EPFL Workshop 1

Logic Synthesis of Recombinase-based

Genetic Circuits

Jie-Hong Roland Jiang

Department of Electrical EngineeringGraduate Institute of Electronics Engineering

National Taiwan University

2017/9/29

Design Automation for Wetware! Hardware

Data representationVoltage

SignalWires“Unlimited” signals

High predictabilityWell-controlled

electrical environment Design principle

Mostly digitalMostly synchronous

Wetware Data representation

Concentration Signal

Molecular speciesLimited signals

Low predictabilityNoisy biochemical

environment Design principle

Analog + digitalMostly asynchronous

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Outline

IntroductionFormalismGenetic Circuit SynthesisGenetic Circuit OptimizationSummary and future work

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Systems and Synthetic Biology Biotechnology has promising applications in health,

medicine, environment, food, energy, etc. Learn circuit design principles from nature

Complex behaviors of bacteria, say, emerge from fundamental biochemical reactions

Engineer circuit components and systems from known biochemical parts Bio-design automation

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Source: openbiolabs.org

Insulin signaling pathways [Boucher et al. 2014]

Why Logic Design in Biology ?

Computation in living cellsSensing / diagnosisDecision makingResponse / control

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Moon et al. 2012

Molecular Biology 101

Central dogma of molecular biology

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Source: Wikipedia

Gene Transcription

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Genetic Recombination A recombinase is an enzyme that achieves one

of the following types of genetic recombination

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[Nern et al. 2011]

Site-Specific Recombination

Site-specific recombinase for inversion (and excision)

Irreversible (mostly) Long-term memory effect cross generations

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attP attB

attR attL

Other Genome Editing Method

CRISPR/Cas9 systems

Excision/insertion in genome editingActivation/inhibition in gene expression

regulation (defective form of Cas9)

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Source: mobitec.com

Outline

IntroductionFormalismGenetic Circuit SynthesisGenetic Circuit OptimizationSummary and future work

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Logic Design with Recombinase

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T T GFP

Bxb1

phiC31

T

GFP

promoter

transcription terminator

targeting sites

green fluorescent protein

Bxb1 phiC31 GFP

0 0 0

1 0 0

0 1 0

1 1 1

Recombinase-based Logic Gates

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GFP

GFP

GFP GFP

T

GFP GFP

(a) (b) (c)

(d) (e)

(f) (g) (h)

T GFP

R1

R3

R2 T GFP

(i)

GFP

R1

R3

R2

R4

OR1

R2R3

R4O

Recombinase Logic Gate: Syntax

Atomic terms

Well-formed sequence

E.g.,

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Recombinase Logic Gate: Semantics

Reduction rules

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Recombinase Logic Gate: Semantics

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Recombinase Logic Gate: Semantics

Example

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Recombinase Logic Gate: Semantics

Example

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Outline

IntroductionFormalismGenetic Circuit SynthesisGenetic Circuit OptimizationSummary and future work

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Multi-level Recombinase Circuits

Example

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AB

AB

ZR1

R2

ZB

A

T

A

B

C D

E

Y

Z

R

Logic Synthesis of Recombinase Circuits

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Logic Synthesis of Recombinase Circuits

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A

B

C D

E

Y

Zn7

n8T

YT

Z

TA

B

C DE

n7

n8

TYT

Z

TABC

D E

T

Synthesis Results

Recombinase circuit synthesis with ABC

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Outline

IntroductionFormalismGenetic Circuit SynthesisGenetic Circuit OptimizationSummary and future work

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Blocking Terminators in Cascaded Circuits

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Optimization by Gate Merging

Merging condition

Gate Y starts with inversed promotercontrolled by the output of gate X

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Gate-Merging Friendly Library

Make DNA sequences start with inverted P

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Mergeability Graph

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Path Covering on Mergeability Graph

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Path Covering by 0/1-ILP

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Optimization Flow

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Optimization Results

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16% length reduction; 36% level reduction

org. synthesis merge aware synthesis

Outline

IntroductionFormalismGenetic Circuit SynthesisGenetic Circuit OptimizationSummary and future work

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Summary

Motivated bio-design automationFormalized the syntax and semantics of

recombinase-based logic gatesUsed existing logic synthesis flow for

genetic circuit synthesis Optimized genetic circuit by gate merging

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Future Work

Recombinase-based genetic circuitsNondeterministic and/or circuit synthesis

Analog computationWet lab validation 2017/9/29 EPFL Workshop 35

[Roquet et al. 2016]

References Tai-Yin Chu, J. Logic synthesis of recombinase-

based genetic circuits. Scientific Reports (to appear).

Chun-Ling Lai, J., Francois Fages. Recombinase-based genetic circuit optimization. BioCAS, 2017.

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Acknowledgement

Collaborators Tai-Yin Chiu, NTUChun-Ning Lai, NTU Francois Fages, INRIA Franck Molina, CNRS

SponsorMinistry of Science of Technology, Taiwan

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Thanks for Your Attention!

Questions?

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