Gene Regulatory Networks Controlling
12 Xenopus Embryogenesis
Ken W.Y. Cho and Ira L. Blitz
CONTENTS
12.1. Historical Background ............................................................................................................................................. 185
12.2. Past Observations ..................................................................................................................................................... 186
12.2.1. Brief Overview of Xenopus Development ................................................................................................ 186
12.2.2. GRNs during Germ Layer Formation ....................................................................................................... 186
12.2.3. GRNs during Gastrulation ........................................................................................................................ 188
12.2.4. GRN Subcircuits in Xenopus Embryos ..................................................................................................... 188
12.3. Present Status of the Field ........................................................................................................................................ 190
12.4. Our Contribution to This Field—Insights ................................................................................................................ 192
12.5. Future Directions and Important Questions ............................................................................................................. 192
References ............................................................................................................................................................................ 193
12.1. HISTORICAL BACKGROUND
The orchestration of cohorts of gene expression at specif c
times and places during animal development needs to be
precisely repeated in every cell in every generation to create
and sustain the life of the organism. Regulatory programs
controlling gene expression in time and space, known as a
gene regulatory network (GRN), are critical to understand
the mechanisms governing developmental processes. A
GRN displays interactions between regulatory effectors,
such as transcription factors (TFs) and cis-regulatory modules (CRMs), and explains how target gene expression is
precisely triggered to be induced or repressed (Peter and
Davidson, 2015). CRMs are typically 100–1000 base pairs in
length and dock a number of TFs, acting as a functional unit,
to regulate expression of a nearby gene (Davidson, 2006). In
general, a gene produces a specifc pattern of transcription
in space and time by integrating the enhancers, insulators
and silencers, and multiple CRMs can combine to produce
complex patterns of gene expression (Gray et al., 1994). All
of this information is hardwired into the animal genome,
and GRN study provides a mechanistic understanding of
these biological processes, often displaying TF and gene
interactions using a wiring diagram.
Genetic modifcation of individual genes has served as
a powerful tool to uncover critical functions in both phenotype and the developmental regulation to achieve it. The
uncovering of the hierarchical regulatory interactions of
the segmentation gene network in Drosophila has led to a
powerful illustration of how TFs organize networks of subordinate genes to guide the behavior of embryonic cells
during development (Schroeder et al., 2004). These discoveries also inform us that developmental genes function in
networks, and it is their function within these networks that
ultimately generates biological outcomes. Thus, identifying
the structure of a network and its functions and activities is
a necessary step toward comprehending the cause of various
embryonic and cellular behaviors at a system-wide level, as
well as predicting phenotypes in disease.
The frst theoretical model describing the mechanisms
controlling gene regulation in higher eukaryotes was postulated by Britten and Davidson (1969). They hypothesized
that individual TFs regulate the expression of diverse batteries of genes to provide specifc phenotypic outcomes. The
authors presented the structure of the regulatory network as
a wiring diagram to describe how genes interact in a network. Because of the unidirectional information f ow (input
=> output) within genomic control systems, a GRN diagram
is distinct from other types of networks, such as proteinprotein interaction networks or metabolic networks, which
typically lack clear directionality. Subsequently, Davidson
and coworkers expanded their approach and performed
more systematic investigation of a GRN, including all the
genes operating in a single network controlling the specifcation of endomesoderm cells in early sea urchin development (Peter and Davidson, 2010). Their endomesoderm
GRN diagram depicted relationships between nearly 50 TFs
and illustrated how changes at a single node (one interaction point between a gene and its regulator) in the network
can impact the transcription of multiple downstream genes
(Nam and Davidson, 2012). By linking the direct input and
output information of each interaction (based on the spatiotemporal expression patterns of the genes, DNA binding
information, and perturbation analysis), it becomes feasible
to predict the potential outcome of a given regulatory interaction (Faure et al., 2012).
Establishment of similar regulatory network diagrams
for vertebrate embryonic development is a necessary next
DOI: 10.1201/9781003050230-14
185
12 Xenopus Embryogenesis
Ken W.Y. Cho and Ira L. Blitz
CONTENTS
12.1. Historical Background ............................................................................................................................................. 185
12.2. Past Observations ..................................................................................................................................................... 186
12.2.1. Brief Overview of Xenopus Development ................................................................................................ 186
12.2.2. GRNs during Germ Layer Formation ....................................................................................................... 186
12.2.3. GRNs during Gastrulation ........................................................................................................................ 188
12.2.4. GRN Subcircuits in Xenopus Embryos ..................................................................................................... 188
12.3. Present Status of the Field ........................................................................................................................................ 190
12.4. Our Contribution to This Field—Insights ................................................................................................................ 192
12.5. Future Directions and Important Questions ............................................................................................................. 192
References ............................................................................................................................................................................ 193
12.1. HISTORICAL BACKGROUND
The orchestration of cohorts of gene expression at specif c
times and places during animal development needs to be
precisely repeated in every cell in every generation to create
and sustain the life of the organism. Regulatory programs
controlling gene expression in time and space, known as a
gene regulatory network (GRN), are critical to understand
the mechanisms governing developmental processes. A
GRN displays interactions between regulatory effectors,
such as transcription factors (TFs) and cis-regulatory modules (CRMs), and explains how target gene expression is
precisely triggered to be induced or repressed (Peter and
Davidson, 2015). CRMs are typically 100–1000 base pairs in
length and dock a number of TFs, acting as a functional unit,
to regulate expression of a nearby gene (Davidson, 2006). In
general, a gene produces a specifc pattern of transcription
in space and time by integrating the enhancers, insulators
and silencers, and multiple CRMs can combine to produce
complex patterns of gene expression (Gray et al., 1994). All
of this information is hardwired into the animal genome,
and GRN study provides a mechanistic understanding of
these biological processes, often displaying TF and gene
interactions using a wiring diagram.
Genetic modifcation of individual genes has served as
a powerful tool to uncover critical functions in both phenotype and the developmental regulation to achieve it. The
uncovering of the hierarchical regulatory interactions of
the segmentation gene network in Drosophila has led to a
powerful illustration of how TFs organize networks of subordinate genes to guide the behavior of embryonic cells
during development (Schroeder et al., 2004). These discoveries also inform us that developmental genes function in
networks, and it is their function within these networks that
ultimately generates biological outcomes. Thus, identifying
the structure of a network and its functions and activities is
a necessary step toward comprehending the cause of various
embryonic and cellular behaviors at a system-wide level, as
well as predicting phenotypes in disease.
The frst theoretical model describing the mechanisms
controlling gene regulation in higher eukaryotes was postulated by Britten and Davidson (1969). They hypothesized
that individual TFs regulate the expression of diverse batteries of genes to provide specifc phenotypic outcomes. The
authors presented the structure of the regulatory network as
a wiring diagram to describe how genes interact in a network. Because of the unidirectional information f ow (input
=> output) within genomic control systems, a GRN diagram
is distinct from other types of networks, such as proteinprotein interaction networks or metabolic networks, which
typically lack clear directionality. Subsequently, Davidson
and coworkers expanded their approach and performed
more systematic investigation of a GRN, including all the
genes operating in a single network controlling the specifcation of endomesoderm cells in early sea urchin development (Peter and Davidson, 2010). Their endomesoderm
GRN diagram depicted relationships between nearly 50 TFs
and illustrated how changes at a single node (one interaction point between a gene and its regulator) in the network
can impact the transcription of multiple downstream genes
(Nam and Davidson, 2012). By linking the direct input and
output information of each interaction (based on the spatiotemporal expression patterns of the genes, DNA binding
information, and perturbation analysis), it becomes feasible
to predict the potential outcome of a given regulatory interaction (Faure et al., 2012).
Establishment of similar regulatory network diagrams
for vertebrate embryonic development is a necessary next
DOI: 10.1201/9781003050230-14
185