Basic HTML Version
Full Abstracts – SYSTEMS AND QUANTITATIVE BIOLOGY
163
115
Reverse-engineering the evolutionary and developmental dynamics of the gap gene system.
Johannes Jaeger, Karl Wotton, Anton Crombach, Damjan
Cicin-Sain. EMBL/CRG Research Unit in Systems Biology CRG - Centre de Regulació Genòmica Barcelona, Spain.
To gain a mechanistic and quantitative understanding of the genotype-phenotype map is one of the big challenges in biology today. Tackling this challenge
requires a quantitative systems-level understanding of the gene networks underlying development across multiple levels, from the molecular to the
organismic. This is difficult due to the large number of factors involved. We depend on computational models for this task. I present a reverse-engineering
approach, where gene regulatory interactions are inferred from quantitative expression data, using data-driven mathematical models (called gene circuits).
We have established that the gap gene network can be consistently reconstructed in this way using both protein or mRNA expression data. Gap gene circuit
models in
Drosophila
reproduce observed gene expression with high precision and temporal resolution and reveal a dynamic mechanism for the control of
positional information through shifts of gap gene expression domains. My group is extending this approach to a comparative study of the gap gene network
between different species of dipterans. No such quantitative systems-level analysis of an evolving developmental gene regulatory network has been achieved
to date. I will present results concerning data quantification and modeling of gap genes in the scuttle fly
Megaselia abdita
, and the moth midge
Clogmia
albipunctata
. We have created and analyzed quantitative data sets for gap gene expression in both of these species, which are now used for model fitting.
Our approach yields precise, quantitative predictions of how changes of gene regulatory feedback affect the timing and positioning of expression domains in
these species. These predictions are now being tested experimentally using RNA interference.
116
Consequences of enhancer architecture for gene expression dynamics and fitness.
Manu Manu
1
, Michael Ludwig
1,2
, Ralf Kittler
2,3
, Kevin White
2,3
,
Martin Kreitman
1,2
. 1) Ecology and Evolution, University of Chicago, Chicago, IL; 2) Institute for Genomics and Systems Biology, University of Chicago,
Chicago, IL; 3) Human Genetics, University of Chicago, Chicago, IL.
During the past decade or so, investigators have identified a number of regulatory features that confer robustness to gene networks. Here we present
evidence that the
cis
-regulatory architecture of genes, that is, the number and placement of transcription-factor binding sites (TFBS), promotes the
reproducibility of gene expression and buffers genetic and environmental perturbation. Eukaryotic
cis
-regulatory regions often contain TFBS outside the
boundaries of enhancers defined by reporter assays. In
Drosophila
, the
cis
-regulatory element driving expression in the second stripe of the
even-skipped
(
eve
) pattern has evolutionarily-conserved binding sites outside the minimal stripe element (MSE). The conservation of these sites suggests that they play a
functional role in development. We used recombineering to make constructs that rescue
eve
-
lethality and that could be imaged live to investigate the effect
of these sites on gene expression dynamics and fitness. We used rescue crosses and quantitative time-course data to show that these binding sites are 1)
dispensable for viability but are necessary for 2) precise placement of the stripe and 3) temperature compensation. Our investigation also led to a surprising
discovery: we found that
eve
, thought to be a stereotypically-expressed morphogen, is expressed differently in male and female embryos during early
development. We traced
eve
's sex-specific expression to an incomplete compensation of
giant
dosage. However, segmentation itself was found to be sex-
independent. This result implies that later autosomal regulation in the segmentation system can correct the deleterious effects of incomplete dosage
compensation. Our results show that enhancer architecture is optimized not just to turn genes "on" or "off" but to do so robustly across different
environments and genetic backgrounds.
117
Epithelial folding during eggshell morphogenesis.
Miriam Osterfield
1
, XinXin Du
2
, Trudi Schüpbach
4,5
, Eric Wieschaus
4,5
, Stanislav Shvartsman
1,3
. 1)
Lewis-Sigler Institute, Princeton Univ, Princeton, NJ; 2) Department of Physics, Princeton University, NJ; 3) Department of Chemical and Biological
Engineering, Princeton University, NJ; 4) Department of Molecular Biology, Princeton University, NJ; 5) Howard Hughes Medical Institute.
The formation of tubular structures is central to the development of many types of organs. To investigate the mechanisms of tubulogenesis, we examine
dorsal appendage formation, the process in which the follicular epithelium surrounding a Drosophila oocyte develops from a simple ovoid surface to a
structure with two protruding tubes. Dorsal appendage tube formation is thought to occur by the process of wrapping. Our analysis shows that during this
process, the apical surface of follicle cells remains continuous. The dorsal appendage tubes form by lateral cell rearrangements in a spatially organized
process of intercalation, coupled to deformation of the sheet. E-cadherin, Bazooka, and myosin proteins all show non-uniform localizations that suggest
specific patterns of tension along cell edges within the apical domain. Using a computational vertex model accounting for cell elasticity and tension in
epithelial sheets, we show that these experimentally predicted patterns of tension are sufficient to account for the three-dimensional deformation of the apical
surface during early stages of tube formation.
118
Quantifying the consistency of interactions in the NADP(H) enzyme network across varying environmental conditions.
Teresa Rzezniczak, Thomas
J.S. Merritt. Department of Chemistry & Biochemistry, Laurentian University, Sudbury, Ontario, Canada.
Interactions between members of biological networks are often quantified under a single set of conditions, however cellular behaviours are dynamic and
interactions can change in response to molecular contexts. The extent which environment plays a role in governing these interactions is still unclear. To
determine the consistency of network interactions, we examined the enzyme network responsible for the reduction of nicotinamide adenine dinucleotide
phosphate (NADP) to NADPH across three different conditions of stress: oxidative stress, starvation and desiccation. We used synthetic, activity-variant
alleles in
Drosophila melanogaster
for
glucose-6-phosphate dehydrogenase
, cytosolic
isocitrate dehydrogenase
and cytosolic
malic enzyme
as well as seven
different genetic backgrounds to lend biological significance to the data. The response of the NADP-reducing enzymes as well as two downstream
phenotypes (triglyceride and carbohydrate concentration) was quantified spectrophotometrically between the control and stressful conditions. Each stressor
was found to affect the activities of NADP-reducing enzymes differently: oxidative stress resulted in metabolic re-routing to the pentose phosphate pathway,
desiccation caused up-regulation of the NADP-reducing enzymes, whereas no response was observed under starvation. In addition, we found significant
changes in the response to the reductions in the NADP-reducing enzymes with differing experimental conditions, suggesting that the way in which the
enzymes interact and the amount of NADPH they contribute to the cellular pool changes with differing conditions. These findings indicate that biological
network interactions are strongly influenced by the molecular context of the cell and underscore the importance of examining network dynamics.