1 / 11

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.

luka
Download Presentation

Transcriptional Networks

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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

More Related