Transcript S. cerevisiae

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
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
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Science 2007
ChIP-chip of two cooperatively-acting TFs in 3 species
(S. cerevisiae, S. mikatae, S. bayanus ~20 my diverged)
Tec1
Ste12
Pseudohyphal growth
Genes
Ste12
Ste12
Mating genes
(haploid cells only)
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Only ~20% of orthologous regions bound in all 3 species
Scer
Ste12 380
Smik
167
Sbay
250 21% bound in all 3 species
Tec1 348
185
126 20% bound in all 3 species
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* non-S. cer but otherwise conserved binding: enriched for Mating Genes
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Borneman et al. Science 2007
Only 20% of bound fragments conserved over 20 my
(75% of these have underlying binding sites conserved)
Tec1
Ste12
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?
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How common will these trends be? Different trends for different functional processes?
PLoS Biol. April 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
Nature. March 2010
Science April 2010
ChIP-chip’d Ste12 in 43 S. cerevisiae segregants
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)
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How do regulatory networks evolve?
Short time-scales: gene target turnover (gain and loss)
Cooption of existing network
Time
Evolved
Responsiveness
Time
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Ancestral GAL control likely by Cph1 … S. cerevisiae lineage picked up Gal4 and Mig1 sites upstream of GAL genes
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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
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How do regulatory networks evolve?
Sub/neo-functionalization through TF duplication & divergence
TF duplication
Time
Evolved TF sensitivity, binding specificity,
and ultimately targets
Time
Gene targets can also duplicate
(especially in WGD)
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Example: Arg80 and Mcm1 duplication
Tuch et al. 2008. 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
Time (>150 my)
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
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How do regulatory networks evolve?
Conundrum:
Clearest cases of regulatory switches are often for highly co-regulated genes,
whose co-regulation is high conserved.
If co-regulation is so important, then how can tolerate many independent changes
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in upstream cis-elements?
Tanay et al. 2005. 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
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Molecular Cell 2008
Motif predictions in RP genes suggest evolved sites
Rap1
S. cerevisiae RPs
GTACAYCCRTACAT
Ifhl
RGE
CYRGGCNG
GAAATTTT
C. albicans RPs
AAAATTTT
Tbf1
Cbf1
TTAGGGCTA
TCACGTG
S. cerevisiae Sulfur genes (and centromeres)
TCACGTG
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
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Motif analysis prediction:
Ancestral regulation by Tbf1, Cbf1, RGE
Lineage to S. cerevisiae picked up Rap1 and IFHL regulation
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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
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They raise the question:
Is wholesale rewiring common
to all modules
Or
facilitated by
very strong pressures to keep
genes co-regulated?
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