Primitive Endoderm Differentiates via a Three-Step Mechanism Involving Nanog and RTK Signaling

SummaryDuring preimplantation mouse development, the inner cell mass (ICM) differentiates into two cell lineages—the epiblast and the primitive endoderm (PrE)—whose precursors are identifiable by reciprocal expression of Nanog and Gata6, respectively. PrE formation depends on Nanog by a non-cell-autonomous mechanism. To decipher early cell- and non-cell-autonomous effects, we performed a mosaic knockdown of Nanog and found that this is sufficient to induce a PrE fate cell autonomously. Strikingly, in Nanog null embryos, Gata6 expression is maintained, showing that initiation of the PrE program is Nanog independent. Treatment of Nanog null embryos with pharmacological inhibitors revealed that RTK dependency of Gata6 expression is initially direct but later indirect via Nanog repression. Moreover, we found that subsequent expression of Sox17 and Gata4—later markers of the PrE—depends on the presence of Fgf4 produced by Nanog-expressing cells. Thus, our results reveal three distinct phases in the PrE differentiation program

Spatio-temporal requirements for transposable element piRNA-mediated silencing during Drosophila oogenesis

International audienceDuring Drosophila oogenesis, transposable element (TE) repression involves the Piwi-interacting RNA (piRNA) pathway which ensures genome integrity for the next generation. We developed a transgenic model to study repression of the Idefix retrotrans-poson in the germline. Using a candidate gene KD-approach, we identified differences in the spatio-temporal requirements of the piRNA pathway components for piRNA-mediated silencing. Some of them (Aub, Vasa, Spn-E) are necessary in very early stages of oogenesis within the germarium and appear to be less important for efficient TE silencing thereafter. Others (Piwi, Ago3, Mael) are required at all stages of oogenesis. Moreover, during early oogenesis, in the dividing cysts within the germarium, Idefix anti-sense transgenes escape host control, and this is associated with very low piwi expression. Silencing of P-element-based transgenes is also strongly weakened in these cysts. This region, termed the 'Piwiless pocket' or Pilp, may ensure that new TE insertions occur and are transmitted to the next generation, thereby contributing to genome dynamics. In contrast, piRNA-mediated silencing is strong in germline stem cells in which TE mobilization is tightly repressed ensuring the continued production of viable germline cysts

GReD-Clermont/omero_batch-plugin: 2.0.0

<h2>Instructions</h2> <ol> <li>Install the <a href="https://omero-guides.readthedocs.io/en/latest/fiji/docs/installation.html">OMERO.insight plugin for Fiji</a> (if you haven't already).</li> <li>Download the JAR file for the <a href="https://github.com/GReD-Clermont/simple-omero-client/releases/5.16.0/"><em>Simple OMERO Client</em> library</a>.</li> <li>Download the <a href="https://github.com/GReD-Clermont/omero_batch-plugin/releases/download/2.0.0/omero_batch-plugin-2.0.0.jar">JAR file for this plugin</a>.</li> <li>Place these JAR files in your plugins folder and make sure to remove any previous version.</li> </ol> <h2>What's Changed</h2> <ul> <li>V2.0 by in #22</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/GReD-Clermont/omero_batch-plugin/compare/1.0.5...2.0.0</p&gt

GReD-Clermont/omero_batch-plugin: 2.0.1

<h2>Instructions</h2> <ol> <li>Install the <a href="https://omero-guides.readthedocs.io/en/latest/fiji/docs/installation.html">OMERO.insight plugin for Fiji</a> (if you haven't already).</li> <li>Download the JAR file for the <a href="https://github.com/GReD-Clermont/simple-omero-client/releases/5.16.0/"><em>Simple OMERO Client</em> library</a>.</li> <li>Download the <a href="https://github.com/GReD-Clermont/omero_batch-plugin/releases/download/2.0.1/omero_batch-plugin-2.0.1.jar">JAR file for this plugin</a>.</li> <li>Place these JAR files in your plugins folder and make sure to remove any previous version.</li> </ol> <h2>What's Changed</h2> <ul> <li>Bugfix: reload project after adding dataset, in #23</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/GReD-Clermont/omero_batch-plugin/compare/2.0.0...2.0.1</p&gt

GReD-Clermont/omero_macro-extensions: 1.3.3

<h2>Instructions</h2> <ol> <li>Install the <a href="https://omero-guides.readthedocs.io/en/latest/fiji/docs/installation.html">OMERO.insight plugin for Fiji</a> (if you haven't already).</li> <li>Download the JAR file for the <a href="https://github.com/GReD-Clermont/simple-omero-client/releases/5.16.0/">library</a>.</li> <li>Download the <a href="https://github.com/GReD-Clermont/omero_macro-extensions/releases/download/1.3.3/omero_macro-extensions-1.3.3.jar">JAR file for this plugin</a>.</li> <li>Place these JAR files in your plugins folder and make sure to remove any previous version.</li> </ol> <h2>What's Changed</h2> <ul> <li>Fix default port for websockets in #17</li> <li>Bump versions, update README and improve ROI deletion in #18</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/GReD-Clermont/omero_macro-extensions/compare/1.3.2...1.3.3</p&gt

GReD-Clermont/simple-omero-client: 5.15.0

What's Changed Add methods for user / group management by @Rdornier in https://github.com/GReD-Clermont/simple-omero-client/pull/74 Full Changelog: https://github.com/GReD-Clermont/simple-omero-client/compare/5.14.2...5.15.

Basement membrane diversification relies on two competitive secretory routes defined by Rab10 and Rab8 and modulated by dystrophin and the exocyst complex

Abstract The basement membrane (BM) is an essential structural element of tissues, and its diversification participates in organ morphogenesis. However, the traffic routes associated with BM formation and the mechanistic modulations explaining its diversification are still poorly understood. Drosophila melanogaster follicular epithelium relies on a BM composed of oriented BM fibrils and a more homogenous matrix. Here, we determined the specific molecular identity and cell exit sites of BM protein secretory routes. First, we found that Rab10 and Rab8 define two parallel routes for BM protein secretion. When both routes were abolished, BM production was fully blocked; however, genetic interactions revealed that these two routes competed. Rab10 promoted lateral and planar-polarized secretion, whereas Rab8 promoted basal secretion, leading to the formation of BM fibrils and homogenous BM, respectively. We also found that the dystrophin-associated protein complex (DAPC) associated with Rab10 and both were present in a planar-polarized tubular compartment containing BM proteins. DAPC was essential for fibril formation and sufficient to reorient secretion towards the Rab10 route. Moreover, we identified a dual function for the exocyst complex in this context. First, the Exo70 subunit directly interacted with dystrophin to limit its planar polarization. Second, the exocyst complex was also required for the Rab8 route. Altogether, these results highlight important mechanistic aspects of BM protein secretion and illustrate how BM diversity can emerge from the spatial control of distinct traffic routes

Jak-Stat pathway induces Drosophila follicle elongation by a gradient of apical contractility

International audienceTissue elongation and its control by spatiotemporal signals is a major developmental question. Currently, it is thought that Drosophila ovarian follicular epithelium elongation requires the planar polarization of the basal domain cytoskeleton and of the extra-cellular matrix, associated with a dynamic process of rotation around the anteroposterior axis. Here we show, by careful kinetic analysis of fat2 mutants, that neither basal planar polarization nor rotation is required during a first phase of follicle elongation. Conversely, a JAK-STAT signaling gradient from each follicle pole orients early elongation. JAK-STAT controls apical pulsatile contractions, and Myosin II activity inhibition affects both pulses and early elongation. Early elongation is associated with apical constriction at the poles and with oriented cell rearrangements, but without any visible planar cell polarization of the apical domain. Thus, a morphogen gradient can trigger tissue elongation through a control of cell pulsing and without a planar cell polarity requirement

NucBase, an easy to use read mapper for small RNAs

<p>Abstract</p> <p>Background</p> <p>High-throughput deep-sequencing technology has generated an unprecedented number of expressed sequence reads that offer the opportunity to get insight into biological systems. Several databases report the sequence of small regulatory RNAs which play a prominent role in the control of transposable elements (TE). However, the huge amount of data reported in these databases remains mostly unexplored because the available tools are hard for biologists to use.</p> <p>Results</p> <p>Here we report NucBase, a new program designed to make an exhaustive search for sequence matches and to align short sequence reads from large nucleic acid databases to genomes or input sequences. NucBase includes a graphical interface which allows biologists to align sequences with ease and immediately visualize matched sequences, their number and their genomic position. NucBase identifies nucleic motives with strict identity to input sequences, and it capably finds candidates with one or several mismatches. It offers the opportunity to identify “core sequences” comprised of a chosen number of consecutive matching nucleotides. This software can be run locally on any Windows, Linux or Mac OS computer with 32-bit architecture compatibility.</p> <p>Conclusions</p> <p>Since this software is easy to use and can detect reads that were undetected by other software, we believe that it will be useful for biologists involved in the field of TE silencing by small non-coding RNAs. We hope NucBase will be useful for a larger community of researchers, since it makes exploration of small nucleic sequences in any organism much easier.</p

Tight Coordination of Growth and Differentiation between Germline and Soma Provides Robustness for Drosophila Egg Development

Organs often need to coordinate the growth of distinct tissues during their development. Here, we analyzed the coordination between germline cysts and the surrounding follicular epithelium during Drosophila oogenesis. Genetic manipulations of the growth rate of both germline and somatic cells influence the growth of the other tissue accordingly. Growth coordination is therefore ensured by a precise, two-way, intrinsic communication. This coordination tends to maintain constant epithelial cell shape, ensuring tissue homeostasis. Moreover, this intrinsic growth coordination mechanism also provides cell differentiation synchronization. Among growth regulators, PI3-kinase and TORC1 also influence differentiation timing cell-autonomously. However, these two pathways are not regulated by the growth of the adjacent tissue, indicating that their function reflects an extrinsic and systemic influence. Altogether, our results reveal an integrated and particularly robust mechanism ensuring the spatial and temporal coordination of tissue size, cell size, and cell differentiation for the proper development of two adjacent tissues