Information Processing in Genetic Regulatory Networks
Ofer Biham
Mor NitzanYishai ShimoniBaruch BarzelAdiel LoingerAzi LipshtatOded RosolioAssaf Pe’erYael Altuvia
Hanah MargalitPascale RombyPierre Fechter
Network and motifs
Transcriptional network of E. coli
Other modules
A
B
A
AB
A
b c d e
A
Motifs
b
Regulation Mechanisms
Different levels of regulation Transcriptional regulation Post-transcriptional regulation (by sRNA-mRNA int.) Post-translational regulation (by protein-protein int.)
gene a gene b
m B
m A
BA
gene a gene b
B
m B
S A
Transcriptional regulation Post-transcriptional regulation
Information processing
Transcriptional regulation
c
m C
C
A
B
Input Functions
Diverse two-dimensional input functions control bacterial sugar Genes, Kaplan, Bren, Zaslaver, Dekel and Alon, Molecular Cell 29, 783 (2008).
Transcription factor
Transcription regulation
Post-transcriptional regulation
ncRNA
Post-transcriptional regulation by ncRNA
Transcription regulation Integrated networkMulti-layer feed-forward loop
Multi-layer regulatory circuits
Asaf Peer, Mor Nitzan, Zohar Itzhaki, Hanah Margalit
Combination of regulations at different levels
gene b
SB
gene agene c
mCm A
CA
Staphylococcus aureus
Pathogenic bacteriaCause a wide range of human diseasesDisease manifestations depend on the
expression of numerous virulence factorsWithin S. aureus virulence
pathways lies a regulator switch that is
induced by a quorum
sensing signal
Quorum sensing for a growing population
At low numbers, violent bacteria will be quickly targeted for degradation
Only at higher numbers, the bacteria become virulent.
Quorum sensing for a dense population
Outer bacteria act as a shieldInner, protected bacteria excrete violent
proteins
S. aureus virulence path
hla
Quorum SensingQuorum Sensing
spa
RNAIII
Rot
Adhesins, camouflage proteins
(defensive state)
Adhesins, camouflage proteins
(defensive state)
Exotoxins, hemolysinα
(offensive state)
Exotoxins, hemolysinα
(offensive state)
The Switch
Target 2Target 1
Regulator
A Simpler Switch
Selector Switch
Target 2Target 1
activator
Selector Switch without activator/repressor
repressor
Target 2Target 1
Top Regulator
Bottom Regulator
Double Selector Switch
The model- rate equations
.
(sRNA regulator)
(mRNA transcripts of TF )
(TF protein)
(TF - promoter complexes)
(mRNA transcripts of target 1)(mRNA transcripts of target 2)(Target 1 proteins)
(Target 2 proteins )
(sRNA - target mRNA complexes)
Switching on and off
Target 2Target 1
sRNA
TF
Time (min)
Response to a spike
Leakage of Target 1
1
(1 ) (1 )
T
T
T s
T m
bTPu
b bTP su d
NLeakage
N N
Target 2Target 1
sRNA
TF
Mixed Feedback Loop
Bifurcation Diagrams
Stochastic Trajectories
Life-times of bistable states
Deterministic vs. Stochastic Models
SS
S A
P
Probability Distribution
sRNA-target interaction
E. Levine, Z. Zhang, T. Kuhlman and T. Hwa, Plos. Biol. (2007)
Fine-tuning of target expression
E. Levine, Z. Zhang, T. Kuhlman and T. Hwa, Plos. Biol. (2007)
miRstargets
Post transcriptional network in HEK293 Cells
Crosstalk between Competing endogeneous RNAs (ceRNAs)
miR-Y
mRNA target 1mRNA target 2
Salmena et al., Cell 146, 353 (2011); Tay et al., Cell 147, 344 (2011);Bosia et al., Plos One 8, e66609 (2013); Figliuzzi et al., Biophys J. 104, 1203 (2013)
Crosstalk between ncRNAs
Crosstalk between mRNAs through their common regulators
Fast Transmission of Signals
(a) Wild-type (c)
(a) Wild-type (b)
T0T0 T1
T1 T2T2 T0
T0 T1T1 T2
T2 T0T0 T1
T1 T2T2
T0T0 T1
T1 T0T0 T1
T1
R0R0 R0
R0
T0T0 T1
T1 T2T2
R0R0 R1
R1 R0R0 R1
R1 R0R0 R1
R1 R0R0 R1
R1
(c) (d)
(b)
T0T0 T1
T1
R0R0
Knock-down of T0
Knock-down of T0
Knock-down of T10
Knock-down of T10
A
C
(a) Wild-type (c)(b)
B
Over-expression
of R0
Over-expression
of R0
T1T1
R0R0 R1
R1
T1T1
R0R0 R1
R1
T1T1
R0R0 R1
R1
Signal Propagation – Experimental Data
T0T0 T1
T1 T2T2
R0R0 R1
R1 R4R4
T3T3 T4
T4
R2R2 R3
R3
T5T5
R5R5
Subnetwork of sRNA Regulators and theirTargets
T0T0 T1
T1 T2T2
R0R0 R1
R1 R4R4
T3T3 T4
T4
R2R2 R3
R3
T5T5
R5R5
Decay Rate of the Signal
Correlations in the Network
Summary
We have studied information processing in genetic regulatory networks that involve different levels of regulation
These networks combine sharp on/off type regulation with fine tuning processes, fast and slow processes, synchronization and subtle coordination
Further progress will require experiments both at the single cell level and at the cell population level
Transcriptional vs. Post-transcriptional regulation
Transcriptional Post-transcriptional
Response time Slow Fast
Regulation type Sharp On/Off Enables fine-tuning
Regulator-target interaction
Non-stoichiometric Stoichiometric
Regulation strength determined by
TF copy number and affinity to promoter
Relative copy numbers of sRNAs and mRNAs and their affinity
Directionality Directional – from regulator to target
Bi-directional
Energetic cost Protein synthesis RNA synthesis
Combination of regulations at different levels
gene b
SB
gene a gene c
mCm A
CA
Target 2Target 1
TF
sRNA
Target 2Target 1
sRNA
TF
Target 2Target 1
TF
TF
Three variants of the DSS
Dynamics of DSS variants
Leakage in target genes