Download gene regulatory networks

The regulatory genome for
animal development
4/11/2012
Chiou-Hwa Yuh
2006/7/7
The framework
• How animal body plans form?
• The mechanism of development has many
layers, what are they?
Outside: spatial and temporal regulation of genes
Deeper: dynamic progression of regulatory states
Core: genomic apparatus---sum of the modular DNA sequence elements that
interacts with transcription factors.
• What is the core of the mechanism of
development?
• The causality underlying the twin phenomena
of animal development and animal evolution--system level organization of the core
genomic regulation apparatus
Differences in body plan
By the end of the 1950s it was clear that the causal differences between the
body plans of a fish and fly, or a sea urchin and a mouse, are somehow encoded
in their DNA genomes. But, what is the mechanism?
Growing complexity
Now, we know a good bit about how the genome actually works in
development, the same question continues to lead us forward: in what
sequences of the genome do in fact resides the causal differences
responsible for morphological diversity, and how exactly do they function?
The Regulatory Apparatus
Encoded in the DNA
Genomes, Genes, and Genomic Space
The regulatory apparatus
encoded in the DNA
The genes and gene regulatory components of animal
genomes.
Animal species vary enormously from one another in the
amount of DNA per haploid genome even with a given
clade.
Why?
Protein sequences variation?
Alternative splicing forms of RNA?
DNA mutation?
Non-coding region of DNA contain the regulatory code!
Genes and genomes
Animal species vary enormously from one another in the amount of DNA per haploid genome.
But, large differences in genome size are not at all reflected quantitatively in mRNA population
complexity.
Hs: human
Rn: Rattus norvegicus (rat)
Mm: Mus musculus (mouse)
Fr: Fugu rubipres (puffer fish)
Sp: Strongylocentrotus purpuratus (sea urchin)
Ci: Ciona intestinalis (ascidian)
Dm: Drosophila melanogaster (fly)
Ag: Anopheles gambiae (mosquito)
Ce: Caenorhabditus (nematode)
A Brief History of Regulatory Thinking
• Almost 50 years ago, as the first sequences
of various proteins from different species
were determined, the potential significance
of macromolecules for understanding
evolutionary processes was quickly
recognized.
• The great similarity among homologous
proteins of different species was noted
early and raised the question to what
degree such sequence changes were
functionally significant.
Most conserved proteins
in worm, human, and yeast
Protein
H4 Histone
H3.3 Histone
Actin B
Ubiquitin
Calmodulin
Tubulin
worm/
human
99% id
99
98
98
96
94
worm/
yeast
91% id
89
88
95
59
75
yeast/
human
92 % id
90
89
96
58
76
Curr Opin Struct Biol. 1999 Jun;9(3):408-15.
Protein families in multicellular organisms.
Copley RR, Schultz J, Ponting CP, Bork P.
Biocomputing European Molecular Biology
Laboratory, Heidelberg, Germany.
A Brief History of Regulatory Thinking
• With the advent of the operon model of gene
regulation, some biologists such as Emile
Zuckerkandl began to consider the possible role
of “controller genes” in evolution, including in the
origin of humans from ape ancestors
[Zuckerkandl E (1964) J Mol Biol 8: 128–147.]
• Eric Davidson’s monograph, "Gene Activity in
Early Development (New York, Academic Press
[c1968]) ," is a classic that provides direction for
research in this complicated field.
A Brief History of Regulatory Thinking
• One of the most widely noted series of theoretical
contributions in this period was Roy Britten and Eric
Davidson's models for gene regulation in higher
organisms, which had an explicit emphasis on the
importance of gene regulation in evolution.
• Britten RJ, Davidson EH (1969) Gene regulation for
higher cells: A theory. Science 165: 349–357.
• Britten RJ, Davidson EH (1971) Repetitive and nonrepetitive RNA sequences and a speculation on the
origins of evolutionary novelty. Quart Rev Biol 46:
111–138.
Evolution is a process of
mutation with selection
At the molecular level, evolution is a process of
mutation with selection.
Molecular evolution is the study of changes in genes and
proteins throughout different branches of the tree of
life.
Phylogeny is the inference of evolutionary relationships.
Traditionally, phylogeny relied on the comparison of
morphological features between organisms. Today,
molecular sequence data are also used for phylogenetic
analyses.
Are those true mechanisms for evolution?
Is there any other explanation and
evidence?
1. Changing in protein sequences—can’t count
for evolution, cause the proteins are very
homologous between species
2. Point mutations and accumulate little by little,
providing the opportunity for selection
3. Stepwise mutational change in cis-regulatory
modules or genes—transpositional deletions,
local genomic rearrangement, replication of
DNA, gene conversion
4. Changing in Gene Regulatory Networks
The Regulatory Apparatus
Encoded in the DNA
Overview of Regulatory Architecture
Gene control circuitry encoded in the DNA
The regulatory interactions mandated by this circuitry determine
whether each gene is expressed in every cell, throughout
developmental space and time and if so, at what amplitude.
• Information is stored in
DNA.
• DNA is transcribed to
messenger RNA.
• mRNA is processed and
transported to the
cytoplasm, where it is
translated to protein.
http://www.accessexcellence.org/AB/GG/central.html
Control of Gene Expression
• In physical terms the control circuitry encoded in DNA is
comprised of cis-regulatory elements plus the set of
genes which encode these specific regulatory proteins (i.e.,
transcription factors).
• A significant subset of proteins regulate the expression of
other genes. Because these proteins are also under
regulatory control, complex feedback loops result.
Product A
Gene A
Product B
Gene B
Trans-regulatory apparatus
• DNA-binding proteins — Directly interact with DNA
• Signaling pathways—modification of the DNA binding
proteins
• Adaptor proteins—through protein protein interaction
• Cofactors —through protein protein interaction
• Other entitles that affect the activity of transcription
factors—phosphorlation, methylation, ubiqutination
But it seems clear that most of this cellular machinery is in
general ubiquitous or in any case relatively nonspecific;
that it is always utilized for many diverse regulatory tasks in
each organism.
By far the most important genomic determinants of animal
diversity are the regulatory elements which encode the
genomic program for development.
General Principles of organization
of the developmental apparatus:
• Signaling affects regulatory gene expression--transcriptional termini of the intracellular signal
transduction pathways required in
development are located in the genomic
regulatory elements that determine
expression of genes encoded transcription
factors.
General Principles of organization
of the developmental apparatus:
• Developmental control systems have the
form of gene regulatory networks
Each regulatory gene has both multiple inputs
(from other regulatory genes), and multiple
outputs (to other regulatory genes), so each
can be conceived as a node of the networks.
General Principles of organization
of the developmental apparatus:
• The nodes of these gene regulatory networks
are unique
Each network node performs a unique job in
contributing to overall regulatory state.
• Regulatory genes perform multiple roles in
development
The repertoire of regulatory genes is
evolutionarily limited. Given factors are
frequently required for different processes in
different forms of development.
The Regulatory Apparatus
Encoded in the DNA
Gene Regulatory Networks
The properties of Developmental
Gene Regulatory Networks
Developmental GRNs involved
multiple sequential cascades of
transcription regulation.
Early transcriptional activity results in
the transient amplification of
asymmetries in herited maternal factors
which pre-define cellular territories.
Signaling within and between these
roughly defines territories refines cell
types boundaries and ensures uniformity
within each territories.
Batteries of structural genes can be
driven by cell-type specific pattern of
transcription factors.
Cis-regulatory target sites in DNA
• Major heritable sequence differences which
underlie its form.
• Consist of genomic DNA sequence —
hardwired.
• Same in every cell of the animal — their
organization is a heritable species character.
Genes encoding transcription
factors
• Lie at the nexus of large regulatory networks
• Consisting of all of their target genes
• Of all the regulatory genes encode the
proteins controlling their activity.
The subjects of this book
• How the hardwired control systems of the
genome work
• How their functions underlies developmental
processes
• How they provide an explanation for
evolutionary change in animal body plan
The definition of modules
•Cis-regulatory modules: silencers, enhancers, insulators.
•Each module is typically 300bp or more in length.
•Contains ten or more binding sites for at least 4 transcription factors.
•The cis-regulatory module of eve stripe 2.
•The cis-regulatory logic of the endo16 promoter.
No. CRM in genome
THE REGULATORY GENOME
NO. ELEMENTS (CRM): 5-10 X NO. OF GENES
SIZE OF ELEMENTS : A FEW HUNDRED BASE PAIRS
TOTAL COMPLEXITY: AT LEAST AS MUCH DNA SEQUENCE
LENGTH IS INCLUDED IN REGULATORY ELEMENTS AS IN SUM OF
PROTEIN CODING REGIONS OF GENES (MAYBE 2-3X AS MUCH)
CRM in genome diagram
(Gene Regulatory Modules)
Gene Regulatory Networks for Development:
What They are, how they work, and what they mean
Five examples of network
subcircuits:
• Every node in each of these examples includes
a gene that encodes a transcription factor.
• These subcircuits would each execute a unit
developmental function.
• They are portrayed as VFGs so their structural
relationships may be visualized at a glance.
Subsircuits that do developmental jobs:
Subdivision of territory by subcircuit AND logic
Institution of regulatory state by setting up a
stable feedback loop:
Eventual specification of confines spatial
expression beginning with broad domain
Exclusion of alternative regulatory state on
specification
Spatial and temporal peak of expression
GRN diagram
BASIC PRINCIPLES OF
DEVELOPMENTAL CONTROL
• THE HERITABLE PROGRAM FOR DEVELOPMENT RESIDES IN THE
GENOMIC REGULATORY CODE.
• THIS SPECIFIES IF, WHEN, AND WHERE EACH GENE WILL BE
EXPRESSED GIVEN THE AMBIENT REGULATORY STATE.
• REGULATORY STATE IS THE SUM OF THE ACTIVITIES OF THE DNABINDING TRANSCRIPTION FACTORS PRESENT IN EACH CELL
NUCLEUS.
• REGULATORY STATES ARE GENERATED BY TRANSCRIPTION OF
GENES ENCODING TRANSCRIPTION FACTORS.
• THESE PROTEINS CONTROL DEPLOYMENT OF THE BIOCHEMICAL
GENE EXPRESSION APPARATUS OF THE CELL.
The Regulatory Demands of
Development
Readout and generation of
Regulatory information in
developmental specification
REGULATION OF GENE EXPRESSION
IN DEVELOPMENT:
EACH DEVELOPMENTAL GENE REGULATORY MODULE
FUNCTIONS AS A HARD-WIRED INFORMATION PROCESSING
SYSTEM IN ITS REGULATORY DNA
Eve stripe CRM experiment
Studying GR -microinjection
What CRM are like?
Development, Vol 124, Issue 10 1851-1864, 1997
The hardwiring of development: organization and function of genomic
regulatory systems
MI Arnone and EH Davidson
The Regulatory Demands of
Development
From Regional Specification to
Terminal Differentiation
These genes can be considered as members of muscle gene batteries:
they share target sites for several specific transcriptional regulators
Regulatory States and GRN,
diagram
Linkages of Process Diagram
Process Diagram and network
Bird’s eye network image that indicates relative positions of network modules in context of
developmental parts and/or stages
Gene Regulatory Networks: The roots of
causality and diversity in animal evolution
什麼是「種」？
種是由屬名和種名構成的，也就是說各種生物以林奈氏（Carolus
Linnaeus）二名法（Binomial Nomenclature）而成，其方法由上
而下為界、門、綱、目、科、屬、種等分類的階層中。
現今生物共分
三域（Domain: 古菌域、真細菌域及真核生物域）
六界：真細菌界（Eubacteria）、古細菌界（Archaea）、原生動物
界（Protista）、植物界（Plantae）、真菌界（Fungi）和動物界
（Animalia）。
這些生物都是以形態分之，其外型同中有異、異中有同，因此可
劃出生物演化路徑，就如一棵演化樹一般。
演化樹裡愈早就岔開的物種相似度會比較低一些，而愈晚才
岔開的物種則各種序列就愈接近
(版權聲明) 依據 Angelalive/公有領域 授權引用。
Changes in the different parts of a gene regulatory network and their
qualitatively diverse evolutionary consequences
 Changes at the
network periphery:
such as continuous
changes in
differentiation gene
batteries and in the
immediate
upstream lineages
which determine the
deployment of these
batteries…
→reflect in species (種)
and geric (屬)
differences
Changes in the different parts of a gene regulatory network and their
qualitatively diverse evolutionary consequences
• Changes in the
internal portions of
the network:
→ redeployment of
plug-ins and making
and breaking I/O
linkages…
→ affect regional
regulatory state
specification, hence
pattern formation,
hence the
morphology of body
part…
→ reflect the Class (綱) ,
Order (目) , and
Family (科) level
diversification
Changes in the different parts of a gene regulatory network and their
qualitatively diverse evolutionary consequences
 The basic stability of
phylum (門) -level
morphological
characters:
→ May be due to the
extreme
conservation of
network kernels.
→ The process that
drive the small
changes observed
as species diverge
cannot be taken as
model for evolution
of the body plans of
animals.
Changes in the different parts of a gene regulatory network and their
qualitatively diverse evolutionary consequences
The parts of Gene Regulatory Networks,
and the Qualities of Evolutionary Change
1. Differentiation gene batteries: differentiation gene batteries
do not make body plans, traditional micro-evolutionary
theory is not useable for treatment of the molecular
mechanisms by which evolution of the animal body plan
has occurred.
2. Promiscuously used, invariant little subcircuits, such as panbilaterian signal transduction systems, plug-ins: signaling
cassettes are used in the development of the diversely
elaborated body parts of the different animal clades, their
redeployment has been a major mechanism of evolutionary
diversification in body plan at all levels, at least from the
Early Cambrian down to the present.
3. Input/output (I/O) devices that act as switches on other
network subcircuits: change in them is what used to be
referred to as changing the “embryological address” to
which a given function is directed.
The parts of Gene Regulatory Networks,
and the Qualities of Evolutionary Change
4. Highly conserved, rigidly and recursively wired subcircuits
which initiate specification of fields from which particular
body parts arise, and which we refer to as the “kernel” of
developmental gene regulatory networks.
Kernels are enormously resistant to change. Neither gene nor
cis-regulatory input could easily be removed from them on
pain of the gross failure of the body part to develop, kernel
could provide an answer to what is perhaps the largest
unsolved problem in bilaterian evolution.
The mechanistic reason that no new phylum or super-phylum
level body parts have appeared since the Cambrian emerges
directly from the intrinsically conservative properties of
kernels: once assembled, the kernels could not be taken apart
and some time in the future redone a different way.
HARDWIRED GENE REGULATORY
NETWORK (GRN) ARCHITECTURE:
GENOMIC CHANGES THAT CAUSE ALTERATIONS IN BODY PLAN IN
EVOLUTION ARE THOSE THAT ALTER THE DEVELOPMENTAL
PROCESS.
THE DEVELOPMENTAL PROCESS IS SPECIFIED BY GRN
ARCHITECTURE.
THEREFORE, EVOLUTION OF ANIMAL BODY PLAN DEPENDS ON
CHANGES IN GRN ARCHITECTURE.
EVOLUTION OF THE BODY PLAN CAN ONLY BE UNDERSTOOD
FULLY BY COMPARATIVE GRN ANALYSIS, SINCE THAT IS THE ONLY
WAY WE CAN PERCEIVE SUCH CHANGES.
The end for the introduction of the “Regulatory Genome” for animal
development
• How the hardwired control systems of the genome
work?
• How their functions underlies developmental
processes?
• How they provide an explanation for evolutionary
change in animal body plan?