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Transcriptional Networks

Transcriptional Networks. GENE. PROMOTER. BINDING SITES: TRANSCRIPTION FACTORS BIND TO THESE. MAY INDUCE AND MAY REPRESS. A B C. AA B D. A BB D. C D F. Compare Expression. Time 4. Time 2. Time 3. Time 1. CAGGTA. GGCGAC. CCCAAC. CGTTAA. CACAAA. CAGGTA. CAGGTA. ACGGGC.

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Transcriptional Networks

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

  2. A B C AA B D A BB D C D F Compare Expression Time 4 Time 2 Time 3 Time 1 CAGGTA GGCGAC CCCAAC CGTTAA CACAAA CAGGTA CAGGTA ACGGGC CACAAA CACAAA CACAAA Time 4 Time 1 Time 3 Time 2

  3. Correlation Time 4 Time 2 Time 3 Time 1 TF A B C A BB D F AA B D C 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.

  4. 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.

  5. Ndt80 binds to... 14 time points Cis-element TCGCGA 1. --AACT(TA) CTAGAT 2. CACAAA** Preliminary Testing 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) Documented Binding Site: AAAA Ndt80 (TF) CACAAA MSE (cis-element) Documentation: promoter analysis, reporter constructs, and binding assays (Chu and Herskowitz, Cell 1998)

  6. 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-

  7. Additional Results Algorithm results list of putative cis-elements TRANSFAC-List of putative regulatory elements for specific genes. 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%

  8. 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

  9. 2,000 bp AAAA CAGGCACAAATCTTACGTTATA... (A) (CAGGCA) 3. Scan regulatory regions of expressed genes. Compile a set of potential cis-elements (AGGCAC) (B) (GGCACA) (C) (C) (B) (A) Time 4 Time 1 Time 3 Time 2 Create Data Sets 1.Compile data: sets of expressed transcription factors Time 4 Time 2 Time 3 Time 1 2. Retrieve regulatory sequences

  10. Time 4 Time 2 Time 3 Time 1 Minimal Set TF A B AA B D A BB D F C 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

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

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