14 research outputs found
ContrĂŽle cytoplasmique des paires d'ARN messager sens-antisens chez Saccharomyces cerevisiae
Recent transcriptome analyses have revealed that convergent gene transcription can produce many 3â overlapping mRNAs in diverse organisms. This phenomenon has been studied in the context of nuclear RNA interference (RNAi) pathway, however little is known about the cytoplasmic fate of 3â overlapping messengers or their impact on gene expression. In this work, we address the outcomes of interaction between sense-antisense mRNA pairs in Saccharomyces cerevisiae, a model organism naturally devoid of RNAi. We demonstrate that the complementary tails of 3â overlapping mRNAs can interact in the cytoplasm in a sequence-specific manner and promote post-transcriptional remodeling of mRNA stability and translation. Our findings are based on the detailed analysis of a convergent mRNA pair, POR1 and OCA2, subsequently generalized using the reconstituted RNAi approach in S. cerevisiae. Genome-wide experiments confirm that in wild-type cells, sense-antisense mRNA pairs form RNA duplexes in vivo and thus have potential roles in modulating the respective mRNA or protein levels under different growth conditions. We show that the fate of hundreds of messenger-interacting messengers is controlled by Xrn1, revealing the extent to which this conserved 5â-3â cytoplasmic exoribonuclease plays an unexpected but key role in the post-transcriptional control of convergent gene expression. In sum, our work opens a perspective to consider an additional, cytoplasmic mechanism of interaction between sense-antisense mRNA pairs, in both RNAi-positive and negative organisms.Les rĂ©centes Ă©tudes transcriptomiques chez divers organismes ont montrĂ© que la transcription des gĂšnes convergents peut produire des ARN messagers (ARNm) chevauchants. Ce phĂ©nomĂšne a Ă©tĂ© analysĂ© dans le contexte de lâinterfĂ©rence par ARN (ARNi) nuclĂ©aire, et peu dâinformation existe quant au destin cytoplasmique des messagers 3â chevauchants ou leur impact sur lâexpression des gĂšnes. Dans ce travail, nous avons abordĂ© les consĂ©quences potentielles de lâinteraction entre des paires dâARNm sens-antisens chez Saccharomyces cerevisiae, un organisme modĂšle naturellement dĂ©pourvu de lâARNi. Nous avons dĂ©montrĂ© que les extrĂ©mitĂ©s 3â complĂ©mentaires des ARNm peuvent interagir dans le cytoplasme et moduler la stabilitĂ© ainsi que la traduction dâARNm. Nos rĂ©sultats sont issus dâune Ă©tude dĂ©taillĂ©e dâune paire dâARNm convergents, POR1 et OCA2, ensuite gĂ©nĂ©ralisĂ©e par lâapproche de lâARNi reconstituĂ©e chez S. cerevisiae. Lâanalyse globale a confirmĂ© que dans les cellules sauvages, les paires dâARNm sens-antisens forment des duplexes dâARN in vivo et ont un rĂŽle potentiel Ă moduler lâexpression dâARNm ou de protĂ©ines respectifs, dans des diffĂ©rentes conditions de croissance. Nous avons montrĂ© que le destin de centaines des messagers convergents est contrĂŽlĂ© par Xrn1, rĂ©vĂ©lant lâimportance de cette exoribonuclĂ©ase 5â-3â cytoplasmique trĂšs conservĂ©e dans la rĂ©gulation post-transcriptionnelle des gĂšnes convergents. Notre travail ouvre donc la perspective de considĂ©rer un nouveau mĂ©canisme de lâinteraction entre les paires dâARNm sens-antisens dans le cytoplasme, chez les organismes contenant ou non la voie de lâinterfĂ©rence par ARN
An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus.
No-Go Decay mRNA cleavage in the ribosome exit tunnel produces 5âČ-OH ends phosphorylated by Trl1
International audienceThe No-Go Decay (NGD) mRNA surveillance pathway degrades mRNAs containing stacks of stalled ribosomes. Although an endoribonuclease has been proposed to initiate cleavages upstream of the stall sequence, the production of two RNA fragments resulting from a unique cleavage has never been demonstrated. Here we use mRNAs expressing a 3âČ-ribozyme to produce truncated transcripts in vivo to mimic naturally occurring truncated mRNAs known to trigger NGD. This technique allows us to analyse endonucleolytic cleavage events at single-nucleotide resolution starting at the third collided ribosome, which we show to be Hel2-dependent. These cleavages map precisely in the mRNA exit tunnel of the ribosome, 8 nucleotides upstream of the first P-site residue and release 5âČ-hydroxylated RNA fragments requiring 5âČ-phosphorylation prior to digestion by the exoribonuclease Xrn1, or alternatively by Dxo1. Finally, we identify the RNA kinase Trl1, alias Rlg1, as an essential player in the degradation of NGD RNAs
Cytoplasmic Control of Sense-Antisense mRNA Pairs
Transcriptome analyses have revealed that convergent gene transcription can produce many 3âČ-overlapping mRNAs in diverse organisms. Few studies have examined the fate of 3âČ-complementary mRNAs in double-stranded RNA-dependent nuclear phenomena, and nothing is known about the cytoplasmic destiny of 3âČ-overlapping messengers or their impact on gene expression. Here, we demonstrate that the complementary tails of 3âČ-overlapping mRNAs can interact in the cytoplasm and promote post-transcriptional regulatory events including no-go decay (NGD) in Saccharomyces cerevisiae. Genome-wide experiments confirm that these messenger-interacting mRNAs (mimRNAs) form RNA duplexes in wild-type cells and thus have potential roles in modulating the mRNA levels of their convergent gene pattern under different growth conditions. We show that the post-transcriptional fate of hundreds of mimRNAs is controlled by Xrn1, revealing the extent to which this conserved 5âČ-3âČ cytoplasmic exoribonuclease plays an unexpected but key role in the post-transcriptional control of convergent gene expression
A unique No-Go Decay cleavage in mRNA exit-tunnel of ribosome produces 5â-OH ends phosphorylated by Trl1
The Surface Rhamnopolysaccharide Epa of Enterococcus faecalis Is a Key Determinant of Intestinal Colonization
Enterococcus faecalis is a commensal bacterium of the human intestine and a major opportunistic pathogen in immunocompromised and elderly patients. The pathogenesis of E. faecalis infection relies in part on its capacity to colonize the gut. Following disruption of intestinal homeostasis, E. faecalis can overgrow, cross the intestinal barrier, and enter the lymph and bloodstream. To identify and characterize E. faecalis genes that are key to intestinal colonization, our strategy consisted in screening mutants for the following phenotypes related to intestinal lifestyle: antibiotic resistance, overgrowth, and competition against microbiota. From the identified colonization genes, epaX encodes a glycosyltransferase located in a variable region of the enterococcal polysaccharide antigen (epa) locus. We demonstrated that EpaX acts on sugar composition, promoting resistance to bile salts and cell wall integrity. Given that EpaX is enriched in hospital-adapted isolates, this study points to the importance of the epa variability as a key determinant for enterococcal intestinal colonization
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Revealing the grammar of small RNA secretion using interpretable machine learning.
Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes. However, the mechanisms that govern their sorting and secretion are not well understood. Here, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequences. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins (RBPs), e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications
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A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression
Antisense RNAs are ubiquitous in human cells, yet their role is largely unexplored. Here we profiled antisense RNAs in the MDA-MB-231 breast cancer cell line and its highly lung metastatic derivative. We identified one antisense RNA that drives cancer progression by upregulating the redox enzyme NADPH quinone dehydrogenase 1 (NQO1), and named it NQO1-AS. Knockdown of either NQO1 or NQO1-AS reduced lung colonization in a mouse model, and investigation into the role of NQO1 indicated that it is broadly protective against oxidative damage and ferroptosis. Breast cancer cells in the lung are dependent on this pathway, and this dependence can be exploited therapeutically by inducing ferroptosis while inhibiting NQO1. Together, our findings establish a role for NQO1-AS in the progression of breast cancer by regulating its sense mRNA post-transcriptionally. Because breast cancer predominantly affects females, the disease models used in this study are of female origin and the results are primarily applicable to females
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Nuclear TARBP2 Drives Oncogenic Dysregulation of RNA Splicing and Decay
Post-transcriptional regulation of RNA stability is a key step in gene expression control. We describe a regulatory program, mediated by the RNA binding protein TARBP2, that controls RNA stability in the nucleus. TARBP2 binding to pre-mRNAs results in increased intron retention, subsequently leading to targeted degradation of TARBP2-bound transcripts. This is mediated by TARBP2 recruitment of the m6A RNA methylation machinery to its target transcripts, where deposition of m6A marks influences the recruitment of splicing regulators, inhibiting efficient splicing. Interactions between TARBP2 and the nucleoprotein TPR then promote degradation of these TARBP2-bound transcripts by the nuclear exosome. Additionally, analysis of clinical gene expression datasets revealed a functional role for TARBP2 in lung cancer. Using xenograft mouse models, we find that TARBP2 affects tumor growth in the lung and that this is dependent on TARBP2-mediated destabilization of ABCA3 and FOXN3. Finally, we establish ZNF143 as an upstream regulator of TARBP2 expression