Basal Promoter Elements • Basal Promoter Element = BPE • TATA Box: (G or A)TATA(A or T)AA • Nature 381:127-151 (1996) • Science 272:830-836 (1996) • CAAT Box: GGCCAATC • GC Box: GCCACACCC • From class lectures • Control Gene Transcription
Diauxic Shift • Decrease in [Glucose] causes changes in gene transcription • Effect of shift on transcription of every ORF in S. cerevisiae quantified by Yeast Gene Expression Database
Questions • Is the sequence quality of one BPE higher than another? • Does diauxic shift regulation correlate with the quality of TATA, CAAT, or GC boxes? • Quality: How well does the actual sequence match the “ideal”?
The Program • I wrote a program which finds the closest match to any given “ideal” sequence. • Scoring: Points given for each ‘correct’ base, then normalized to 1. • The search is exhaustive. • Entire sequence between previous stop codon and start codon scanned for matches
3 types of diauxic regulation • Upregulated (22 sequences): • <2X at [Glucose] = 14 g/L • >5X at [Glucose] = 0.2 g/L • Downregulated (18 sequences): • >0.47X at [Glucose] = 14 g/L • <0.23X at [Glucose] = 0.2 g/L • Control (10 sequences) • Never >2X or <0.5X
Method • The program analyzed each sequence. • Average BPE quality scores for Upregulated, Downregulated, and Control sequences were computed.
Future Directions • Are the ideal sequences accurate for Saccharomyces? • Does the quality of the boxes correlate with other relative events? • e.g., pH, temperature, salt concentration • Do other protein binding sequences correlate with diauxic shift?