Mouse oocytes sequester aggregated proteins in degradative super-organelles

Oocytes are among the longest-lived cells in the body and need to preserve their cytoplasm to support proper embryonic development. Protein aggregation is a major threat for intracellular homeostasis in long-lived cells. How oocytes cope with protein aggregation during their extended life is unknown. Here, we find that mouse oocytes accumulate protein aggregates in specialized compartments that we named endolysosomal vesicular assemblies (ELVAs). Combining live-cell imaging, electron microscopy, and proteomics, we found that ELVAs are non-membrane-bound compartments composed of endolysosomes, autophagosomes, and proteasomes held together by a protein matrix formed by RUFY1. Functional assays revealed that in immature oocytes, ELVAs sequester aggregated proteins, including TDP-43, and degrade them upon oocyte maturation. Inhibiting degradative activity in ELVAs leads to the accumulation of protein aggregates in the embryo and is detrimental for embryo survival. Thus, ELVAs represent a strategy to safeguard protein homeostasis in long-lived cells.

MicroRNAs Regulate Ca2+ Homeostasis in Murine Embryonic Stem Cells

MicroRNAs (miRNAs) are important regulators of embryonic stem cell (ESC) biology, and their study has identified key regulatory mechanisms. To find novel pathways regulated by miRNAs in ESCs, we undertook a bioinformatics analysis of gene pathways differently expressed in the absence of miRNAs due to the deletion of Dicer, which encodes an RNase that is essential for the synthesis of miRNAs. One pathway that stood out was Ca2+ signaling. Interestingly, we found that Dicer-/- ESCs had no difference in basal cytoplasmic Ca2+ levels but were hyperresponsive when Ca2+ import into the endoplasmic reticulum (ER) was blocked by thapsigargin. Remarkably, the increased Ca2+ response to thapsigargin in ESCs resulted in almost no increase in apoptosis and no differences in stress response pathways, despite the importance of miRNAs in the stress response of other cell types. The increased Ca2+ response in Dicer-/- ESCs was also observed during purinergic receptor activation, demonstrating a physiological role for the miRNA regulation of Ca2+ signaling pathways. In examining the mechanism of increased Ca2+ responsiveness to thapsigargin, neither store-operated Ca2+ entry nor Ca2+ clearance mechanisms from the cytoplasm appeared to be involved. Rather, it appeared to involve an increase in the expression of one isoform of the IP3 receptors (Itpr2). miRNA regulation of Itpr2 expression primarily appeared to be indirect, with transcriptional regulation playing a major role. Therefore, the miRNA regulation of Itpr2 expression offers a unique mechanism to regulate Ca2+ signaling pathways in the physiology of pluripotent stem cells.

DRP1 levels determine the apoptotic threshold during embryonic differentiation through a mitophagy-dependent mechanism

The changes that drive differentiation facilitate the emergence of abnormal cells that need to be removed before they contribute to further development or the germline. Consequently, in mice in the lead-up to gastrulation, ∼35% of embryonic cells are eliminated. This elimination is caused by hypersensitivity to apoptosis, but how it is regulated is poorly understood. Here, we show that upon exit of naive pluripotency, mouse embryonic stem cells lower their mitochondrial apoptotic threshold, and this increases their sensitivity to cell death. We demonstrate that this enhanced apoptotic response is induced by a decrease in mitochondrial fission due to a reduction in the activity of dynamin-related protein 1 (DRP1). Furthermore, we show that in naive pluripotent cells, DRP1 prevents apoptosis by promoting mitophagy. In contrast, during differentiation, reduced mitophagy levels facilitate apoptosis. Together, these results indicate that during early mammalian development, DRP1 regulation of mitophagy determines the apoptotic response.

A developmentally programmed splicing failure contributes to DNA damage response attenuation during mammalian zygotic genome activation

Transition from maternal to embryonic transcriptional control is crucial for embryogenesis. However, alternative splicing regulation during this process remains understudied. Using transcriptomic data from human, mouse, and cow preimplantation development, we show that the stage of zygotic genome activation (ZGA) exhibits the highest levels of exon skipping diversity reported for any cell or tissue type. Much of this exon skipping is temporary, leads to disruptive noncanonical isoforms, and occurs in genes enriched for DNA damage response in the three species. Two core spliceosomal components, Snrpb and Snrpd2, regulate these patterns. These genes have low maternal expression at ZGA and increase sharply thereafter. Microinjection of Snrpb/d2 messenger RNA into mouse zygotes reduces the levels of exon skipping at ZGA and leads to increased p53-mediated DNA damage response. We propose that mammalian embryos undergo an evolutionarily conserved, developmentally programmed splicing failure at ZGA that contributes to the attenuation of cellular responses to DNA damage.

Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development

Cell competition is emerging as a quality-control mechanism that eliminates unfit cells in a wide range of settings from development to the adult. However, the nature of the cells normally eliminated by cell competition and what triggers their elimination remains poorly understood. In mice, 35% of epiblast cells are eliminated before gastrulation. Here we show that cells with mitochondrial defects are eliminated by cell competition during early mouse development. Using single-cell transcriptional profiling of eliminated mouse epiblast cells, we identify hallmarks of cell competition and mitochondrial defects. We demonstrate that mitochondrial defects are common to a range of different loser cell types and that manipulating mitochondrial function triggers cell competition. Moreover, we show that in the mouse embryo, cell competition eliminates cells with sequence changes in mt-Rnr1 and mt-Rnr2, and that even non-pathological changes in mitochondrial DNA sequences can induce cell competition. Our results suggest that cell competition is a purifying selection that optimizes mitochondrial performance before gastrulation.

MicroRNAs control the apoptotic threshold in primed pluripotent stem cells through regulation of BIM

Pernaute et al. identify miRNA-mediated regulation as a key mechanism controlling apoptosis in the post-implantation epiblast. Three miRNA families, miR-20, miR-92, and miR-302, control the mitochondrial apoptotic machinery by fine-tuning the levels of expression of the proapoptotic protein BIM. These miRNA families are needed to maintain cell survival in stem cells that are primed for not only differentiation but also cell death.

Mammalian primed pluripotent stem cells have been shown to be highly susceptible to cell death stimuli due to their low apoptotic threshold, but how this threshold is regulated remains largely unknown. Here we identify microRNA (miRNA)-mediated regulation as a key mechanism controlling apoptosis in the post-implantation epiblast. Moreover, we found that three miRNA families, miR-20, miR-92, and miR-302, control the mitochondrial apoptotic machinery by fine-tuning the levels of expression of the proapoptotic protein BIM. These families therefore represent an essential buffer needed to maintain cell survival in stem cells that are primed for not only differentiation but also cell death.

HOIP deficiency causes embryonic lethality by aberrant TNFR1-mediated endothelial cell death

Linear ubiquitination is crucial for innate and adaptive immunity. The linear ubiquitin chain assembly complex (LUBAC), consisting of HOIL-1, HOIP, and SHARPIN, is the only known ubiquitin ligase that generates linear ubiquitin linkages. HOIP is the catalytically active LUBAC component. Here, we show that both constitutive and Tie2-Cre-driven HOIP deletion lead to aberrant endothelial cell death, resulting in defective vascularization and embryonic lethality at midgestation. Ablation of tumor necrosis factor receptor 1 (TNFR1) prevents cell death, vascularization defects, and death at midgestation. HOIP-deficient cells are more sensitive to death induction by both tumor necrosis factor (TNF) and lymphotoxin-α (LT-α), and aberrant complex-II formation is responsible for sensitization to TNFR1-mediated cell death in the absence of HOIP. Finally, we show that HOIP's catalytic activity is necessary for preventing TNF-induced cell death. Hence, LUBAC and its linear-ubiquitin-forming activity are required for maintaining vascular integrity during embryogenesis by preventing TNFR1-mediated endothelial cell death.

Competitive interactions eliminate unfit embryonic stem cells at the onset of differentiation

A fundamental question in developmental biology is whether there are mechanisms to detect stem cells with mutations that, although not adversely affecting viability, would compromise their ability to contribute to further development. Here, we show that cell competition is a mechanism regulating the fitness of embryonic stem cells (ESCs). We find that ESCs displaying defective bone morphogenetic protein signaling or defective autophagy or that are tetraploid are eliminated at the onset of differentiation by wild-type cells. This elimination occurs in an apoptosis-dependent manner and is mediated by secreted factors. Furthermore, during this process, we find that establishment of differential c-Myc levels is critical and that c-Myc overexpression is sufficient to induce competitive behavior in ESCs. Cell competition is, therefore, a process that allows recognition and elimination of defective cells during the early stages of development and is likely to play important roles in tissue homeostasis and stem cell maintenance.

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Defective ESCs are eliminated at the onset of differentiation by wild-type cells

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Elimination of unfit cells is apoptosis dependent and mediated by secreted factors

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Higher c-Myc levels are established in wild-type ESCs cocultured with unfit cells

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c-Myc overexpression induces a competitive advantage in ESCs

Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1

The structural complexity of the vertebrate brain is mirrored by its unparalleled transcriptome complexity. In particular, two post-transcriptional processes, alternative splicing and RNA editing, greatly diversify brain transcriptomes. Here we report a close connection between these two processes: we show A-to-I RNA editing in Nova1, a key brain-specific regulator of alternative splicing. Nova1 editing levels increase during embryonic development in mouse and chicken brains and show significant variation across postnatal brain regions. Evolutionary conservation of both editing and editing-associated RNA secondary structure of the Nova1 mRNA for 300 million years attests to the functional importance of Nova1 editing. Using a combination of different assays in human HEK293T cell lines, we report a novel post-translational role for this RNA editing. Whereas functional assays showed no effect of RNA editing on the regulatory splicing activity of the encoded proteins, we found evidence that edited forms exhibit reduced proteasome targeting and increased protein half-life. In addition, we found evidence for similar regulation of protein half-life by an evolutionarily conserved alternative splicing event in Nova1. These results open new venues of research on the multi-level integration of gene expression by: (1) revealing the novel role of RNA editing in regulating protein stability, and (2) establishing protein stability as a new target of multifaceted regulation.

An early developmental role for miRNAs in the maintenance of extraembryonic stem cells in the mouse embryo

The two first cell fate decisions taken in the mammalian embryo generate three distinct cell lineages: one embryonic, the epiblast, and two extraembryonic, the trophoblast and primitive endoderm. miRNAs are essential for early development, but it is not known if they are utilized in the same way in these three lineages. We find that in the pluripotent epiblast they inhibit apoptosis by blocking the expression of the proapoptotic protein Bcl2l11 (Bim) but play little role in the initiation of gastrulation. In contrast, in the trophectoderm, miRNAs maintain the trophoblast stem cell compartment by directly inhibiting expression of Cdkn1a (p21) and Cdkn1c (p57), and in the primitive endoderm, they prevent differentiation by maintaining ERK1/2 phosphorylation through blocking the expression of Mapk inhibitors. Therefore, we show that there are fundamental differences in how stem cells maintain their developmental potential in embryonic and extraembryonic tissues through miRNAs.

Secale cereale inter-microsatellites (SCIMs): chromosomal location and genetic inheritance

The polymerase chain reaction (PCR) was used to locate Sectale cereale (inter-simple sequence repeat ISSR) or Secale cereale inter-microsatellite (SCIM) markers using wheat-rye addition lines in order to develop a set of molecular markers distributed on the seven rye chromosomes. The number of SCIM markers located on 1R, 2R, 3R, 4R, 5R, 6R and 7R chromosomes were 4, 3, 12, 3, 2, 9 and 8, respectively. Therefore, a total of 41 new SCIMs were located on the seven rye chromosomes. The segregation of the 63 different SCIM markers in three different F2 was studied. The observed ISSR segregations were the 3:1 (50.7%), the 15:1 (12.7%) and the 1:1 (14.2%). The linkage analysis carried out indicated that seven of the segregating SCIMs were linked to chromosome 7R and two were linked to chromosome 4R. The use of the SCIM markers as a source of molecular markers that could be linked to interesting genes or other important agronomic traits is discussed.

A new aluminum tolerance gene located on rye chromosome arm 7RS

Rye has one of the most efficient groups of genes for aluminum tolerance (Alt) among cultivated species of Triticeae. This tolerance is controlled by, at least, three independent and dominant loci (Alt1, Alt2, and Alt3) located on chromosome arms 6RS, 3RS, and 4RL, respectively. The segregation of Alt genes and several random amplified polymorphic DNA (RAPD), Secale cereale inter-microsatellite (SCIM), and Secale cereale microsatellite (SCM) markers in three F(2) between a tolerant cultivar (Ailés) and a non-tolerant inbred line (Riodeva) were studied. The segregation ratio obtained for aluminum tolerance in the three F(2) populations analyzed was 3:1 (tolerant:non-tolerant), indicating that tolerance is controlled by one dominant locus. SCIM811(1376) was linked to an Alt gene in the three F(2) populations studied, and three different SCIMs and one RAPD (SCIM811(1376), SCIM812(626), SCIM812(1138), and OPQ4(725)) were linked to the Alt gene in two F(2) populations. This result indicated that the same Alt gene was segregating in the three crosses. SCIM819(1434) and OPQ4(578) linked to the tolerance gene in one F(2) population were located using wheat-rye ditelosomic addition lines on the 7RS chromosome arm. The Alt locus is mapped between SCIM819(1434) and the OPQ4(578) markers. Two microsatellite loci (SCM-40 and SCM-86), previously located on chromosome 7R, were also linked to the Alt gene. Therefore, the Alt gene segregating in these F(2) populations is new and probably could be orthologous to the Alt genes located on wheat chromosome arm 4DL, on barley chromosome arm 4HL, on rye chromosome arm 4RL, and rice chromosome 3. This new Alt gene located on rye chromosome arm 7RS was named Alt4. A map of rye chromosome 7R with the Alt4 gene, 16 SCIM and RAPD, markers and two SCM markers was obtained.