cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8293439.v2
title: A two-step probing method to compare lysine accessibility across macromolecular complex conformations

description: Structural models of large and dynamic molecular complexes are appearing in increasing numbers, in large part because of recent technical advances in cryo-electron microscopy. However, the inherent complexity of such biological assemblies comprising dozens of moving parts often limits the resolution of structural models and leaves the puzzle as to how each functional configuration transitions to the next. Orthogonal biochemical information is crucial to understanding the molecular interactions that drive those rearrangements. We present a two-step method for chemical probing detected by tandem mass-spectrometry to globally assess the reactivity of lysine residues within purified macromolecular complexes. Because lysine side chains often balance the negative charge of RNA in ribonucleoprotein complexes, the method is especially useful for detecting changes in protein-RNA interactions. By probing the <i>E. coli</i> 30S ribosome subunit, we established that the reactivity pattern of lysine residues quantitatively reflects structure models derived from X-ray crystallography. We also used the strategy to assess differences in three conformations of purified human spliceosomes in the context of recent cryo-electron microscopy models. Our results demonstrate that the probing method yields powerful biochemical information that helps contextualize architectural rearrangements of intermediate resolution structures of macromolecular complexes, often solved in multiple conformations.
DOI: 10.6084/m9.figshare.8343428.v1
title: Low levels of exosomal long non-coding RNA <i>HOTTIP</i> is a prognostic biomarker in colorectal cancer

description: Molecular risk stratification of colorectal cancer can improve patient outcome. A panel of lncRNAs (<i>H19, HOTTIP, HULC</i> and <i>MALAT1</i>) derived from serum exosomes of patients with non-metastatic CRC and healthy donors was analyzed. Exosomes from healthy donors carried significantly more <i>H19, HULC</i> and <i>HOTTIP</i> transcripts in comparison to CRC patients. Correlation analysis between lncRNAs and clinical data revealed a statistical significance between low levels of exosomal <i>HOTTIP</i> and poor overall survival. This was confirmed by multivariate analysis that <i>HOTTIP</i> is an independent prognostic marker for overall survival (HR: 4.5, CI: 1.69 – 11.98, p=0.0027). Here, <i>HOTTIP</i> poses to be a valid biomarker for patients with a CRC to predict post-surgical survival time.
DOI: 10.6084/m9.figshare.8247800.v2
title: Transcriptome stability profiling using 5’-bromouridine IP chase (BRIC-seq) identifies novel and functional microRNA targets in human melanoma cells

description: RNA half-life is closely related to its cellular physiological function, so stability determinants may have regulatory functions. Micro(mi)RNAs have primarily been studied with respect to post-transcriptional mRNA regulation and target degradation. Here we study the impact of the tumour suppressive melanoma miRNA miR-211 on transcriptome stability and phenotype in the non-pigmented melanoma cell line, A375. Using 5ʹ-bromouridine IP chase (BRIC)-seq, transcriptome-wide RNA stability profiles revealed highly regulated genes and pathways important in this melanoma cell line. By combining BRIC-seq, RNA-seq and <i>in silico</i> predictions, we identified both existing and novel direct miR-211 targets. We validated <i>DUSP3</i> as one such novel miR-211 target, which itself sustains colony formation and invasion in A375 cells via MAPK/PI3K signalling. miRNAs have the capacity to control RNA turnover as a gene expression mechanism, and RNA stability profiling is an excellent tool for interrogating functionally relevant gene regulatory pathways and miRNA targets when combined with other high-throughput and <i>in silico</i> approaches.
DOI: 10.6084/m9.figshare.8247800.v1
title: Transcriptome stability profiling using 5’-bromouridine IP chase (BRIC-seq) identifies novel and functional microRNA targets in human melanoma cells

description: RNA half-life is closely related to its cellular physiological function, so stability determinants may have regulatory functions. Micro(mi)RNAs have primarily been studied with respect to post-transcriptional mRNA regulation and target degradation. Here we study the impact of the tumour suppressive melanoma miRNA miR-211 on transcriptome stability and phenotype in the non-pigmented melanoma cell line, A375. Using 5ʹ-bromouridine IP chase (BRIC)-seq, transcriptome-wide RNA stability profiles revealed highly regulated genes and pathways important in this melanoma cell line. By combining BRIC-seq, RNA-seq and <i>in silico</i> predictions, we identified both existing and novel direct miR-211 targets. We validated <i>DUSP3</i> as one such novel miR-211 target, which itself sustains colony formation and invasion in A375 cells via MAPK/PI3K signalling. miRNAs have the capacity to control RNA turnover as a gene expression mechanism, and RNA stability profiling is an excellent tool for interrogating functionally relevant gene regulatory pathways and miRNA targets when combined with other high-throughput and <i>in silico</i> approaches.
DOI: 10.6084/m9.figshare.8293391
title: High-throughput analysis revealed mutations’ diverging effects on <i>SMN1</i> exon 7 splicing

description: Splicing-affecting mutations can disrupt gene function by altering the transcript assembly. To ascertain splicing dysregulation principles, we modified a minigene assay for the parallel high-throughput evaluation of different mutations by next-generation sequencing. In our model system, all exonic and six intronic positions of the <i>SMN1</i> gene’s exon 7 were mutated to all possible nucleotide variants, which amounted to 180 unique single-nucleotide mutants and 470 double mutants. The mutations resulted in a wide range of splicing aberrations. Exonic splicing-affecting mutations resulted either in substantial exon skipping, supposedly driven by predicted exonic splicing silencer or cryptic donor splice site (5′ss) and <i>de novo</i> 5′ss strengthening and use. On the other hand, a single disruption of exonic splicing enhancer was not sufficient to cause major exon skipping, suggesting these elements can be substituted during exon recognition. While disrupting the acceptor splice site led only to exon skipping, some 5′ss mutations potentiated the use of three different cryptic 5′ss. Generally, single mutations supporting cryptic 5′ss use displayed better pre-mRNA/U1 snRNA duplex stability and increased splicing regulatory element strength across the original 5′ss. Analyzing double mutants supported the predominating splicing regulatory elements’ effect, but U1 snRNA binding could contribute to the global balance of splicing isoforms. Based on these findings, we suggest that creating a new splicing enhancer across the mutated 5′ss can be one of the main factors driving cryptic 5′ss use.
DOI: 10.6084/m9.figshare.9114344
title: HuR interacts with lincBRN1a and lincBRN1b during neuronal stem cells differentiation

description: LncRNAs play crucial roles in cellular processes and their regulatory effects in the adult brain and neural stem cells (NSCs) remain to be entirely characterized. We report that 10 lncRNAs (LincENC1, FABL, lincp21, HAUNT, PERIL, lincBRN1a, lincBRN1b, HOTTIP, TUG1 and FENDRR) are expressed during murine NSCs differentiation and interact with the RNA-binding protein ELAVL1/HuR. Furthermore, we characterize the function of two of the deregulated lncRNAs, lincBRN1a and lincBRN1b, during NSCs’ differentiation. Their inhibition leads to the induction of differentiation, with a concomitant decrease in stemness and an increase in neuronal markers, indicating that they exert key functions in neuronal cells differentiation. Furthermore, we describe here that HuR regulates their half-life, suggesting their synergic role in the differentiation process. We also identify six human homologs (PANTR1, TUG1, HOTTIP, TP53COR, ELDRR and FENDRR) of the mentioned 10 lncRNAs and we report their deregulation during human iPSCs differentiation into neurons. In conclusion, our results strongly indicate a key synergic role for lncRNAs and HuR in neuronal stem cells fate.
DOI: 10.6084/m9.figshare.8327783
title: The σ<sup>B</sup>-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in <i>Listeria monocytogenes</i> through a direct interaction with the <i>ilvA</i> transcript

description: The facultative intracellular pathogen <i>Listeria monocytogenes</i> can persist and grow in a diverse range of environmental conditions, both outside and within its mammalian host. The alternative sigma factor Sigma B (σ<sup>B</sup>) plays an important role in this adaptability and is critical for the transition into the host. While some of the functions of the σ<sup>B</sup> regulon in facilitating this transition are understood the role of σ<sup>B</sup>-dependent small regulatory RNAs (sRNAs) remain poorly characterized. In this study, we focused on elucidating the function of Rli47, a σ<sup>B</sup>-dependent sRNA that is highly induced in the intestine and in macrophages. Using a combination of <i>in silico</i> and <i>in vivo</i> approaches, a binding interaction was predicted with the Shine-Dalgarno region of the <i>ilvA</i> mRNA, which encodes threonine deaminase, an enzyme required for branched-chain amino acid biosynthesis. Both <i>ilvA</i> transcript levels and threonine deaminase activity were increased in a deletion mutant lacking the <i>rli47</i> gene. The Δ<i>rli47</i> mutant displayed a shorter growth lag in isoleucine-depleted growth media relative to the wild-type, and a similar phenotype was also observed in a mutant lacking σ<sup>B</sup>. The impact of the Δ<i>rli47</i> on the global transcription profile of the cell was investigated using RNA-seq, and a significant role for Rli47 in modulating amino acid metabolism was uncovered. Taken together, the data point to a model where Rli47 is responsible for specifically repressing isoleucine biosynthesis as a way to restrict growth under harsh conditions, potentially contributing to the survival of <i>L. monocytogenes</i> in niches both outside and within the mammalian host.
DOI: 10.6084/m9.figshare.8327783.v2
title: The σ<sup>B</sup>-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in <i>Listeria monocytogenes</i> through a direct interaction with the <i>ilvA</i> transcript

description: The facultative intracellular pathogen <i>Listeria monocytogenes</i> can persist and grow in a diverse range of environmental conditions, both outside and within its mammalian host. The alternative sigma factor Sigma B (σ<sup>B</sup>) plays an important role in this adaptability and is critical for the transition into the host. While some of the functions of the σ<sup>B</sup> regulon in facilitating this transition are understood the role of σ<sup>B</sup>-dependent small regulatory RNAs (sRNAs) remain poorly characterized. In this study, we focused on elucidating the function of Rli47, a σ<sup>B</sup>-dependent sRNA that is highly induced in the intestine and in macrophages. Using a combination of <i>in silico</i> and <i>in vivo</i> approaches, a binding interaction was predicted with the Shine-Dalgarno region of the <i>ilvA</i> mRNA, which encodes threonine deaminase, an enzyme required for branched-chain amino acid biosynthesis. Both <i>ilvA</i> transcript levels and threonine deaminase activity were increased in a deletion mutant lacking the <i>rli47</i> gene. The Δ<i>rli47</i> mutant displayed a shorter growth lag in isoleucine-depleted growth media relative to the wild-type, and a similar phenotype was also observed in a mutant lacking σ<sup>B</sup>. The impact of the Δ<i>rli47</i> on the global transcription profile of the cell was investigated using RNA-seq, and a significant role for Rli47 in modulating amino acid metabolism was uncovered. Taken together, the data point to a model where Rli47 is responsible for specifically repressing isoleucine biosynthesis as a way to restrict growth under harsh conditions, potentially contributing to the survival of <i>L. monocytogenes</i> in niches both outside and within the mammalian host.
DOI: 10.6084/m9.figshare.8247800
title: Transcriptome stability profiling using 5’-bromouridine IP chase (BRIC-seq) identifies novel and functional microRNA targets in human melanoma cells

description: RNA half-life is closely related to its cellular physiological function, so stability determinants may have regulatory functions. Micro(mi)RNAs have primarily been studied with respect to post-transcriptional mRNA regulation and target degradation. Here we study the impact of the tumour suppressive melanoma miRNA miR-211 on transcriptome stability and phenotype in the non-pigmented melanoma cell line, A375. Using 5ʹ-bromouridine IP chase (BRIC)-seq, transcriptome-wide RNA stability profiles revealed highly regulated genes and pathways important in this melanoma cell line. By combining BRIC-seq, RNA-seq and <i>in silico</i> predictions, we identified both existing and novel direct miR-211 targets. We validated <i>DUSP3</i> as one such novel miR-211 target, which itself sustains colony formation and invasion in A375 cells via MAPK/PI3K signalling. miRNAs have the capacity to control RNA turnover as a gene expression mechanism, and RNA stability profiling is an excellent tool for interrogating functionally relevant gene regulatory pathways and miRNA targets when combined with other high-throughput and <i>in silico</i> approaches.
DOI: 10.6084/m9.figshare.9114344.v2
title: HuR interacts with lincBRN1a and lincBRN1b during neuronal stem cells differentiation

description: LncRNAs play crucial roles in cellular processes and their regulatory effects in the adult brain and neural stem cells (NSCs) remain to be entirely characterized. We report that 10 lncRNAs (LincENC1, FABL, lincp21, HAUNT, PERIL, lincBRN1a, lincBRN1b, HOTTIP, TUG1 and FENDRR) are expressed during murine NSCs differentiation and interact with the RNA-binding protein ELAVL1/HuR. Furthermore, we characterize the function of two of the deregulated lncRNAs, lincBRN1a and lincBRN1b, during NSCs’ differentiation. Their inhibition leads to the induction of differentiation, with a concomitant decrease in stemness and an increase in neuronal markers, indicating that they exert key functions in neuronal cells differentiation. Furthermore, we describe here that HuR regulates their half-life, suggesting their synergic role in the differentiation process. We also identify six human homologs (PANTR1, TUG1, HOTTIP, TP53COR, ELDRR and FENDRR) of the mentioned 10 lncRNAs and we report their deregulation during human iPSCs differentiation into neurons. In conclusion, our results strongly indicate a key synergic role for lncRNAs and HuR in neuronal stem cells fate.
DOI: 10.6084/m9.figshare.8327783.v1
title: The σ<sup>B</sup>-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in <i>Listeria monocytogenes</i> through a direct interaction with the <i>ilvA</i> transcript

description: The facultative intracellular pathogen <i>Listeria monocytogenes</i> can persist and grow in a diverse range of environmental conditions, both outside and within its mammalian host. The alternative sigma factor Sigma B (σ<sup>B</sup>) plays an important role in this adaptability and is critical for the transition into the host. While some of the functions of the σ<sup>B</sup> regulon in facilitating this transition are understood the role of σ<sup>B</sup>-dependent small regulatory RNAs (sRNAs) remain poorly characterized. In this study, we focused on elucidating the function of Rli47, a σ<sup>B</sup>-dependent sRNA that is highly induced in the intestine and in macrophages. Using a combination of <i>in silico</i> and <i>in vivo</i> approaches, a binding interaction was predicted with the Shine-Dalgarno region of the <i>ilvA</i> mRNA, which encodes threonine deaminase, an enzyme required for branched-chain amino acid biosynthesis. Both <i>ilvA</i> transcript levels and threonine deaminase activity were increased in a deletion mutant lacking the <i>rli47</i> gene. The Δ<i>rli47</i> mutant displayed a shorter growth lag in isoleucine-depleted growth media relative to the wild-type, and a similar phenotype was also observed in a mutant lacking σ<sup>B</sup>. The impact of the Δ<i>rli47</i> on the global transcription profile of the cell was investigated using RNA-seq, and a significant role for Rli47 in modulating amino acid metabolism was uncovered. Taken together, the data point to a model where Rli47 is responsible for specifically repressing isoleucine biosynthesis as a way to restrict growth under harsh conditions, potentially contributing to the survival of <i>L. monocytogenes</i> in niches both outside and within the mammalian host.
DOI: 10.6084/m9.figshare.8293391.v1
title: High-throughput analysis revealed mutations’ diverging effects on <i>SMN1</i> exon 7 splicing

description: Splicing-affecting mutations can disrupt gene function by altering the transcript assembly. To ascertain splicing dysregulation principles, we modified a minigene assay for the parallel high-throughput evaluation of different mutations by next-generation sequencing. In our model system, all exonic and six intronic positions of the <i>SMN1</i> gene’s exon 7 were mutated to all possible nucleotide variants, which amounted to 180 unique single-nucleotide mutants and 470 double mutants. The mutations resulted in a wide range of splicing aberrations. Exonic splicing-affecting mutations resulted either in substantial exon skipping, supposedly driven by predicted exonic splicing silencer or cryptic donor splice site (5′ss) and <i>de novo</i> 5′ss strengthening and use. On the other hand, a single disruption of exonic splicing enhancer was not sufficient to cause major exon skipping, suggesting these elements can be substituted during exon recognition. While disrupting the acceptor splice site led only to exon skipping, some 5′ss mutations potentiated the use of three different cryptic 5′ss. Generally, single mutations supporting cryptic 5′ss use displayed better pre-mRNA/U1 snRNA duplex stability and increased splicing regulatory element strength across the original 5′ss. Analyzing double mutants supported the predominating splicing regulatory elements’ effect, but U1 snRNA binding could contribute to the global balance of splicing isoforms. Based on these findings, we suggest that creating a new splicing enhancer across the mutated 5′ss can be one of the main factors driving cryptic 5′ss use.
DOI: 10.6084/m9.figshare.9114344.v1
title: HuR interacts with lincBRN1a and lincBRN1b during neuronal stem cells differentiation

description: LncRNAs play crucial roles in cellular processes and their regulatory effects in the adult brain and neural stem cells (NSCs) remain to be entirely characterized. We report that 10 lncRNAs (LincENC1, FABL, lincp21, HAUNT, PERIL, lincBRN1a, lincBRN1b, HOTTIP, TUG1 and FENDRR) are expressed during murine NSCs differentiation and interact with the RNA-binding protein ELAVL1/HuR. Furthermore, we characterize the function of two of the deregulated lncRNAs, lincBRN1a and lincBRN1b, during NSCs’ differentiation. Their inhibition leads to the induction of differentiation, with a concomitant decrease in stemness and an increase in neuronal markers, indicating that they exert key functions in neuronal cells differentiation. Furthermore, we describe here that HuR regulates their half-life, suggesting their synergic role in the differentiation process. We also identify six human homologs (PANTR1, TUG1, HOTTIP, TP53COR, ELDRR and FENDRR) of the mentioned 10 lncRNAs and we report their deregulation during human iPSCs differentiation into neurons. In conclusion, our results strongly indicate a key synergic role for lncRNAs and HuR in neuronal stem cells fate.
DOI: 10.16904/1000001.3
title: Forest Type NFI

description: This dataset presents an remote sensing based approach for a countrywide mapping of broadleaved and coniferous trees in Switzerland with a spatial resolution of 3 m x 3 m. The data available is a raster of 25 m x 25 m with the fraction of broadleaf trees. The classification approach incorporates a random forest classifier, explanatory variables from multispectral aerial imagery and a Digital Terrain Model (DTM) from Airborne Laser Scanning (ALS) data, digitized training polygons and independent validation data from the National Forest Inventory (NFI). Whereas high model overall accuracies (0.99)and kappa (0.98) were achieved, the comparison of the tree type map with independent NFI data revealed significant deviations that are related to underestimations of broadleaved trees (median of 3.17%).
DOI: 10.16904/1000001.6
title: Forest Type NFI

description: This dataset presents an remote sensing based approach for a countrywide mapping of broadleaved and coniferous trees in Switzerland with a spatial resolution of 3 m x 3 m. The data available is a raster of 25 m x 25 m with the fraction of broadleaf trees. The classification approach incorporates a random forest classifier, explanatory variables from multispectral aerial imagery and a Digital Terrain Model (DTM) from Airborne Laser Scanning (ALS) data, digitized training polygons and independent validation data from the National Forest Inventory (NFI). Whereas high model overall accuracies (0.99)and kappa (0.98) were achieved, the comparison of the tree type map with independent NFI data revealed significant deviations that are related to underestimations of broadleaved trees (median of 3.17%).
DOI: 10.5281/zenodo.4740115
title: MD simulation trajectory and related files for POPC bilayer in medium low hydration (CHARMM36, Gromacs 4.5)

description: Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36 force field in medium low hydration (dx.doi.org/10.1021/jp101759q), 20ns, T=303K, 72 POPC molecules, 1080 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1021/jp101759q).
DOI: 10.5281/zenodo.607232
title: MD simulation trajectory and related files for POPC bilayer in medium low hydration (CHARMM36, Gromacs 4.5)

description: Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36 force field in medium low hydration (dx.doi.org/10.1021/jp101759q), 20ns, T=303K, 72 POPC molecules, 1080 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1021/jp101759q).
DOI: 10.6084/m9.figshare.13379084.v1
title: Data and R codes from: Garrido et al. 2021. The dilution effect behind the scenes: disentangling mechanisms by the quantification of reciprocal pathogen-multihost responses'

description: Data and R codes from: <i>Garrido et al. 2021. The dilution effect behind the scenes: disentangling mechanisms by the quantification of reciprocal pathogen-multihost responses</i>'
DOI: 10.5519/qd.4st0pbw1
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (53 records)
DOI: 10.25345/c55n78
title: MassIVE MSV000087371 - GNPS_Srigolactone_Hemp_exsudat-10-12_method_MS02
title: Research in hemp exudate of cannabis sativa strigolactone by MS/MS with various Strigolactone control and a blank in acetonitrile.