Introduction to Systems Biology, Functional

Genomics and Molecular Networks

CMMB 461
University of Calgary
Wikipedia
Gordon Chua 1
 CMMB 461 Course Outline
Dr. Gordon Chua: BI 560; [email protected]
Office Hours: Thursdays 1-3 PM
Suggested readings: primary literature (reviews, papers)
Tentative Course Schedule:
Sept. 6: Introduction to Systems Biology, Functional Genomics and Molecular Networks
Sept. 9-18: Conventional and Next Generation Sequencing
Sept. 20-25 Expression Microarrays
Sept. 27-Oct. 11: Forward and Reverse Genetics
Oct. 14: THANKSGIVING DAY: NO LECTURES
Oct. 16-21: Transcription Factor Overexpression
Oct. 23: IN CLASS MIDTERM
Oct. 25: Workshop: “How to get the most of your degree and career planning”
Oct. 30-Nov 4: Chromatin Immunoprecipitation and One Hybrid
Nov. 6-8: Posttranscriptional Regulation and Protein-RNA Interactions
Nov. 11-15: READING BREAK: NO LECTURES
Nov. 18: Translational control and Ribosome profiling
Nov. 20-27: Proteomics
Nov. 29-Dec 4: Synthetic Genetic Array Analysis
Dec 6: Review

Mark Breakdown:
Assignments (I and II): 30%
Midterm Exam: 25%
Final Exam: 45%

Letter Grade Scale:

A+: 95%; A: 90%; A-: 85%; B+: 80%; B: 75%; B-: 70; C+: 65%; C: 60%; C-: 55%; D+: 53%; D: 50%
 Suggested readings
•Kitano (2002) Science 295: 1662-1664 (systems biology
review)
http://www.ncbi.nlm.nih.gov/pubmed/11872829

•Vukmirovic and Tilghman (2000) Nature 405:820-822

(functional genomics review)
http://www.ncbi.nlm.nih.gov/pubmed/10866207

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 Genotype ? Phenotype
•Gene: DNA sequence involved in making RNA and protein
- long string of ACTG, genes are the part of ACTG

•Genotype: gene(s) inherited by an organism

•Phenotype: visible traits (e.g. body plan, behaviour, illnesses/diseases)

•Genome: entire DNA sequence (ACGT) of an organism

•Decoding how living things work is a daunting task due to the immense
complexity, however, the benefits are tremendous
ATCGGCATTACGATTTTTCAAGAATTCTTGAACCCGGGTTTGGAA...

Wikipedia
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 Central dogma of molecular biology
“Information flow in all living things”
Encodes genetic heritable instructions
DNA (genes) for the development and
functioning of all known living organisms

Reverse
Transcription (genes turned on)
transcription
(cDNA)
RNA
Translation (protein synthesis)

Structural proteins, metabolic

Protein enzymes, gene-regulatory proteins
- its the protein that determine the phenotype
•Although DNA is the information molecule that
directs protein expression, proteins ultimately
Phenotype determine the phenotype of the cell because they
control every reaction in the cell.
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 Gene and Protein Expression
•Eukaryotic chromosome: DNA of linear order of coding and noncoding genes

•GENE EXPRESSION: “turning on” a gene to produce RNA and protein (coding gene)

•PROTEIN EXPRESSION: the type and abundance of proteins in the cell

- coding rna - messenger

non-conding - snrna, trna
(makes up majority of the
total rna)

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Phenotypic Variation: what makes individuals different
from one another?
1. Different alleles (slight variation in gene sequence results in
changes in amino acid sequence of proteins)

2. Differential regulation of gene and protein expression

Gene for eye colour

• Alleles for eye pigment gene: blue, green, brown, etc.
• Amount of gene and protein expression: pale versus deep colour
National Geographic; Wikipedia

• Unique alleles and differential regulation

of thousands of genes among individuals
leads to countless phenotypic possibilities
in a population.

• Individuals that possess common alleles

and gene regulation leads to more similar
protein expression and phenotypes
(immediate family, relatives). 7
 Levels of Eukaryotic Gene Regulation

IMP

• Changes at any level of gene regulation

would potentially alter protein expression
and cause variation in phenotype
Wikipedia
Sri Lanka Foundation 8
 Differential expression of genome gives rise to
different cell types and tissues
•An organism’s phenotype is
dependent on cell number, type
and function.

•Every cell in an organism has

an identical genome (DNA
sequence) - every organism have the same ACTG
sequence

•An adult human has approx.

1014 cells composed of 250
different cell types.

•Which genes are being turned

on and off (transcription) that
produce the diverse phenotypes
in different cell types?
Wikipedia 9
 Transcription of tissue-specific genes in frog

Wikipedia

Can you infer what are these tissues based on

the most highly transcribed genes?

eye

heart

If we can control tissue-specific transcription, then

possible for transdifferentiation (changing one tissue
into another type of tissue) – applications?
Chan et al. (2009) J. Biol. 8:33 10
Cellular processes involve the concerted action of
macromolecules
•Complexes of proteins, nucleic acids and lipids form molecular
machineries to carry out cellular processes

•e.g. kinetochore (DNA-protein), ribosome (RNA-protein), vacuolar-type

H+ ATPase (lipid-protein)

- don;t need to remember number, gene names etcFront. Plant Sci. (2013) 4:276 11
 Cellular process are also regulated by signal-transduction
pathways by ordered associations of multiple proteins
•Extracellular stimulus/hormone can communicate to genes by signal
transduction pathways

•Pathway components include ligand, cell surface receptor, kinase

cascade, transcriptional regulator

•Ensures proper gene expression or physiological response from

stimulus

Wikipedia 12
 What is needed to fully decipher and understand
how life works?
•Identify all the parts/macromolecules in the cell /organism
(nucleic acids, proteins, lipid, metabolites )

•Measure the abundance and dynamics of each

macromolecule

•Determine the regulation (multiple levels) and function of

each macromolecule

•Determine interactions between macromolecules and

their biological significance

•This is a daunting task!!!

Nature Cell Biology/Wikipedia 13

 Why sequence genomes?
To understand how the types and abundance of RNA and proteins result in a
phenotype of an organism, we need to identify all the genes in the genome

12364 completed genomes (January 2014):

(Archaeal: 277; eubacterial: 11775; eukaryotes: 312)

M. pneumoniae H. pylori H. influenza V. cholerae E. coli P. aeruginosa

0.8 Mb 1.7 Mb 1.8 Mb 4.0 Mb 4.6 Mb 6.3 Mb
680 genes 1589 genes 1738 genes 3890 genes 4406 genes 5570 genes

S. cerevisiae C. elegans D. melano. A. thaliana H. glaber H. sapiens

12.1 Mb 95.5 Mb 180 Mb 120 Mb 2700 Mb 3200 Mb
5,860 genes 23,209 genes 14,100 genes 25,498 genes 22,561 genes 25,000 genes
http://www.genomesonline.org http://www.youtube.com/watch?v=mVZI7NBgcWM 14
 What is Systems Biology?
•“Systems biology is the study of an organism, viewed as an
integrated and interacting network of genes, proteins and
biochemical reactions which give rise to life.” –ISB, Seattle

•The approach is to analyze all the components and their

interactions at once to obtain a systems view of an cell/organism
(opposite of reductionism)

•This recent field of science was driven by the human genome

sequence project and the development of high-throughput
technologies to monitor global levels of molecules and interactions
simultaneously in a cell

•Obtaining a systems understanding of a cells/organism has the

potential to benefit human society (e.g. health, agriculture,
ecology, environment)
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System-level understanding: how does it all work?

1. Systems Structures:

2. System Dynamics:

3. System Control:

4. System Design:
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 Systems-level understanding of a
biological system (cell)
1. System structures: What are the parts list?

•Macromolecules: Genes, RNA, proteins, lipids, metabolites

•Macromolecular interactions (e.g. transcriptional regulation,

protein binding and biochemical activity, genetic)

•How do these various interactions give rise to the

phenotype of the cell/organism?

Histone-DNA interactions (Wikipedia) AJPCell 292:1645-1659 (2007): F-actin-actinin co-localization

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 Network structures: how to show the myriad of
macromolecular interactions
Networks are made of nodes (genes, proteins, etc) and edges
(binding and regulatory interactions)

Protein complexes:

Gene regulation
TF
(mRNA synthesis)

•Edges of protein-protein interactions: no directionality

•Edges of gene regulatory interactions: directionality

•Connectivity: number of interactions between nodes

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 Network of a signal transduction pathway
Hormone
A
Receptor Plasma Membrane
MAPKKK
P P MAPKK B
Proteasome P MAPK
C
P
P P
P
H D

Cytoskeleton F E G
Metabolism

Arrow = activating interaction

P “T”=repressing interaction
P

Nucleus
(transcription)
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Regulatory network of the BRCA1 tumor
suppressor gene

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 Cellular networks of budding yeast
•Saccharomyces cerevisiae: most extensively studied eukaryotic
organism (6000 genes in genome)

•However deciphering the cellular networks are far from complete

Transcriptional- Protein interaction

regulatory network
network

Genetic-interaction
network Metabolic network

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 2. System dynamics: how do the biological networks change over time,
during development or to various environmental conditions?

expression
mRNA
Embryonic stem cells Nerve cells time

What parameters of mRNA/proteins change in the cell?

1. Abundance (synthesis and degradation)

2. Interactions (complex components)
3. Activity (enzymes)

•Need to measure these parameters of all these parts over

time/particular condition to study the dynamics (big task)

•Detecting these changes allows inference of gene function

Wikipedia 22
 3. Systems control: what control mechanisms exist to keep the
cell fairly robust to perturbations to minimize malfunctions?

Perturbations = genetic mutations/environmental insult

1. Negative-feedback and feed-forward control

A B A B C

“AND”: delayed activation of “C”

“OR”: protection from transient
X Y
inactivation
2. Redundancy/backup
essential
process

3. Structural stability: chaperones, DNA repair and checkpoints

4. Modularity: sub networks are physically or functionally insulated so

that failure of a component will not result in catastrophe

Nature Methods 10: 597-598 (2013) 23

4. Systems design: can we rewire the network to cause
a desired phenotype?
•“Rewire”: perturbation of specific gene activity predicted by systems
theory rather than trial and error to change global gene expression

•Desired phenotype: reprogram cell fates or restore disease cell to

normal cell

•Overexpression of 3-4 transcription factors simultaneously to change

somatic cells into an embryonic stem cell (what are the benefits?)

Nerve cells Embryonic stem cells

Is it possible to reprogram cancer cells to differentiate into a more

benign state with this approach (differentiation therapy)?

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 Framework for Systems Biology
Approach involve a continuous interplay between experimental
discoveries (wet lab) and hypothesis-driven model
simulations/predictions (dry lab)

1. Define all components in the system and model based on

pre-existing genetic and biochemical knowledge

2. Systematically perturb and monitor components of the

system

3. Reconcile the experimentally observed responses with

those predicted by the model

4. Design and perform new perturbations experiments to

distinguish between multiple and competing models

Ideker et al. (2001) Annu. Rev. Genomics Hum. Genet.2: 343-372 25

 Understanding gene function
•Now that we have identified all the genes, what next to do to
decode how life works?

•Determine function of genes by several approaches/assays:

1. Perturb gene function and study

phenotype

2. Measure mRNA expression in

various cells

3. Measure protein abundance,

cellular localization, and
interactions

4. Predict and elucidate structure

of protein from gene and amino
Vukmirovic & Tilghman (2000) Nature 405:820-822
acid sequences
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 Functional genomics
•Goal: To determine the function of every gene in the genome

•Approach: high-throughput “omics” technologies to

functionally characterize all the genes in the genome in a
single experiment
1. Reverse genetics: delete every gene and study phenotype

2. Genetic Interaction mapping: create all double mutant

combinations and assay for lethality (SGA technology)

3. Transcriptomics: determine abundance of all RNA

molecules (DNA microarrays/RNA-Seq)

4. Proteomics/Interactomics: determine abundance and

interactions of all proteins (2-hybrid/mass spectrometry)

5. Metabolomics: determine abundance of metabolites (mass

spectrometry, NMR)
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Learning objectives: you should be able to…
•Describe the types of macromolecules in a cell and explain how their
regulation and interactions can give rise to a specific phenotype

•Explain how the availability of genome sequences has significantly

advanced the field of systems biology

•Describe the four components involved in achieving a systems level

understanding of the cell

•Describe the main goal and technologies of functional genomics

•Describe biological network structure and types

Questions to ponder on:

•How can knowledge of molecular networks be used to develop a
potential treatment for cancer?
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