar, we identified the promoter sequences of some genes, then predicted and analyzed the conserved motifs of the promoters of the testis specific expressed genes The main results are as follows.1. Identify 1341 promoter sequences.This work identified 3137 annotation genes corresponding to full-length cDNA based on the BLAST of full-length cDNA sequences and predicted genes. Using the BLAT to alignment the full-length cDNA sequences and the silkworm genome sequences obtained 1492 Candidate promoter sequences, among the total,743 located on the positive-sense strand and 749 located on the negative-sense strand. Loction of TSS site analysis showed that 1341 promoter sequences located in the 30000bp upstream of the start codon, these sequences were used to analyze the structure features of the promoter.2. Analyze the structure features of the promoter.We identified CpG island in 113 promoters refer to Takai’s classical standard. On the condition of p<le-4, the numbers of promoter containing TATA-box, INR, GC-box, CAAT-box elements are 279,565,398,200, respectively. The arrangements of these elements are conserved, mostly located on 1500bp upstream of the TSS sites. 3. Predict 5 conserved cis-elements in testis specific promoters.Microarray showed that 46 out of all genes corresponding to 1341 promoter are tissue-specific expressed.The number of tissue-specific genes in testis, ovary, midgut, Malpighian tubules, head, silkgland, fat body is 23,6,6,4,3,1,1 respectively. We obtained 10 overrepresented motifs by further analysis of promoter regulatory elements of the testis-specific expressed genes. By test of overrepresented motifs in testis-specific promoters and 3 control groups, the frequency of motif1, motif5, motif6, motif7, motif8 in the testis-specific promoters is much higher than in the 3 control groups, imply that these five testis-specific motifs play an important role in the transcriptional regulation of tissue-specific genes expression.

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