Consrevation and evolvability in regulatory network evolution

1
Consrevation and evolvability in regulatory
network evolution

• Aviv Regev
• Bauer Center for Genomics Research
• Harvard University

2
Regulatory modules

• Module - Sets of proteins that co-operate to
  achieve a specific task
• Turned on or off coordinately as cells are
  exposed to different environments

sites
RNA
3
DNA microarrays Measuring expression
Genes
Conditions
Gasch et al., 2000
4
From expression to regulation
sites
RNA
5
From expression to regulation
Control regions
Gene I
AGCTAGCTGAGACTGCACAC TTCGGACTGCGCTATATAGA GACTGCAG
CTAGTAGAGCTC CTAGAGCTCTATGACTGCCG ATTGCGGGGCGTCTGA
GCTC TTTGCTCTTGACTGCCGCTT
AGCTAGCTGAGACTGCACAC TTCGGACTGCGCTATATAGA GACTGCAG
CTAGTAGAGCTC CTAGAGCTCTATGACTGCCG ATTGCGGGGCGTCTGA
GCTC TTTGCTCTTGACTGCCGCTT
Gene II
clustering
Gene III
Genes
Gene IV
Gene V
Gene VI
Experiments
GACTGC
6
From expression to regulation
7
Comparative expression analysis

• Module phenotype (expression) is conserved

Bergman et al., PLoS 2004
Stuart et al., Science 2003
8
Ortho-modules Ortho-regulation?

• Expression modules are conserved across evolution
  (Stuart et al., 2003, Ihmels et al., 2004)
• Are the regulatory mechanisms conserved?

Genes
9
Comparative Genomics
10
(No Transcript)
11
Evolution of cis-regulation in Ascomycota fungi
12
Evolution of cis-regulation in Ascomycota fungi
Putative co-regulated S. cerevisiaegene sets
Known S. cerevisiaecis-elements
Putative S. cerevisiaecis-elements
MEME
42 gene sets with 35 enriched motifs
Test for motif enrichment in projected
orthologousgene sets
13
Phylogenetic cis-profiles conservation

• The number of regulatory systems conserved across
  species correlates with their divergence times
• In 80 of cases in which a given cis-regulatory
  element was enrichmed, the ortholog of its S.
  cerevisiae binding protein could be identified

14
Conservation of promoter organization position
of site

• Compared the fraction of elements in 50-bp
  windows upstream of their target genes to the
  fraction of elements in the same 50-bp window
  upstream of all genes in the same genome.
• Not simply site conservation

15
Conservation of promoter organization site
distances
16
Sequence evolution in cis elements RPN4
17
Divergence in Sequence-specificity on Rpn4p
Sce specific
Cal specific
Hybrid
18
Phylogenetic cis-profiles divergence

• No co-regulation or evolved cis-regualtory
  mechanism?

19
Evolution of cis-regulation in Ascomycota fungi
Putative co-regulated S. cerevisiaegene sets
Known S. cerevisiaecis-elements
Putative S. cerevisiaecis-elements
MEME
42 gene sets with 35 enriched motifs
Test for motif enrichment in projected
orthologousgene sets
Putative enriched cis-elements in other species
MEME
20
Phylogenetic cis-profiles Divergence
21
Conclusions

• Conservation of cis-regulatory systems,
• Addition and removal of targets under a given
  program
• Co-evolution of binding protein and binding site
• Divergence of regulatory mechanisms controlling
  tightly co-expressed genes. How?

22
(No Transcript)
23
Ortho-modules Ortho-regulation?

• Expression modules are conserved across evolution
  (Stuart et al., 2003, Ihmels et al., 2004)
• Are the regulatory mechanisms conserved?

Genes
S. Cerevisiae (budding yeast)
S. Pombe (fission yeast)
24
Orthologous transcriptional modules
S. cerevisiae
S. pombe
Arrays
Orthologs
Genes
Sce promoters
Spo promoters
25
Ortho-modules Ortho-regulation
S phase
Respiration
Amino acid metabolism
Plt10-29
S. Pombe
Plt10-9
Plt10-23
S. pombe
S. pombe
S. cerevisiae
S. cerevisiae
S. cerevisiae
Mbp1-Swi6
Res1/2-Cdc10
Hap2-3-4-5
Cpf1-Php2-Php5
Gcn4
???
26
Ortho-modules Divergent regulation
Ribosomal proteins
Ribosome biogenesis
Stress
Plt10-56
S. Pombe
Plt10-151
Plt10-32
S. Pombe
S. cerevisiae
S. Pombe
S. cerevisiae
S. cerevisiae
RAP1
Homol-D
PAC
PAC
STRE
CRE
RRPE
Homol-E
IFHL
27
Ribosomal proteins module
S. cerevisiae
S. pombe
RPL1B
RPL101
RPS6B
RPS601
HomolD
RPS1701
RPS17B
RPS25A
IFHL
RPS2501
HomolE
RPL31A
RPL31
RPS6A
RPS2601

• Gradual evolution of site or switching from one
  mechanism to another?
• How could this shift have occurred without
  destroying the coordination?

28
Ascomycota Fungi
gt 15 sequenced genomes
29
Phylogenetic cis-profiling
S. cerevisiae
S. pombe
PutativeModule
Sce
Spo
30
Ortho-modules Ortho-regulation
S phase
Respiration
AA metabolism
31
Parsimonious reconstruction
S. cerevisiae
S. pombe
32
Site evolution from Homol-E to IFHL
S. cerevisiae
S. paradoxus
S. mikatae
S. kudriavzevii
S. bayanus
S. castellii
C. glabrata
S. kluyveri

K. waltii
K. lactis
A. gossypii
D. hansenii
C. albicans
Y. lipolytica
(G/C)CCTA
N. crassa
TAGGG
A. nidulans
S. pombe
33
Ribosomal protein module cis redundancy
S. cerevisiae
IFHL/HomolE
S. paradoxus
RAP1
RAP1 program
Homol-D
S. mikatae
S. kudriavzevii
Homol-D loss
S. bayanus
S. castellii
C. glabrata
Redundant program
S. kluyveri
RAP1 gain
K. waltii
K. lactis
A. gossypii
D. hansenii
C. albicans
Homol-D program
Y. lipolytica
N. crassa
A. nidulans
S. pombe
34
From Homol-D to RAP1
BRCT
Myb
TA
Sil
sc RAP1
S. cerevisiae
IFHL/HomolE
S. paradoxus
RAP1
Homol-D
S. mikatae
S. kudriavzevii
Homol-D loss
S. bayanus
S. castellii
C. glabrata
S. kluyveri
TA gain
RAP1 gain
K. waltii
K. lactis
A. gossypii
D. hansenii
C. albicans
Y. lipolytica
N. crassa
H. sapiens
A. nidulans
S. pombe
35
From Homol-D to RAP1
S. cerevisiae
IFHL/HomolE
S. paradoxus
RAP1
Homol-D
S. mikatae
S. kudriavzevii
Homol-D loss
S. bayanus
S. castellii
C. glabrata
S. kluyveri
TA gain
RAP1 gain
K. waltii
K. lactis
A. gossypii
D. hansenii
C. albicans
Y. lipolytica
N. crassa
A. nidulans
S. pombe
36
Mechanisms of evolution of module regulation
Conservation
trans switching
Binding Site Evolution
Full switching
Mediated replacement
37
The evolution of regulatory modules

• Flexible transition between different regulatory
  mechanisms to perform a similar function
• How do novel sites emerge and invade many genes?
• Why redundancy? Why switch?
• How can we experimentally validate evolutionary
  findings?

38
(No Transcript)
39
WGD, oxygen requirements and fermentation
cerevisiae
Rapid anaerobic growth
paradoxus
mikatae
bayanus
glabrata
castellii
lactis
Rapid aerobic growth
gossypii
waltii
hansenii
albicans
lipolytica
crassa
graminearum
grisea
nidulans
pombe
40
Comparative expression profiling

• S. cerevisiae mitochondrial modules are not
  correlated with cytoplasmic ribosomal protein and
  ribosome biogenesis modules
• C. albicans mitochondrial modules strongly
  correlated with cytoplasmic ribosomal ones

41
Regulatory divergence
42
Regulatory divergence
43
A phylogenetic cis-profile

• Massive loss of RGE site from MRPs post-WGD

44
Conclusions

• Emergence of anaerobic growth capacity in yeast
  is associated with a global rewiring of the yeast
  transcriptional network.
• Loss of motif across dozens of promoters
• What about the TF binding to the RGE site?
• Can whole genome duplication facilitate the
  evolution of new function through cis-regulatory
  function?