1. http://cs273a.stanford.edu [Bejerano Fall10/11] 1 Thank you for the midterm feedback! Projects will be assigned shortly.

2. http://cs273a.stanford.edu [Bejerano Fall10/11] 2 Lecture 12 Mid Term Feedback Feedback Cis-Regulation Cellular Signaling

3. MidTerm Feedback Feedback General comments: Programming requirements –CS106A enough? Coverage: Depth vs. Breadth UCSC Primer Fit Homework vs. lectures You’re enjoying this class :) Let’s also reflect about doing your homework briefly. http://cs273a.stanford.edu [Bejerano Fall10/11] 3

4. Big Picture Context We are surveying the functional classes of elements encoded by the human genome. We have previously discussed: Repetitive sequences Protein coding genes Non coding RNAs Today we’ll cover the last (known :) large class of functional elements. http://cs273a.stanford.edu [Bejerano Fall10/11] 4

5. 5 Gene Regulation gene (how to) control region (when & where) DNA DNA binding proteins RNA gene Protein coding

6. http://cs273a.stanford.edu [Bejerano Fall10/11] 6 unicellular multicellular Unicellular vs. Multicellular

7. http://cs273a.stanford.edu [Bejerano Fall10/11] 7 Vertebrate Transcription Regulation

8. http://cs273a.stanford.edu [Bejerano Fall10/11] 8 Pol II Transcription Key components: Proteins DNA sequence DNA epigenetics Protein components: General Transcription factors Activators Co-activators

9. http://cs273a.stanford.edu [Bejerano Fall10/11] 9 Activators & Co-Activators Protein - DNA Protein - Protein

10. http://cs273a.stanford.edu [Bejerano Fall10/11] 10 The Core Promoter

11. http://cs273a.stanford.edu [Bejerano Fall10/11] 11 Chromatin Remodeling “off” “on”

12. http://cs273a.stanford.edu [Bejerano Fall10/11] 12 CpG islands

13. 13 Nucleosome tail modifications Lysine acetylations. Histone Acetyl-Transferases (HAT) & Histone Deacetylases (HDAC). Lysine and Argenine Metylations. –Modified by histone- metyl-transferase. Phosphorilation. Ubiquitination. –H2A ubiquitination affects 10-15% of this histone in most eukaryotic cells ADP-ribosylation.

14. http://cs273a.stanford.edu [Bejerano Fall10/11] 14

15. http://cs273a.stanford.edu [Bejerano Fall10/11] 15 Transcription Factor (TF) Binding Sites

16. http://cs273a.stanford.edu [Bejerano Fall10/11] 16 TFs in the Human Genome

17. http://cs273a.stanford.edu [Bejerano Fall10/11] 17 Combinatorial Regulatory Code Gene 2,000 different proteins can bind specific DNA sequences. A regulatory region encodes 3-10 such protein binding sites. When all are bound by proteins the regulatory region turns “on”, and the nearby gene is activated to produce protein. Proteins DNA Protein binding site

18. http://cs273a.stanford.edu [Bejerano Fall10/11] 18 Synergy / non-linear additivity Gene DNA

19. http://cs273a.stanford.edu [Bejerano Fall10/11] 19 Enhancers

20. http://cs273a.stanford.edu [Bejerano Fall10/11] 20 Basal factors RNAP II Enhancer with bound protein promoter Enhancers: action over very large distances

21. http://cs273a.stanford.edu [Bejerano Fall10/11] 21 Transient Transgenic Enhancer Assay Reporter Gene Minimal Promoter Conserved Element Construct is injected into 1 cell embryos Taken out at embryonic day 10.5-14.5 Assayed for reporter gene activity in situ transgenic

22. http://cs273a.stanford.edu [Bejerano Fall10/11] 22 Vertebrate Enhancer Combinatorics Sall1 limb neural tube brain

23. http://cs273a.stanford.edu [Bejerano Fall10/11] 23 Vertebrate Enhancer Combinatorics

24. http://cs273a.stanford.edu [Bejerano Fall10/11] 24 What are Enhancers? What do enhancers encode? Surely a cluster of TF binding sites. [but TFBS prediction is hard, fraught with false positives] What else? DNA Structure related properties? So how do we recognize enhancers? Sequence conservation across multiple species [weak but generic]

25. http://cs273a.stanford.edu [Bejerano Fall10/11] 25 Most Non-Coding Elements likely work in cis… 9Mb “IRX1 is a member of the Iroquois homeobox gene family. Members of this family appear to play multiple roles during pattern formation of vertebrate embryos.” gene deserts regulatory jungles Every orange tick mark is roughly 100-1,000bp long, each evolves under purifying selection, and does not code for protein.

26. http://cs273a.stanford.edu [Bejerano Fall10/11] 26 Many non-coding elements tested are cis-regulatory

27. http://cs273a.stanford.edu [Bejerano Fall10/11] 27 Vertebrate Gene Regulation gene (how to) control region (when & where) DNA proximal: in 10 3 letters distal: in 10 6 letters DNA binding proteins

28. http://cs273a.stanford.edu [Bejerano Fall10/11] 28 Gene Expression Domains: Independent

29. http://cs273a.stanford.edu [Bejerano Fall10/11] 29 Signal Transduction

30. 30 Cell Communication Lodish, 20-1

31. 31 Wnt and Hedgehog signaling Jacob & Lum Science 2007

32. 32 Signaling Pathways Important in Developmental Biology Wnt/Frizzled through  -catenin Hedgehog TGF-  family through Smads Growth factors via JAK-STATs Notch Integrin TNF