cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20310627.v1
title: Investigating the role of RNA structures in transcriptional pausing using in vitro assays and in silico analyses

description: Transcriptional pausing occurs across the bacterial genome but the importance of this mechanism is still poorly understood. Only few pauses were observed during the previous decades, leaving an important gap in understanding transcription mechanisms. Using the well-known <i>Escherichia coli hisL</i> and <i>trpL</i> pause sites as models, we describe here the relation of pause sites with upstream RNA structures suspected to stabilize pausing. We find that the transcription factor NusA influences the pause half-life at <i>leuL, pheL</i> and <i>thrL</i> pause sites. Using a mutagenesis approach, we observe that transcriptional pausing is affected in all tested pause sites, suggesting that the upstream RNA sequence is important for transcriptional pausing. Compensatory mutations assessing the presence of RNA hairpins did not yield clear conclusions, indicating that complex RNA structures or transcriptional features may be playing a role in pausing. Moreover, using a bioinformatic approach, we explored the relation between a DNA consensus sequence important for pausing and putative hairpins among thousands of pause sites in <i>E. coli</i>. We identified 2125 sites presenting hairpin-dependent transcriptional pausing without consensus sequence, suggesting that this mechanism is widespread across <i>E. coli</i>. This study paves the way to understand the role of RNA structures in transcriptional pausing.
DOI: 10.6084/m9.figshare.21104650.v2
title: RNA structure-altering mutations underlying positive selection on Spike protein reveal novel putative signatures to trace crossing host-species barriers in <i>Betacoronavirus</i>

description: Similar to other RNA viruses, the emergence of <i>Betacoronavirus</i> relies on cross-species viral transmission, which requires careful health surveillance monitoring of protein-coding information as well as genome-wide analysis. Although the evolutionary jump from natural reservoirs to humans may be mainly traced-back by studying the effect that hotspot mutations have on viral proteins, it is largely unexplored if other impacts might emerge on the structured RNA genome of <i>Betacoronavirus</i>. In this survey, the protein-coding and viral genome architecture were simultaneously studied to uncover novel insights into cross-species horizontal transmission events. We analysed 1,252,952 viral genomes of SARS-CoV, MERS-CoV, and SARS-CoV-2 distributed across the world in bats, intermediate animals, and humans to build a new landscape of changes in the RNA viral genome. Phylogenetic analyses suggest that bat viruses are the most closely related to the time of most recent common ancestor of <i>Betacoronavirus</i>, and missense mutations in viral proteins, mainly in the S protein S1 subunit: SARS-CoV (G &gt; T; A577S); MERS-CoV (C &gt; T; S746R and C &gt; T; N762A); and SARS-CoV-2 (A &gt; G; D614G) appear to have driven viral diversification. We also found that codon sites under positive selection on S protein overlap with non-compensatory mutations that disrupt secondary RNA structures in the RNA genome complement. These findings provide pivotal factors that might be underlying the eventual jumping the species barrier from bats to intermediate hosts. Lastly, we discovered that nearly half of the <i>Betacoronavirus</i> genomes carry highly conserved RNA structures, and more than 90% of these RNA structures show negative selection signals, suggesting essential functions in the biology of <i>Betacoronavirus</i> that have not been investigated to date. Further research is needed on negatively selected RNA structures to scan for emerging functions like the potential of coding virus-derived small RNAs and to develop new candidate antiviral therapeutic strategies.
DOI: 10.6084/m9.figshare.25458844
title: RefEx2 Datasets for Mouse FANTOM5

description: RefEx2 is a project to collect, organize, and curate transcriptome datasets of various species as reference resources for gene expression data analysis. It provides 6 reference datasets for four different species: humans, mice, Drosophila melanogaster, and Arabidopsis thaliana. This directory contains the following datasets on mouse FANTOM5:220428_fantom5_mouse_refextable_sample_stats.tsv.gzProcessed data matrixfantom5_mouse_refextable_grouped_sample_descGrouped sample descriptionfantom5_mouse_refextable_sampleID_mapping.tsvSample ID mappingsMouse_FANTOM5_refined_original_sample_annotation.tsvOriginal sample annotations provided by the FANTOM5 project, modified in part by RefEx2.No. of genes: 21,369<br>No. of samples: 535Key ID: NCBI gene<br>Original data: https://fantom.gsc.riken.jp/5/data/<br>Reference(s): DOI: 10.1038/sdata.2017.112, DOI: 10.1093/nar/gkaa1054
DOI: 10.6084/m9.figshare.25458844.v1
title: RefEx2 Datasets for Mouse FANTOM5

description: RefEx2 is a project to collect, organize, and curate transcriptome datasets of various species as reference resources for gene expression data analysis. It provides 6 reference datasets for four different species: humans, mice, Drosophila melanogaster, and Arabidopsis thaliana. This directory contains the following datasets on mouse FANTOM5:220428_fantom5_mouse_refextable_sample_stats.tsv.gzProcessed data matrixfantom5_mouse_refextable_grouped_sample_descGrouped sample descriptionfantom5_mouse_refextable_sampleID_mapping.tsvSample ID mappingsMouse_FANTOM5_refined_original_sample_annotation.tsvOriginal sample annotations provided by the FANTOM5 project, modified in part by RefEx2.No. of genes: 21,369<br>No. of samples: 535Key ID: NCBI gene<br>Original data: https://fantom.gsc.riken.jp/5/data/<br>Reference(s): DOI: 10.1038/sdata.2017.112, DOI: 10.1093/nar/gkaa1054
DOI: 10.6084/m9.figshare.20198979
title: Editome landscape of CCM-derived endothelial cells

description: By regulating several phases of gene expression, RNA editing modifications contribute to maintaining physiological RNA expression levels. RNA editing dysregulation can affect RNA molecule half-life, coding/noncoding RNA interaction, alternative splicing, and circular RNA biogenesis. Impaired RNA editing has been observed in several pathological conditions, including cancer and Alzheimer’s disease. No data has been published yet on the editome profile of endothelial cells (ECs) isolated from human cerebral cavernous malformation (CCM) lesions. Here, we describe a landscape of editome modifications in sporadic CCM-derived ECs (CCM-ECs) by comparing editing events with those observed in human brain microvascular endothelial cells (HBMECs). With a whole transcriptome-based variant calling pipeline, we identified differential edited genes in CCM-ECs that were enriched in pathways related to angiogenesis, apoptosis and cell survival, inflammation and, in particular, to thrombin signalling mediated by protease-activated receptors and non-canonical Wnt signalling. These pathways, not yet associated to CCM development, could be a novel field for further investigations on CCM molecular mechanisms. Moreover, enrichment analysis of differentially edited miRNAs suggested additional small noncoding transcripts to consider for development of targeted therapies.
DOI: 10.6084/m9.figshare.20198979.v1
title: Editome landscape of CCM-derived endothelial cells

description: By regulating several phases of gene expression, RNA editing modifications contribute to maintaining physiological RNA expression levels. RNA editing dysregulation can affect RNA molecule half-life, coding/noncoding RNA interaction, alternative splicing, and circular RNA biogenesis. Impaired RNA editing has been observed in several pathological conditions, including cancer and Alzheimer’s disease. No data has been published yet on the editome profile of endothelial cells (ECs) isolated from human cerebral cavernous malformation (CCM) lesions. Here, we describe a landscape of editome modifications in sporadic CCM-derived ECs (CCM-ECs) by comparing editing events with those observed in human brain microvascular endothelial cells (HBMECs). With a whole transcriptome-based variant calling pipeline, we identified differential edited genes in CCM-ECs that were enriched in pathways related to angiogenesis, apoptosis and cell survival, inflammation and, in particular, to thrombin signalling mediated by protease-activated receptors and non-canonical Wnt signalling. These pathways, not yet associated to CCM development, could be a novel field for further investigations on CCM molecular mechanisms. Moreover, enrichment analysis of differentially edited miRNAs suggested additional small noncoding transcripts to consider for development of targeted therapies.
DOI: 10.6084/m9.figshare.21603042
title: Comparative analysis of piRNA sequences, targets and functions in nematodes

description: Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in <i>C. briggsae</i>, a sibling species of the model organism <i>C. elegans</i>. Our analyses define 25,883 piRNA producing-loci in <i>C. briggsae</i>. piRNA sequences in <i>C. briggsae</i> are extremely divergent from their counterparts in <i>C. elegans</i>, yet both species adopt similar genomic organization that drive piRNA expression. By examining production of Piwi-mediated secondary small RNAs, we identified a set of protein-coding genes that are evolutionarily conserved piRNA targets. In contrast to <i>C. elegans</i>, small RNAs targeting ribosomal RNAs or histone transcripts are not hyper-accumulated in <i>C. briggsae</i> Piwi mutants. Instead, we found that transcripts with few introns are prone to small RNA overamplification. Together our work highlights evolutionary conservation and divergence of the nematode piRNA pathway and provides insights into its role in endogenous gene regulation.
DOI: 10.6084/m9.figshare.21603042.v2
title: Comparative analysis of piRNA sequences, targets and functions in nematodes

description: Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in <i>C. briggsae</i>, a sibling species of the model organism <i>C. elegans</i>. Our analyses define 25,883 piRNA producing-loci in <i>C. briggsae</i>. piRNA sequences in <i>C. briggsae</i> are extremely divergent from their counterparts in <i>C. elegans</i>, yet both species adopt similar genomic organization that drive piRNA expression. By examining production of Piwi-mediated secondary small RNAs, we identified a set of protein-coding genes that are evolutionarily conserved piRNA targets. In contrast to <i>C. elegans</i>, small RNAs targeting ribosomal RNAs or histone transcripts are not hyper-accumulated in <i>C. briggsae</i> Piwi mutants. Instead, we found that transcripts with few introns are prone to small RNA overamplification. Together our work highlights evolutionary conservation and divergence of the nematode piRNA pathway and provides insights into its role in endogenous gene regulation.
DOI: 10.6084/m9.figshare.21603042.v1
title: Comparative analysis of piRNA sequences, targets and functions in nematodes

description: Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in <i>C. briggsae</i>, a sibling species of the model organism <i>C. elegans</i>. Our analyses define 25,883 piRNA producing-loci in <i>C. briggsae</i>. piRNA sequences in <i>C. briggsae</i> are extremely divergent from their counterparts in <i>C. elegans</i>, yet both species adopt similar genomic organization that drive piRNA expression. By examining production of Piwi-mediated secondary small RNAs, we identified a set of protein-coding genes that are evolutionarily conserved piRNA targets. In contrast to <i>C. elegans</i>, small RNAs targeting ribosomal RNAs or histone transcripts are not hyper-accumulated in <i>C. briggsae</i> Piwi mutants. Instead, we found that transcripts with few introns are prone to small RNA overamplification. Together our work highlights evolutionary conservation and divergence of the nematode piRNA pathway and provides insights into its role in endogenous gene regulation.
DOI: 10.6084/m9.figshare.18865633
title: Structural maturation of the HIV-1 RNA 5’ untranslated region by Pr55<sup>Gag</sup> and its maturation products

description: Maturation of the HIV-1 viral particles shortly after budding is required for infectivity. During this process, the Pr55<sup>Gag</sup> precursor undergoes a cascade of proteolytic cleavages, and whilst the structural rearrangements of the viral proteins are well understood, the concomitant maturation of the genomic RNA (gRNA) structure is unexplored, despite evidence that it is required for infectivity. To get insight into this process, we systematically analysed the interactions between Pr55<sup>Gag</sup> or its maturation products (NCp15, NCp9 and NCp7) and the 5ʹ gRNA region and their structural consequences, <i>in vitro</i>. We show that Pr55<sup>Gag</sup> and its maturation products mostly bind at different RNA sites and with different contributions of their two zinc knuckle domains. Importantly, these proteins have different transient and permanent effects on the RNA structure, the late NCp9 and NCp7 inducing dramatic structural rearrangements. Altogether, our results reveal the distinct contributions of the different Pr55<sup>Gag</sup> maturation products on the gRNA structural maturation.
DOI: 10.6084/m9.figshare.18865633.v1
title: Structural maturation of the HIV-1 RNA 5’ untranslated region by Pr55<sup>Gag</sup> and its maturation products

description: Maturation of the HIV-1 viral particles shortly after budding is required for infectivity. During this process, the Pr55<sup>Gag</sup> precursor undergoes a cascade of proteolytic cleavages, and whilst the structural rearrangements of the viral proteins are well understood, the concomitant maturation of the genomic RNA (gRNA) structure is unexplored, despite evidence that it is required for infectivity. To get insight into this process, we systematically analysed the interactions between Pr55<sup>Gag</sup> or its maturation products (NCp15, NCp9 and NCp7) and the 5ʹ gRNA region and their structural consequences, <i>in vitro</i>. We show that Pr55<sup>Gag</sup> and its maturation products mostly bind at different RNA sites and with different contributions of their two zinc knuckle domains. Importantly, these proteins have different transient and permanent effects on the RNA structure, the late NCp9 and NCp7 inducing dramatic structural rearrangements. Altogether, our results reveal the distinct contributions of the different Pr55<sup>Gag</sup> maturation products on the gRNA structural maturation.
DOI: 10.6084/m9.figshare.25458847
title: RefEx2 Datasets for Arabidopsis thaliana TraVA

description: RefEx2 is a project to collect, organize, and curate transcriptome datasets of various species as reference resources for gene expression data analysis. It provides 6 reference datasets for four different species: humans, mice, Drosophila melanogaster, and Arabidopsis thaliana. This directory contains the following datasets on Arabidopsis thaliana TraVA:ath_TraVA_refextable_sample_stats.tsv.gzProcessed data matrixath_TraVA_refextable_grouped_sample_desc.tsvGrouped sample descriptionath_TraVA_refextable_sampleID_mapping.tsvSample ID mappingsNo. of genes: 32,431<br>No. of samples: 85Key ID: NCBI gene<br>Original data: PRJNA314076, PRJNA324514<br>Reference(s): DOI: 10.1111/tpj.13312
DOI: 10.6084/m9.figshare.19521505
title: Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site

description: The internal ribosome entry site (IRES) RNA of bovine viral diarrhoea virus (BVDV), an economically significant <i>Pestivirus</i>, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and <i>in silico</i> modelling approaches to gain insight into the secondary and tertiary structures of BVDV IRES RNA. Our study demonstrated that BVDV IRES RNA in solution forms a modular architecture composed of three distinct structural domains (I–III). Two regions within domain III are represented in tertiary interactions to form an H-type pseudoknot. Computational modelling of the pseudoknot motif provided a fine-grained picture of the tertiary structure and local arrangement of helices in the BVDV IRES. Furthermore, comparative genomics and consensus structure predictions revealed that the pseudoknot is evolutionarily conserved among many <i>Pestivirus</i> species. These studies provide detailed insight into the structural arrangement of BVDV IRES RNA H-type pseudoknot and encompassing motifs that likely contribute to the optimal functionality of viral cap-independent translation element.
DOI: 10.6084/m9.figshare.20525597
title: The A to I editing landscape in melanoma and its relation to clinical outcome

description: RNA editing refers to non-transient RNA modifications that occur after transcription and prior to translation by the ribosomes. RNA editing is more widespread in cancer cells than in non-transformed cells and is associated with tumorigenesis of various cancer tissues. However, RNA editing can also generate neo-antigens that expose tumour cells to host immunosurveillance. Global RNA editing in melanoma and its relevance to clinical outcome currently remain poorly characterized. The present study compared RNA editing as well as gene expression in tumour cell lines from melanoma patients of short or long metastasis-free survival, patients relapsing or not after immuno- and targeted therapy and tumours harbouring <i>BRAF</i> or <i>NRAS</i> mutations. Overall, our results showed that <i>NTRK</i> gene expression can be a marker of resistance to BRAF and MEK inhibition and gives some insights of candidate genes as potential biomarkers. In addition, this study revealed an increase in Adenosine-to-Inosine editing in Alu regions and in non-repetitive regions, including the hyperediting of the <i>MOK</i> and <i>DZIP3</i> genes in relapsed tumour samples during targeted therapy and of the <i>ZBTB11</i> gene in NRAS mutated melanoma cells. Therefore, RNA editing could be a promising tool for identifying predictive markers, tumour neoantigens and targetable pathways that could help in preventing relapses during immuno- or targeted therapies.
DOI: 10.6084/m9.figshare.20525597.v1
title: The A to I editing landscape in melanoma and its relation to clinical outcome

description: RNA editing refers to non-transient RNA modifications that occur after transcription and prior to translation by the ribosomes. RNA editing is more widespread in cancer cells than in non-transformed cells and is associated with tumorigenesis of various cancer tissues. However, RNA editing can also generate neo-antigens that expose tumour cells to host immunosurveillance. Global RNA editing in melanoma and its relevance to clinical outcome currently remain poorly characterized. The present study compared RNA editing as well as gene expression in tumour cell lines from melanoma patients of short or long metastasis-free survival, patients relapsing or not after immuno- and targeted therapy and tumours harbouring <i>BRAF</i> or <i>NRAS</i> mutations. Overall, our results showed that <i>NTRK</i> gene expression can be a marker of resistance to BRAF and MEK inhibition and gives some insights of candidate genes as potential biomarkers. In addition, this study revealed an increase in Adenosine-to-Inosine editing in Alu regions and in non-repetitive regions, including the hyperediting of the <i>MOK</i> and <i>DZIP3</i> genes in relapsed tumour samples during targeted therapy and of the <i>ZBTB11</i> gene in NRAS mutated melanoma cells. Therefore, RNA editing could be a promising tool for identifying predictive markers, tumour neoantigens and targetable pathways that could help in preventing relapses during immuno- or targeted therapies.
DOI: 10.6084/m9.figshare.19471868
title: Mechanistic insights into non-coding Y RNA processing

description: Y RNAs (84–112 nt) are non-coding RNAs transcribed by RNA polymerase III and are characterized by a distinctive secondary structure. Human Y RNAs interact with the autoimmune proteins SSB and RO60 that together form a ribonucleoprotein (RNP) complex termed RoRNP and Y RNAs also perform regulatory roles in DNA and RNA replication and stability, which has major implications for diseases including cancer. During cellular stress and apoptosis, Y RNAs are cleaved into 3’ and 5’ end fragments termed Y RNA-derived small RNAs (ysRNAs). Although some ysRNA functions in stress, apoptosis and cancer have been reported, their fundamental biogenesis has not been described. Here we report that 3’ end <i>RNY5</i> cleavage is structure dependent. In high throughput mutagenesis experiments, cleavage occurred between the 2<sup>nd</sup> and 3<sup>rd</sup> nt above a double stranded stem comprising high GC content. We demonstrate that an internal loop above stem S3 is critical for producing 3’ end ysRNAs (31 nt) with mutants resulting in longer or no ysRNAs. We show a UGGGU sequence motif at position 22 of <i>RNY5</i> is critical for producing 5’ end ysRNAs (22–25 nt). We show that intact RO60 is critical for ysRNA biogenesis. We conclude that ribonuclease L (RNASEL) contributes to Y RNA cleavage in mouse embryonic fibroblasts but is not the only endoribonuclease important in human cells.
DOI: 10.6084/m9.figshare.19471868.v1
title: Mechanistic insights into non-coding Y RNA processing

description: Y RNAs (84–112 nt) are non-coding RNAs transcribed by RNA polymerase III and are characterized by a distinctive secondary structure. Human Y RNAs interact with the autoimmune proteins SSB and RO60 that together form a ribonucleoprotein (RNP) complex termed RoRNP and Y RNAs also perform regulatory roles in DNA and RNA replication and stability, which has major implications for diseases including cancer. During cellular stress and apoptosis, Y RNAs are cleaved into 3’ and 5’ end fragments termed Y RNA-derived small RNAs (ysRNAs). Although some ysRNA functions in stress, apoptosis and cancer have been reported, their fundamental biogenesis has not been described. Here we report that 3’ end <i>RNY5</i> cleavage is structure dependent. In high throughput mutagenesis experiments, cleavage occurred between the 2<sup>nd</sup> and 3<sup>rd</sup> nt above a double stranded stem comprising high GC content. We demonstrate that an internal loop above stem S3 is critical for producing 3’ end ysRNAs (31 nt) with mutants resulting in longer or no ysRNAs. We show a UGGGU sequence motif at position 22 of <i>RNY5</i> is critical for producing 5’ end ysRNAs (22–25 nt). We show that intact RO60 is critical for ysRNA biogenesis. We conclude that ribonuclease L (RNASEL) contributes to Y RNA cleavage in mouse embryonic fibroblasts but is not the only endoribonuclease important in human cells.