cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24132255.v2
title: Translational control of murine adiponectin expression by an upstream open reading frame element

description: Adiponectin, an adipocyte-specific secretory protein encoded by the <i>ADIPOQ</i> gene has a causal role in insulin resistance. Anti-diabetic drugs increase plasma adiponectin by a poorly understood, post-transcriptional mechanism enhancing insulin sensitivity. Deletion analysis of a reporter bearing the mouse <i>Adipoq</i> mRNA 5’-leader identified an inhibitory <i>cis</i>-regulatory sequence. The 5’-leader harbours two potential upstream open reading frames (uORFs) overlapping the principal downstream ORF. Mutation of the uORF ATGs increased reporter translation ~3-fold, indicative of a functional uORF. uORFs are common in mammalian mRNAs; however, only a select group resist translational repression by the integrated stress response (ISR). Thapsigargin (TG), which induces endoplasmic reticulum (ER) stress and the ISR, enhanced expression of a reporter bearing the <i>Adipoq</i> 5’-leader; polysome profiling verified translation-stimulation. TG-stimulated translation was absent in cells defective in Ser<sup>51</sup> phosphorylation of eukaryotic initiation factor 2α (eIF2α), required for the ISR. To determine its role in expression and function of endogenous adiponectin, the upstream uORF was disrupted by CRISPR-Cas9-mediated mutagenesis of differentiated mouse 3T3-L1 adipocytes. uORF disruption in adipocytes increased adiponectin expression, triacylglycerol accumulation, and glucose uptake, and inhibited paracrine muscle and liver cell expression of gluconeogenic enzymes, establishing an important role of the uORF in adiponectin-mediated responses to stress.
DOI: 10.6084/m9.figshare.24132255.v1
title: Translational control of murine adiponectin expression by an upstream open reading frame element

description: Adiponectin, an adipocyte-specific secretory protein encoded by the <i>ADIPOQ</i> gene has a causal role in insulin resistance. Anti-diabetic drugs increase plasma adiponectin by a poorly understood, post-transcriptional mechanism enhancing insulin sensitivity. Deletion analysis of a reporter bearing the mouse <i>Adipoq</i> mRNA 5’-leader identified an inhibitory <i>cis</i>-regulatory sequence. The 5’-leader harbours two potential upstream open reading frames (uORFs) overlapping the principal downstream ORF. Mutation of the uORF ATGs increased reporter translation ~3-fold, indicative of a functional uORF. uORFs are common in mammalian mRNAs; however, only a select group resist translational repression by the integrated stress response (ISR). Thapsigargin (TG), which induces endoplasmic reticulum (ER) stress and the ISR, enhanced expression of a reporter bearing the <i>Adipoq</i> 5’-leader; polysome profiling verified translation-stimulation. TG-stimulated translation was absent in cells defective in Ser<sup>51</sup> phosphorylation of eukaryotic initiation factor 2α (eIF2α), required for the ISR. To determine its role in expression and function of endogenous adiponectin, the upstream uORF was disrupted by CRISPR-Cas9-mediated mutagenesis of differentiated mouse 3T3-L1 adipocytes. uORF disruption in adipocytes increased adiponectin expression, triacylglycerol accumulation, and glucose uptake, and inhibited paracrine muscle and liver cell expression of gluconeogenic enzymes, establishing an important role of the uORF in adiponectin-mediated responses to stress.
DOI: 10.6084/m9.figshare.21804773
title: Identification of circular RNAs hosted by the <i>RPGR</i> ORF15 genomic locus

description: Mutations in the retina-specific isoform of the gene encoding retinitis pigmentosa GTPase regulator (RPGR<sup>orf15</sup>) cause X-linked retinitis pigmentosa, a severe and early onset inherited retinal degeneration. The underlying pathogenic mechanisms and variability in disease severity remain to be fully elucidated. The present study examines structural features of the ORF15 exonic region to provide new insights into the disease pathogenesis. Using canine and human RNA samples, we identified several novel <i>RPGR</i> ORF15-like linear RNA transcripts containing cryptic introns (exitrons) within the annotated exon ORF15. Furthermore, using outward-facing primers designed inside exitrons in the ORF15 exonic region, we found many of previously unidentified circular RNAs (circRNAs) that formed via back fusion of linear parts of the <i>RPGR<sup>orf15</sup></i> pre-mRNAs. These circRNAs (resistant to RNAse R treatment) were found in all studied cells and tissues. Notably, some circRNAs were present in cytoplasmic and polysomal RNA fractions. Although certain <i>RPGR</i> circRNAs may be cell type specific, we found some of the same circRNAs expressed in different cell types, suggesting similarities in their biogenesis and functions. Sequence analysis of <i>RPGR</i> circRNAs revealed several remarkable features, including identification of N6-methyladenosine (m6A) consensus sequence motifs and high prevalence of predictive microRNA binding sites pointing to the functional roles of these circRNAs. Our findings also illustrate the presence of non-canonical <i>RPGR</i> circRNA biogenesis pathways independent of the known back splicing mechanism. The obtained data on novel <i>RPGR</i> circRNAs further underline structural complexity of the <i>RPGR</i> ORF15 region and provide a potential molecular basis for the disease phenotypic heterogeneity.
DOI: 10.6084/m9.figshare.21804773.v1
title: Identification of circular RNAs hosted by the <i>RPGR</i> ORF15 genomic locus

description: Mutations in the retina-specific isoform of the gene encoding retinitis pigmentosa GTPase regulator (RPGR<sup>orf15</sup>) cause X-linked retinitis pigmentosa, a severe and early onset inherited retinal degeneration. The underlying pathogenic mechanisms and variability in disease severity remain to be fully elucidated. The present study examines structural features of the ORF15 exonic region to provide new insights into the disease pathogenesis. Using canine and human RNA samples, we identified several novel <i>RPGR</i> ORF15-like linear RNA transcripts containing cryptic introns (exitrons) within the annotated exon ORF15. Furthermore, using outward-facing primers designed inside exitrons in the ORF15 exonic region, we found many of previously unidentified circular RNAs (circRNAs) that formed via back fusion of linear parts of the <i>RPGR<sup>orf15</sup></i> pre-mRNAs. These circRNAs (resistant to RNAse R treatment) were found in all studied cells and tissues. Notably, some circRNAs were present in cytoplasmic and polysomal RNA fractions. Although certain <i>RPGR</i> circRNAs may be cell type specific, we found some of the same circRNAs expressed in different cell types, suggesting similarities in their biogenesis and functions. Sequence analysis of <i>RPGR</i> circRNAs revealed several remarkable features, including identification of N6-methyladenosine (m6A) consensus sequence motifs and high prevalence of predictive microRNA binding sites pointing to the functional roles of these circRNAs. Our findings also illustrate the presence of non-canonical <i>RPGR</i> circRNA biogenesis pathways independent of the known back splicing mechanism. The obtained data on novel <i>RPGR</i> circRNAs further underline structural complexity of the <i>RPGR</i> ORF15 region and provide a potential molecular basis for the disease phenotypic heterogeneity.
DOI: 10.6084/m9.figshare.24224935
title: Anticodon sequence determines the impact of mistranslating tRNA<sup>Ala</sup> variants

description: Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNA<sup>Ala</sup> and the anticodon plays no role in charging, tRNA<sup>Ala</sup> variants with anticodon mutations have the potential to mis-incorporate alanine. Here, we characterize the impact of the 60 non-alanine tRNA<sup>Ala</sup> anticodon variants on the growth of <i>Saccharomyces cerevisiae</i>. Overall, 36 tRNA<sup>Ala</sup> anticodon variants decreased growth in single- or multi-copy. Mass spectrometry analysis of the cellular proteome revealed that 52 of 57 anticodon variants, not decoding alanine or stop codons, induced mistranslation when on single-copy plasmids. Variants with G/C-rich anticodons resulted in larger growth deficits than A/U-rich variants. In most instances, synonymous anticodon variants impact growth differently, with anticodons containing U at base 34 being the least impactful. For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNA<sup>Ala</sup> variant mistranslating unique sets of peptides and proteins. We suggest that these differences in decoding specificity are also important in determining the impact of tRNA<sup>Ala</sup> anticodon variants.
DOI: 10.6084/m9.figshare.24224935.v1
title: Anticodon sequence determines the impact of mistranslating tRNA<sup>Ala</sup> variants

description: Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNA<sup>Ala</sup> and the anticodon plays no role in charging, tRNA<sup>Ala</sup> variants with anticodon mutations have the potential to mis-incorporate alanine. Here, we characterize the impact of the 60 non-alanine tRNA<sup>Ala</sup> anticodon variants on the growth of <i>Saccharomyces cerevisiae</i>. Overall, 36 tRNA<sup>Ala</sup> anticodon variants decreased growth in single- or multi-copy. Mass spectrometry analysis of the cellular proteome revealed that 52 of 57 anticodon variants, not decoding alanine or stop codons, induced mistranslation when on single-copy plasmids. Variants with G/C-rich anticodons resulted in larger growth deficits than A/U-rich variants. In most instances, synonymous anticodon variants impact growth differently, with anticodons containing U at base 34 being the least impactful. For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNA<sup>Ala</sup> variant mistranslating unique sets of peptides and proteins. We suggest that these differences in decoding specificity are also important in determining the impact of tRNA<sup>Ala</sup> anticodon variants.
DOI: 10.6084/m9.figshare.24550918
title: Long non-coding RNA APDC plays important regulatory roles in metabolism of bone and adipose tissues

description: The long noncoding RNA (lncR) ANRIL in the human genome is an established genetic risk factor for atherosclerosis, periodontitis, diabetes, and cancer. However, the regulatory role of lncR-ANRIL in bone and adipose tissue metabolism remains unclear. To elucidate the function of lncRNA ANRIL in a mouse model, we investigated its ortholog, AK148321 (referred to as lncR-APDC), located on chr4 of the mouse genome, which is hypothesized to have similar biological functions to ANRIL. We initially revealed that lncR-APDC in mouse bone marrow cells (BMSCs) and lncR-ANRIL in human osteoblasts (hFOBs) are both increased during early osteogenesis. Subsequently, we examined the osteogenesis, adipogenesis, osteoclastogenesis function with lncR-APDC deletion/overexpression cell models. In vivo, we compared the phenotypic differences in bone and adipose tissue between APDC-KO and wild-type mice. Our findings demonstrated that lncR-APDC deficiency impaired osteogenesis while promoting adipogenesis and osteoclastogenesis. Conversely, the overexpression of lncR-APDC stimulated osteogenesis, but impaired adipogenesis and osteoclastogenesis. Furthermore, KDM6B was downregulated with lncR-APDC deficiency and upregulated with overexpression. Through binding-site analysis, we identified miR-99a as a potential target of lncR-APDC. The results suggest that lncR-APDC exerts its osteogenic function via miR-99a/KDM6B/Hox pathways. Additionally, osteoclasto-osteogenic imbalance was mediated by lncR-APDC through MAPK/p38 and TLR4/MyD88 activation. These findings highlight the pivotal role of lncR-APDC as a key regulator in bone and fat tissue metabolism. It shows potential therapeutic for addressing imbalances in osteogenesis, adipogenesis, and osteoclastogenesis.
DOI: 10.6084/m9.figshare.24550918.v1
title: Long non-coding RNA APDC plays important regulatory roles in metabolism of bone and adipose tissues

description: The long noncoding RNA (lncR) ANRIL in the human genome is an established genetic risk factor for atherosclerosis, periodontitis, diabetes, and cancer. However, the regulatory role of lncR-ANRIL in bone and adipose tissue metabolism remains unclear. To elucidate the function of lncRNA ANRIL in a mouse model, we investigated its ortholog, AK148321 (referred to as lncR-APDC), located on chr4 of the mouse genome, which is hypothesized to have similar biological functions to ANRIL. We initially revealed that lncR-APDC in mouse bone marrow cells (BMSCs) and lncR-ANRIL in human osteoblasts (hFOBs) are both increased during early osteogenesis. Subsequently, we examined the osteogenesis, adipogenesis, osteoclastogenesis function with lncR-APDC deletion/overexpression cell models. In vivo, we compared the phenotypic differences in bone and adipose tissue between APDC-KO and wild-type mice. Our findings demonstrated that lncR-APDC deficiency impaired osteogenesis while promoting adipogenesis and osteoclastogenesis. Conversely, the overexpression of lncR-APDC stimulated osteogenesis, but impaired adipogenesis and osteoclastogenesis. Furthermore, KDM6B was downregulated with lncR-APDC deficiency and upregulated with overexpression. Through binding-site analysis, we identified miR-99a as a potential target of lncR-APDC. The results suggest that lncR-APDC exerts its osteogenic function via miR-99a/KDM6B/Hox pathways. Additionally, osteoclasto-osteogenic imbalance was mediated by lncR-APDC through MAPK/p38 and TLR4/MyD88 activation. These findings highlight the pivotal role of lncR-APDC as a key regulator in bone and fat tissue metabolism. It shows potential therapeutic for addressing imbalances in osteogenesis, adipogenesis, and osteoclastogenesis.
DOI: 10.6084/m9.figshare.23999751
title: Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex

description: The peripheral and central auditory subsystems together form a complex sensory network that allows an organism to hear. The genetic programs of the two subsystems must therefore be tightly coordinated during development. Yet, their interactions and common expression pathways have never been systematically explored. MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression and are essential for normal development of the auditory system. We performed mRNA and small-RNA sequencing of organs from both auditory subsystems at three critical developmental timepoints (E16, P0, P16) to obtain a comprehensive and unbiased insight of their expression profiles. Our analysis reveals common and organ-specific expression patterns for differentially regulated mRNAs and miRNAs, which could be clustered with a particular selection of functions such as inner ear development, Wnt signalling, K+ transport, and axon guidance, based on gene ontology. Bioinformatics detected enrichment of predicted targets of specific miRNAs in the clusters and predicted regulatory interactions by monitoring opposite trends of expression of miRNAs and their targets. This approach identified six miRNAs as strong regulatory candidates for both subsystems. Among them was miR-96, an established critical factor for proper development in both subsystems, demonstrating the strength of our approach. We suggest that other miRNAs identified by this analysis are also common effectors of proper hearing acquirement. This first combined comprehensive analysis of the developmental program of the peripheral and central auditory systems provides important data and bioinformatics insights into the shared genetic program of the two sensory subsystems and their regulation by miRNAs.
DOI: 10.6084/m9.figshare.23999751.v1
title: Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex

description: The peripheral and central auditory subsystems together form a complex sensory network that allows an organism to hear. The genetic programs of the two subsystems must therefore be tightly coordinated during development. Yet, their interactions and common expression pathways have never been systematically explored. MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression and are essential for normal development of the auditory system. We performed mRNA and small-RNA sequencing of organs from both auditory subsystems at three critical developmental timepoints (E16, P0, P16) to obtain a comprehensive and unbiased insight of their expression profiles. Our analysis reveals common and organ-specific expression patterns for differentially regulated mRNAs and miRNAs, which could be clustered with a particular selection of functions such as inner ear development, Wnt signalling, K+ transport, and axon guidance, based on gene ontology. Bioinformatics detected enrichment of predicted targets of specific miRNAs in the clusters and predicted regulatory interactions by monitoring opposite trends of expression of miRNAs and their targets. This approach identified six miRNAs as strong regulatory candidates for both subsystems. Among them was miR-96, an established critical factor for proper development in both subsystems, demonstrating the strength of our approach. We suggest that other miRNAs identified by this analysis are also common effectors of proper hearing acquirement. This first combined comprehensive analysis of the developmental program of the peripheral and central auditory systems provides important data and bioinformatics insights into the shared genetic program of the two sensory subsystems and their regulation by miRNAs.
DOI: 10.25318/4510008501-fra
title: Estimations du nombre des organisations sans but lucratif actifs, des revenus et de l'emploi selon l’activité, inactif

description: Estimations du nombre d'organismes sans but lucratif (OSBL) actifs, le revenu et l'emploi générés selon la Classification internationale des organisations à but non lucratif (CIOBNL) et la classification géographique et d’emplacement en région rurale et petite ville ou en région urbaine.
DOI: 10.6084/m9.figshare.23548151
title: Novel compounds that synergize with aminoglycoside G418 or eRF3 degraders for translational readthrough of nonsense mutant <i>TP53</i> and <i>PTEN</i>

description: The <i>TP53</i> and <i>PTEN</i> tumour suppressor genes are inactivated by nonsense mutations in a significant fraction of human tumours. <i>TP53</i> nonsense mutant tumours account for approximately one million new cancer cases per year worldwide. We have screened chemical libraries with the aim of identifying compounds that induce translational readthrough and expression of full-length p53 protein in cells with nonsense mutation in this gene. Here we describe two novel compounds with readthrough activity, either alone or in combination with other known readthrough-promoting substances. Both compounds induced levels of full-length p53 in cells carrying R213X nonsense mutant <i>TP53</i>. Compound C47 showed synergy with the aminoglycoside antibiotic and known readthrough inducer G418, whereas compound C61 synergized with eukaryotic release factor 3 (eRF3) degraders CC−885 and CC−90009. C47 alone showed potent induction of full-length PTEN protein in cells with different <i>PTEN</i> nonsense mutations. These results may facilitate further development of novel targeted cancer therapy by pharmacological induction of translational readthrough.
DOI: 10.6084/m9.figshare.23548151.v1
title: Novel compounds that synergize with aminoglycoside G418 or eRF3 degraders for translational readthrough of nonsense mutant <i>TP53</i> and <i>PTEN</i>

description: The <i>TP53</i> and <i>PTEN</i> tumour suppressor genes are inactivated by nonsense mutations in a significant fraction of human tumours. <i>TP53</i> nonsense mutant tumours account for approximately one million new cancer cases per year worldwide. We have screened chemical libraries with the aim of identifying compounds that induce translational readthrough and expression of full-length p53 protein in cells with nonsense mutation in this gene. Here we describe two novel compounds with readthrough activity, either alone or in combination with other known readthrough-promoting substances. Both compounds induced levels of full-length p53 in cells carrying R213X nonsense mutant <i>TP53</i>. Compound C47 showed synergy with the aminoglycoside antibiotic and known readthrough inducer G418, whereas compound C61 synergized with eukaryotic release factor 3 (eRF3) degraders CC−885 and CC−90009. C47 alone showed potent induction of full-length PTEN protein in cells with different <i>PTEN</i> nonsense mutations. These results may facilitate further development of novel targeted cancer therapy by pharmacological induction of translational readthrough.
DOI: 10.6084/m9.figshare.23808561
title: <i>Escherichia coli</i> transcriptome assembly from a compendium of RNA-seq data sets

description: Owing to the complexities of bacterial RNA biology, the transcriptomes of even the best studied bacteria are not fully understood. To help elucidate the transcriptional landscape of <i>E. coli</i>, we compiled a compendium of 3,376 RNA-seq data sets composed of more than 7 trillion sequenced bases, which we evaluate with a transcript assembly pipeline. We report expression profiles for all annotated <i>E. coli</i> genes as well as 5,071 other transcripts. Additionally, we observe hundreds of instances of co-transcribed genes that are novel with respect to existing operon databases. By integrating data from a large number of sequencing experiments corresponding to a wide range of conditions, we are able to obtain a comprehensive view of the <i>E. coli</i> transcriptome.
DOI: 10.6084/m9.figshare.23808561.v1
title: <i>Escherichia coli</i> transcriptome assembly from a compendium of RNA-seq data sets

description: Owing to the complexities of bacterial RNA biology, the transcriptomes of even the best studied bacteria are not fully understood. To help elucidate the transcriptional landscape of <i>E. coli</i>, we compiled a compendium of 3,376 RNA-seq data sets composed of more than 7 trillion sequenced bases, which we evaluate with a transcript assembly pipeline. We report expression profiles for all annotated <i>E. coli</i> genes as well as 5,071 other transcripts. Additionally, we observe hundreds of instances of co-transcribed genes that are novel with respect to existing operon databases. By integrating data from a large number of sequencing experiments corresponding to a wide range of conditions, we are able to obtain a comprehensive view of the <i>E. coli</i> transcriptome.