Last time … * Constraint on transcription factor binding sites Sites with the most ‘information content’ generally evolve slowest * Stabilizing selection via binding site turnover * Gain and loss of orthologous binding sites can correlate with gain and loss of target genes

2 How do regulatory networks evolve? Module = group of genes co-regulated by the same regulatory system * Evolution of individual gene targets * Evolution of activating signals * Wholesale evolution of the entire module Transcription factor sites occur upstream of totally different genes, responding to totally different signals

3 ChIP-chip of two cooperatively-acting TFs in 3 species (S. cerevisiae, S. mikatae, S. bayanus ~20 my diverged) Tec1Ste12 Pseudohyphal growth Genes Mating genes (haploid cells only) Science 2007

4 Scer Smik Sbay Ste12 Tec % bound in all 3 species 20% bound in all 3 species Only ~20% of orthologous regions bound in all 3 species

5 * non-S. cer but otherwise conserved binding: enriched for Mating Genes

6 Only 20% of bound fragments conserved over 20 my (75% of these have underlying binding sites conserved) Tec1Ste12 Borneman et al. Science 2007 Substantial ‘rewiring’ of transcriptional circuits: * Gain and loss of individual gene targets * S.cer loss/evolution of the module of mating genes How common will these trends be? Different trends for different functional processes?

7 Science April 2010 PLoS Biol. April 2010 ChIP-seq (NF  B and RNA-Pol II) and RNA-seq in 10 humans from 3 different populations Lots of variation (up to 25% variation in binding levels) ChIP-chip’d Ste12 in 43 S. cerevisiae segregants Nature. March 2010 ChIP-chip of 6 developmental TFs in D. mel vs. D. yakuba (5 my) * only 1-5% of genes are variable targets (gene target turnover) * lots of evidence of TF binding site turnover within CONSERVED target regions

8 How do regulatory networks evolve? Short time-scales: gene target turnover (gain and loss) Time Evolved Responsiveness Cooption of existing network

9 Ancestral GAL control likely by Cph1 … S. cerevisiae lineage picked up Gal4 and Mig1 sites upstream of GAL genes

10 In addition to changes in upstream cis-elements … Major changes in the Gal4 transcription factor & upstream along S. cerevisiae lineage: * Gained a domain that interacts with the Galactose-responsive Gal80 protein * Other changes in the upstream response (Gal1-Gal3 duplication) contributed to sensitized pathway

11 How do regulatory networks evolve? Sub/neo-functionalization through TF duplication & divergence Time TF duplication Evolved TF sensitivity, binding specificity, and ultimately targets Gene targets can also duplicate (especially in WGD)

12 Example: Arg80 and Mcm1 duplication Tuch et al PLoS Biol. Mcm1 is a co-factor that works with many different site-specific TFs Tuch. et al. performed ChIP-chip on Mcm1 orthologs in multiple fungi. * Found dramatic differences in inferred Mcm1-TF interactions and modules One case in particular: Arginine biosynthesis genes Mcm1 + Arg81 at arg genes is ancestral Duplication of Mcm1 (Arg80) at WGD Loss of Mcm1 binding at arg genes Presumably taken over by Arg80 Time (>150 my)

13 How do regulatory networks evolve? If co-regulation is so important, then how can tolerate many independent changes in upstream cis-elements? Conundrum: Clearest cases of regulatory switches are often for highly co-regulated genes, whose co-regulation is high conserved.

14 Tanay et al PNAS Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast They argued that a period of redundancy of all 3 systems allowed loss of one system

15 Molecular Cell 2008 Motif predictions in RP genes suggest evolved sites S. cerevisiae RPs C. albicans RPs Rap1IfhlRGE GTACAYCCRTACATCYRGGCNGGAAATTTT AAAATTTT Tbf1 TTAGGGCTA Cbf1 TCACGTG S. cerevisiae Sulfur genes (and centromeres) C. albicans Sulfur genes (and a whole bunch of things) TCACGTG ChIP-chip’d Ca_Tbf1 and Ca_Cbf1 to show binding upstream RP genes

16 Motif analysis prediction: Ancestral regulation by Tbf1, Cbf1, RGE Lineage to S. cerevisiae picked up Rap1 and IFHL regulation

17 Here they ChIP’d 6 TFs implicated in RP regulation in S. cerevisiae and/or C. albicans Ifh1-Fhl1 co-activators are conserved in Sc-Ca (>200 my) Required co-factors have evolved: Hmo1 and Rap1 required for Ifh1-Fhl1 binding in S. cerevisiae * Hmo1 is a ‘generalist’ in C. albicans In C. albicans, Cbf1 (generalist) and Tbf1 (specialist) are required for Ifh1-Fhl1 binding

18 They raise the question: Is wholesale rewiring common to all modules Or facilitated by very strong pressures to keep genes co-regulated?