Analysis of her1 and her7 Mutants Reveals a Spatio Temporal Separation of the Somite Clock Module

Choorapoikayil, Suma; Willems, Bernd; Ströhle, Peter; Gajewski, Martin

doi:10.1371/journal.pone.0039073

Cited by 24 publications

(23 citation statements)

References 29 publications

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“…3) and amplitude (Fig. 4) Stochastic simulations predict how synchronization of oscillations will be affected when various genes are mutated in the segmentation clock network The segmentation clock is synchronized across neighboring cells via the Delta-Notch signal transduction pathway (Jiang et al, 2000;Horikawa et al, 2006;Mara et al, 2007;Riedel-Kruse et al, 2007;Ozbudak and Lewis, 2008;Delaune et al, 2012); synchronized gene expression is lost among neighboring cells when Notch signaling is impaired, which has been reproduced by our model (P=4×10 her7 −/− mutant embryos exhibit segmentation defects that are confined to the posterior axis (Choorapoikayil et al, 2012;Schröter et al, 2012;Hanisch et al, 2013). Our model shows that synchronized gene expression among cells has been impaired in these embryos in comparison with wild type (P=2.8×10 …”

Section: −/−supporting

confidence: 61%

Short-lived Her proteins drive robust synchronized oscillations in the zebrafish segmentation clock

Knierer

Sperlea

et al. 2013

Development

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SUMMARYOscillations are prevalent in natural systems. A gene expression oscillator, called the segmentation clock, controls segmentation of precursors of the vertebral column. Genes belonging to the Hes/her family encode the only conserved oscillating genes in all analyzed vertebrate species. Hes/Her proteins form dimers and negatively autoregulate their own transcription. Here, we developed a stochastic two-dimensional multicellular computational model to elucidate how the dynamics, i.e. period, amplitude and synchronization, of the segmentation clock are regulated. We performed parameter searches to demonstrate that autoregulatory negative-feedback loops of the redundant repressor Her dimers can generate synchronized gene expression oscillations in wild-type embryos and reproduce the dynamics of the segmentation oscillator in different mutant conditions. Our model also predicts that synchronized oscillations can be robustly generated as long as the half-lives of the repressor dimers are shorter than 6 minutes. We validated this prediction by measuring, for the first time, the half-life of Her7 protein as 3.5 minutes. These results demonstrate the importance of building biologically realistic stochastic models to test biological models more stringently and make predictions for future experimental studies.

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Section: −/−supporting

confidence: 61%

Short-lived Her proteins drive robust synchronized oscillations in the zebrafish segmentation clock

Knierer

Sperlea

et al. 2013

Development

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“…We and others have also reported that traveling wave-like expression patterns are significantly disturbed in her7 −/− mutants; there is also a large variation from embryo to embryo from the same mutant clutch (Choorapoikayil et al, 2012;Hanisch et al, 2013;Schroter et al, 2012). Our model nicely recapitulates this phenotype.…”

Section: −/−mentioning

confidence: 54%

“…We and others have recently reported that her1 −/− embryos halt their oscillations earlier in the PSM and manifest only one or two expression waves at mid-somitogenesis stages; this results in the formation of one less stripe in the anterior PSM in her1 −/− mutants (Choorapoikayil et al, 2012;Hanisch et al, 2013) compared with wild-type, hes6 −/− and her7 −/− ;hes6 −/− embryos (Schroter et al, 2012). Our model reproduced this observation successfully (Fig.…”

Section: −/−mentioning

confidence: 85%

Spatial gradients of protein-level time delays set the pace of the traveling segmentation clock waves

Holland

Sperlea

et al. 2014

Development

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The vertebrate segmentation clock is a gene expression oscillator controlling rhythmic segmentation of the vertebral column during embryonic development. The period of oscillations becomes longer as cells are displaced along the posterior to anterior axis, which results in traveling waves of clock gene expression sweeping in the unsegmented tissue. Although various hypotheses necessitating the inclusion of additional regulatory genes into the core clock network at different spatial locations have been proposed, the mechanism underlying traveling waves has remained elusive. Here, we combined molecularlevel computational modeling and quantitative experimentation to solve this puzzle. Our model predicts the existence of an increasing gradient of gene expression time delays along the posterior to anterior direction to recapitulate spatiotemporal profiles of the traveling segmentation clock waves in different genetic backgrounds in zebrafish. We validated this prediction by measuring an increased time delay of oscillatory Her1 protein production along the unsegmented tissue. Our results refuted the need for spatial expansion of the core feedback loop to explain the occurrence of traveling waves. Spatial regulation of gene expression time delays is a novel way of creating dynamic patterns; this is the first report demonstrating such a control mechanism in any tissue and future investigations will explore the presence of analogous examples in other biological systems.

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“…In all vertebrates, somites provide one of the first outward appearances of the metameric body plan, periodically pinching off from the presomitic mesoderm (PSM) in bilaterally symmetrical pairs as precursors to the axial muscles and vertebral column (Oates et al, 2012). To date, detailed studies of the gene dynamics underlying somitogenesis have relied heavily on examination of one-channel (Henry et al, 2002;Oates and Ho, 2002;Mara et al, 2007;Gomez et al, 2008;Ferjentsik et al, 2009;Choorapoikayil et al, 2012;Schroter et al, 2012) and two-channel (Holley et al, 2000;Oates and Ho, 2002;Jülich et al, 2005) CARD images that display expression of one or two mRNAs per embryo. Here, using in situ HCR, we demonstrate quantitative subcellular analyses of four mRNAs in the same embryo.…”

Section: Introductionmentioning

confidence: 99%

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

et al. 2018

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For decades, in situ hybridization methods have been essential tools for studies of vertebrate development and disease, as they enable qualitative analyses of mRNA expression in an anatomical context. Quantitative mRNA analyses typically sacrifice the anatomy, relying on embryo microdissection, dissociation, cell sorting and/or homogenization. Here, we eliminate the trade-off between quantitation and anatomical context, using quantitative in situ hybridization chain reaction (qHCR) to perform accurate and precise relative quantitation of mRNA expression with subcellular resolution within whole-mount vertebrate embryos. Gene expression can be queried in two directions: read-out from anatomical space to expression space reveals co-expression relationships in selected regions of the specimen; conversely, read-in from multidimensional expression space to anatomical space reveals those anatomical locations in which selected gene co-expression relationships occur. As we demonstrate by examining gene circuits underlying somitogenesis, quantitative read-out and read-in analyses provide the strengths of flow cytometry expression analyses, but by preserving subcellular anatomical context, they enable bi-directional queries that open a new era for in situ hybridization.

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Analysis of her1 and her7 Mutants Reveals a Spatio Temporal Separation of the Somite Clock Module

Cited by 24 publications

References 29 publications

Short-lived Her proteins drive robust synchronized oscillations in the zebrafish segmentation clock

Short-lived Her proteins drive robust synchronized oscillations in the zebrafish segmentation clock

Spatial gradients of protein-level time delays set the pace of the traveling segmentation clock waves

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

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