Transcriptional Networks BINDING SITES: TRANSCRIPTION FACTORS BIND TO THESE. MAY INDUCE AND MAY REPRESS.

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Presentation transcript:

Transcriptional Networks BINDING SITES: TRANSCRIPTION FACTORS BIND TO THESE. MAY INDUCE AND MAY REPRESS.

Compare Expression Time 1 Time 2 Time 3 Time 4 ACGGGC GGCGAC CACAAA CAGGTA CCCAAC CGTTAA CACAAA CAGGTA Time 1 Time 2 Time 3 Time 4 ABCABC CDFCDF AA B D A BB D

Correlation Time 1 Time 2 Time 3 Time 4 ABCABC CDFCDF AA B D A BB D F Correlation:Find the highest correlations between expression level of TF of interest (red) and number of cis-element occurrence (normalized). AA means high numbers of A. TF

ARTIFICIAL PROMOTERS T1 T2 B1, B2 B3, B4, B2 CANDIDATES FOR BINDING ARTIFICIAL PROMOTER: B1 B3 B4 If find expression, then B2 is out and T1 binds to B1 for sure.

Preliminary Testing Ndt80 (TF) Documented Binding Site: CACAAA MSE (cis-element) Documentation: promoter analysis, reporter constructs, and binding assays (Chu and Herskowitz, Cell 1998) AAAA Preliminary Algorithm Results: Ndt80 binds to... 7 time points Cis-element 1. TCGCGA 2. TAAACT 3. CTAGAT 4. CACAAA** Out of 4,096 possible candidate cis-elements **Documented binding site (see below) Ndt80 binds to time points Cis-element TCGCGA 1. --AACT(TA) CTAGAT 2. CACAAA**

Additional Results meiosis specific sites CACAAA - MSE SITE(Ndt80 binds) GGCGGC - URS SITE CCCCTT - LATE SPORULATION mitotic sites GCGCGC ACGCGT ACGCGG TGTGG CGCGAA - G1 PHASE CCACA - G1 PHASE GCAG - G2 PHASE diauxic shift ACTAA-

Additional Results TRANSFAC-List of putative regulatory elements for specific genes. Algorithm results list of putative cis- elements SEARCH ALL YEAST CIS-ELEMENTS IN TRANSFAC HIT RATE<10% YEAST CIS-ELEMENTS IN TRANSFAC ON GENES UP OR DOWN REGULATED IN SPORULATION HIT RATE<70%

Rosetta Dataset Results: microarray expession of 300 yeast deletion lines plus several drug treatments *close to reverse complements 8 other TFs share the binding site Most involved in amino acid biosynthesis

Create Data Sets 1.Compile data: sets of expressed transcription factors Time 1 Time 2 Time 3 Time 4 CAGGCACAAATCTTACGTTATA... (CAGGCA) (AGGCAC) (GGCACA) 3. Scan regulatory regions of expressed genes. Compile a set of potential cis-elements Time 1 Time 2 Time 3 Time 4 2,000 bp AAAA (A) (B) (C) (A) (C) (B) 2. Retrieve regulatory sequences

Minimal Set Time 1 Time 2 Time 3 Time 4 ABAB CDFCDF AA B D A BB D F B. Minimal Set. Find time point where 1) TF of interest (red) is present. 2)contains the fewest # of cis-elements. Eliminate cis- element candidates absent from this time point TF

Transcriptional Networks Specificity Modularity Time 1Time 2Time 3 Repression Induction e.g. cis-element AAAA