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Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics.
Gildor T
,
Ben-Tabou de-Leon S
.
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Accurate temporal control of gene expression is essential for normal development and must be robust to natural genetic and environmental variation. Studying gene expression variation within and between related species can delineate the level of expression variability that development can tolerate. Here we exploit the comprehensive model of sea urchin gene regulatory networks and generate high-density expression profiles of key regulatory genes of the Mediterranean sea urchin, Paracentrotus lividus (Pl). The high resolution of our studies reveals highly reproducible gene initiation times that have lower variation than those of maximal mRNA levels between different individuals of the same species. This observation supports a threshold behavior of gene activation that is less sensitive to input concentrations. We then compare Mediterranean sea urchin gene expression profiles to those of its Pacific Ocean relative, Strongylocentrotus purpuratus (Sp). These species shared a common ancestor about 40 million years ago and show highly similar embryonic morphologies. Our comparative analyses of five regulatory circuits operating in different embryonic territories reveal a high conservation of the temporal order of gene activation but also some cases of divergence. A linear ratio of 1.3-fold between gene initiation times in Pl and Sp is partially explained by scaling of the developmental rates with temperature. Scaling the developmental rates according to the estimated Sp-Pl ratio and normalizing the expression levels reveals a striking conservation of relative dynamics of gene expression between the species. Overall, our findings demonstrate the ability of biological developmental systems to tightly control the timing of gene activation and relative dynamics and overcome expression noise induced by genetic variation and growth conditions.
Fig 1.
Sp and Pl development.
A, Comparison of Pl (top) and Sp (bottom) embryo development up to prism stage. B, Schematic diagrams of sea urchin cell lineages [28]. Red–skeletogenic mesoderm, light purple–non skeletogenic mesoderm, blue–endoderm, yellow–oral ectoderm, green–aboral ectoderm, dark purple–small micromeres.
Fig 2. Mild variations of mRNA maximal levels and highly repeatable gene initiation times in Pl expression profiles.
A,
blimp1b mRNA level in three biological repeats (blue, red and green lines) and average of the three replicates (black dashed line). Expression is presented in Log10 scale. B, Example for the use of the sigmoid fit to measure the initiation time, t0 (See text). Blue dots are the measured expression of blimp1b at #1 biological repeat, blue line is the sigmoidal function using the fit parameters obtained from Matlab. Red dashed line indicates the time of half rise, t0, which is one of the parameters of the sigmoid function. Black dashed lines indicate the parameters a, b, c of the sigmoid function. C, Maximal mRNA level at the three biological repeats. Error bars represent technical standard error. D, Gene initiation time of the zygotic genes in Pl extracted using the sigmoid fit. Error bars represent 95% confidence bounds reported by Matlab. E, The ratio between estimated initiation times in pairs of biological repeats, interception was set at zero. Linear relations with slopes of ~1 indicate highly reproducible developmental rates within the species.
Fig 3. Comparison of transcriptional expression profiles of five regulatory circuits that operate at different embryonic territories.Circuit diagrams are based on experimental studies in Sp. A-C, Skeletogenic circuit: A, schematic diagram; B, time course in Sp; C, time course in Pl. The color code of the genes matches throughout A-C and the same is for the rest of the circuits. D-F, aboral non-skeletogenic mesoderm circuit (pigment cell specification), G-I, Endoderm specification circuit, J-L, aboral ectoderm circuit. M-O, oral ectoderm circuit. Each point in Pl time courses is an average of three biological repeats, see material and methods for experimental details.
Fig 4. Linear relationship between gene initiation times in Sp and Pl.Gene initiation times for each species was calculated using the sigmoid fit. Black line is the result of a linear regression of the Sp-Pl slope (slope of ×1.3, R2 = 0.84, interception was set to zero). The genes six1/2 and VEGF were excluded from the linear regression as their temporal expression profiles indicate changes in their regulation.
Fig 5. High similarities between Sp and Pl normalized expression profiles scaled according to developmental rates.Corresponding developmental time points in the two species are provided in S1 Table. A, Skeletogenic mesoderm circuit; B, aboral non-skeletogenic mesoderm (pigment) circuit; C, endoderm circuit; D, Aboral ectoderm circuit; E, oral ectoderm circuit.
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