1. Current Topics in Evolutionary Genomics Wen-Hsiung Li and Justin Borevitz

2. Potential Topics: I. Evolution of Gene Expression II. Evolution of transcriptional regulatory code III. Evolution of regulatory networks IV. Evolution of new and duplicate genes V. Protein Protein interactions VI. Genetic variation within and between species VII. Effects of recombination and gene conversion on GC content and substitution rate

3. I. Evolution of Gene Expression Examine how gene expression has diverged between species (or between duplicate genes). A study may examine only changes in expression but not changes in regulatory sequences. There have been many studies on this topic.

4. II. Evolution of transcriptional regulatory code Regulatory code of a gene : (1) Regulatory sequences of the gene, especially the cis elements. (2) Combinatorial rules of the cis elements.

5. Cis-regulatory circuit of MFA2 a cell cycle gene

6. II. Evolution of transcriptional regulatory code This topic may include evolution of regulatory sequences and also methods for inferring transcription factor binding sites (TFBSs). It is a fairly new topic but is receiving a great deal of attention.

7. III. Evolution of regulatory networks A regulatory or gene network (module): What are the genes in a regulatory pathway? Which are the upstream genes and which are the downstream genes? Under what conditions is the regulatory network on?

8. III. Evolution of regulatory networks This is a new topic and, to my knowledge, not much progress has been made yet because few regulatory modules are known for certain. It has a great future because it is new and because it is complex.

9. Other Potential Topics: IV. Evolution of duplicate genes V. Emergence of new genes VI. Genetic variation within and between species VII. Effects of recombination and gene conversion on GC content and substitution rate

10. How the class should be organized and conducted? Meet once a week for 2 to 2 1/2 hours? Select papers for each class: Open to suggestions. Look for new developments. In each class two persons present materials on two related topics for discussion (not much detail). Every participant should read the papers and participate in discussion.

11. How the class should be organized and conducted?

12. Assignments of Topics: I. Evolution of Gene Expression JJ, Megan II. Evolution of transcriptional regulatory code Geoff, Shinhan III. Evolution of regulatory networks Josh, Elliot IV. Evolution of duplicate and new genes Sidi, Jun

13. Assignments of Topics: V. Protein Protein Interactions Josh, Ying VI. Genetic variation within and between species David, Julie VII. Effects of recombination and gene conversion on GC content and substitution rate Loic, Roman

14. I. Evolution of Gene Expression Brem, R.B., Yvert, G., Clinton, R. & Kruglyak, L. Science 296, 752-755 (2002). Genetic dissection of transcriptional regulation in budding yeast. Science 296(5568):752-5. Yvert G, Brem RB, Whittle J, Akey JM, Foss E, Smith EN, Mackelprang R, Kruglyak L. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet. 2003 Sep;35(1):57-64.

15. Rifkin SA, Kim J, White KP. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet. 33, 138-144 (2003). Meiklejohn CD, Parsch J, Ranz JM, Hartl DL. Rapid evolution of male-biased gene expression in Drosophila. Proc Natl Acad Sci U S A. 100:9894-9 (2003). Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science. 2003 Jun 13;300(5626):1742-5.