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Beckmann B.M.,European Molecular Biology Laboratory EMBL | Beckmann B.M.,Humboldt University of Berlin | Horos R.,European Molecular Biology Laboratory EMBL | Fischer B.,European Molecular Biology Laboratory EMBL | And 13 more authors.
Nature Communications | Year: 2015

RNA-binding proteins (RBPs) exert a broad range of biological functions. To explore the scope of RBPs across eukaryotic evolution, we determined the in vivo RBP repertoire of the yeast Saccharomyces cerevisiae and identified 678 RBPs from yeast and additionally 729 RBPs from human hepatocytic HuH-7 cells. Combined analyses of these and recently published data sets define the core RBP repertoire conserved from yeast to man. Conserved RBPs harbour defined repetitive motifs within disordered regions, which display striking evolutionary expansion. Only 60% of yeast and 73% of the human RBPs have functions assigned to RNA biology or structural motifs known to convey RNA binding, and many intensively studied proteins surprisingly emerge as RBPs (termed 'enigmRBPs'), including almost all glycolytic enzymes, pointing to emerging connections between gene regulation and metabolism. Analyses of the mitochondrial hydroxysteroid dehydrogenase (HSD17B10) uncover the RNA-binding specificity of an enigmRBP. Source


Stoeckius M.,Max Delbruck Center Berlin | Grun D.,Max Delbruck Center Berlin | Kirchner M.,Max Delbruck Center Berlin | Ayoub S.,Max Delbruck Center Berlin | And 6 more authors.
EMBO Journal | Year: 2014

The oocyte-to-embryo transition (OET) is thought to be mainly driven by post-transcriptional gene regulation. However, expression of both RNAs and proteins during the OET has not been comprehensively assayed. Furthermore, specific molecular mechanisms that regulate gene expression during OET are largely unknown. Here, we quantify and analyze transcriptome-wide, expression of mRNAs and thousands of proteins in Caenorhabditis elegans oocytes, 1-cell, and 2-cell embryos. This represents a first comprehensive gene expression atlas during the OET in animals. We discovered a first wave of degradation in which thousands of mRNAs are cleared shortly after fertilization. Sequence analysis revealed a statistically highly significant presence of a polyC motif in the 3′ untranslated regions of most of these degraded mRNAs. Transgenic reporter assays demonstrated that this polyC motif is required and sufficient for mRNA degradation after fertilization. We show that orthologs of human polyC-binding protein specifically bind this motif. Our data suggest a mechanism in which the polyC motif and binding partners direct degradation of maternal mRNAs. Our data also indicate that endogenous siRNAs but not miRNAs promote mRNA clearance during the OET. Synopsis The first molecular quantification of transcriptome and proteome changes during the oocyte-to-embryo transition reveals coordinated degradation of thousands of mRNAs shortly after fertilization. First quantification of transcriptome and proteome changes between the Caenorhabditis elegans oocyte and fertilized, totipotent 1-cell embryo in any organism Discovered a wave of destruction where thousands of mRNAs are cleared right after fertilization A novel polyC motif in 3′ untranslated regions (3′ UTRs) explains the targeted degradation of mRNAs Conserved RNA-binding proteins bind the polyC motif in vitro, offering a mechanism for mRNA clearance. The first molecular quantification of transcriptome and proteome changes during the oocyte-to-embryo transition reveals coordinated degradation of thousands of mRNAs shortly after fertilization. © 2014 The Authors. Source


Blevins R.,Imperial College London | Bruno L.,Imperial College London | Carroll T.,Imperial College London | Elliott J.,Imperial College London | And 8 more authors.
PLoS genetics | Year: 2015

The development and homeostasis of multicellular organisms relies on gene regulation within individual constituent cells. Gene regulatory circuits that increase the robustness of gene expression frequently incorporate microRNAs as post-transcriptional regulators. Computational approaches, synthetic gene circuits and observations in model organisms predict that the co-regulation of microRNAs and their target mRNAs can reduce cell-to-cell variability in the expression of target genes. However, whether microRNAs directly regulate variability of endogenous gene expression remains to be tested in mammalian cells. Here we use quantitative flow cytometry to show that microRNAs impact on cell-to-cell variability of protein expression in developing mouse thymocytes. We find two distinct mechanisms that control variation in the activation-induced expression of the microRNA target CD69. First, the expression of miR-17 and miR-20a, two members of the miR-17-92 cluster, is co-regulated with the target mRNA Cd69 to form an activation-induced incoherent feed-forward loop. Another microRNA, miR-181a, acts at least in part upstream of the target mRNA Cd69 to modulate cellular responses to activation. The ability of microRNAs to render gene expression more uniform across mammalian cell populations may be important for normal development and for disease. Source


Stoeckius M.,Max Delbruck Center Berlin | Grun D.,Max Delbruck Center Berlin | Rajewsky N.,Max Delbruck Center Berlin
EMBO Journal | Year: 2014

Development of the early embryo is thought to be mainly driven by maternal gene products and post-transcriptional gene regulation. Here, we used metabolic labeling to show that RNA can be transferred by sperm into the oocyte upon fertilization. To identify genes with paternal expression in the embryo, we performed crosses of males and females from divergent Caenorhabditis elegans strains. RNA sequencing of mRNAs and small RNAs in the 1-cell hybrid embryo revealed that about one hundred sixty paternal mRNAs are reproducibly expressed in the embryo and that about half of all assayed endogenous siRNAs and piRNAs are also of paternal origin. Together, our results suggest an unexplored paternal contribution to early development. Synopsis This paper establishes significant paternal RNA contributions in C. elegans zygotes, a result with major bearings on their potential functional relevance. Metabolic labeling of males shows that male RNA is transferred into the oocyte upon fertilization. We performed a cross of hybrid strains and sequenced RNA from the 1-cell-fertilized embryo. Computational analyses of these data allow to quantify maternal and paternal RNA in the fertilized embryo. We discover numerous mRNAs and different classes of non-coding RNAs of paternal origin in the fertilized embryo. This paper establishes significant paternal RNA contributions in C. elegans zygotes, a result with major bearings on their potential functional relevance. © 2014 The Authors. Source


Grun D.,Max Delbruck Center Berlin | Kirchner M.,Max Delbruck Center Berlin | Thierfelder N.,Max Delbruck Center Berlin | Stoeckius M.,Max Delbruck Center Berlin | And 2 more authors.
Cell Reports | Year: 2014

Spatiotemporal control of gene expression is crucial for development and subject to evolutionary changes. Although proteins are the final product of most genes, the developmental proteome of an animal has not yetbeen comprehensively defined, and the correlation between mRNA and protein abundance during development is largely unknown. Here, we globally measuredand compared protein and mRNA expression changes during the life cycle of the nematodes C.elegans and C.briggsae, separated by ~30 million years of evolution. We observed that developmental mRNA and protein changes were highly conserved to a surprisingly similar degree but were poorly correlated within a species, suggesting important and widespread posttranscriptional regulation. Posttranscriptional control was particularly well conserved if mRNA fold changes were buffered on the protein level, indicating a predominant repressive function. Finally, among divergently expressed genes, we identified insulin signaling, a pathway involved in lifespan determination, as a putative target of adaptive evolution. © 2014 The Authors. Source

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