Secondary Water Supply Systems
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB22937 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The secondary structure of RNA is necessary for its maturation, regulation, and processing. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we identify evolutionarily conserved features of RNA secondary structure in metazoans by applying our high-throughput, sequencing-based, structure-mapping approach to Drosophila melanogaster and Caenorhabditis elegans. This analysis reveals key structural patterns across protein-coding transcripts that indicate RNA folding is influential to protein translation and microRNA-mediated targeting and/or regulation of mRNAs in animals. Additionally, we uncover a novel population of highly base-paired RNAs, many of which are likely functional, long, non-coding RNAs. Finally, we identify and characterize ~180 structural motifs of mRNAs that are under positive or negative selection in these metazoans, thereby revealing a large set of RNA structures that are likely functional. Overall, our findings highlight the significance of secondary structure within RNA molecules, and provide the first comprehensive evidence of widespread RNA secondary structure conservation in animals.
2012-01-26 | GSE29571 | GEO
Project description:The secondary structure of RNA is necessary for its maturation, regulation, and processing. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we identify evolutionarily conserved features of RNA secondary structure in metazoans by applying our high-throughput, sequencing-based, structure-mapping approach to Drosophila melanogaster and Caenorhabditis elegans. This analysis reveals key structural patterns across protein-coding transcripts that indicate RNA folding is influential to protein translation and microRNA-mediated targeting and/or regulation of mRNAs in animals. Additionally, we uncover a novel population of highly base-paired RNAs, many of which are likely functional, long, non-coding RNAs. Finally, we identify and characterize ~180 structural motifs of mRNAs that are under positive or negative selection in these metazoans, thereby revealing a large set of RNA structures that are likely functional. Overall, our findings highlight the significance of secondary structure within RNA molecules, and provide the first comprehensive evidence of widespread RNA secondary structure conservation in animals. Double-stranded (dsRNA) specific RNA sequencing (dsRNA-seq) and single-stranded (ssRNA) specific RNA sequencing (ssRNA-seq) in Drosophila DL1 cells and C. elegans mixed stage N2 worms. Each of the four samples (dsRNA/Dmel, ssRNA/Dmel, dsRNA/Cel, and ssRNA/Cel) was sequenced separately on both Illumina GA-IIx and Hiseq2000, giving a total of eight datasets. Two corresponding smRNA libraries (smRNA-seq) of the same DL1 cells and mixed stage N2 worms are also presented.
2012-01-26 | E-GEOD-29571 | biostudies-arrayexpress
Project description:The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, processing, and functionality. However, the global influence of this feature on plant gene expression is still for the most part unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of polyA+-selected (RNA-seq), small (smRNA-seq), and ribosome-bound (ribo-seq) RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing further evidence that secondary structure is necessary for RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We also reveal that RNA folding is significantly anti-correlated with overall transcript abundance, which is likely due to the increased propensity of highly structured mRNAs to be degraded and/or processed into smRNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. Overall, our findings provide the first global assessment of RNA folding and its significant regulatory effects in a plant transcriptome. Single-stranded RNA sequencing (ssRNA-seq) and ribosome-bound RNA sequencing (ribo-seq) in immature buds. A single replicate of each library.
2012-11-15 | E-GEOD-40209 | biostudies-arrayexpress
Project description:We investigated the metabolism of six secondary metabolite producing fungi of the Penicillium genus, during nutrient depletion in the stationary phase of batch fermentations and assessed conserved metabolic responses across species using genome-wide transcriptional profiling. Coexpression analysis revealed that expression of secondary metabolite biosynthetic genes correlates with expression of genes associated with pathways responsible for generation of precursor metabolites for secondary metabolism. Our results highlight the main metabolic routes for precursor supply of the secondary metabolism during nutrient depletion, and suggests that regulation of fungal metabolism is tailored to meet the demands for secondary metabolite production. These findings can aid in identifying wild type species, which are optimized for production of specific secondary metabolites, and therefore can be utilized as high yielding cell factories.
2017-11-17 | GSE106983 | GEO
Project description:The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, processing, and functionality. However, the global influence of this feature on plant gene expression is still for the most part unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of polyA+-selected (RNA-seq), small (smRNA-seq), and ribosome-bound (ribo-seq) RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing further evidence that secondary structure is necessary for RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We also reveal that RNA folding is significantly anti-correlated with overall transcript abundance, which is likely due to the increased propensity of highly structured mRNAs to be degraded and/or processed into smRNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. Overall, our findings provide the first global assessment of RNA folding and its significant regulatory effects in a plant transcriptome.
2012-11-15 | GSE40209 | GEO
Project description:Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation.
2015-10-21 | GSE63817 | GEO
Project description:Messenger RNA secondary structure is critical to all aspects of post-transcriptional regulation. However, the global regulatory and evolutionary significance of mRNA secondary structure remains largely illusive. Here, we describe a transcriptome-wide analysis of RNA secondary structure in humans and two non-human primates, based on a high-throughput, nuclease-mediated, structure mapping approach. Using this methodology, we uncover global patterns of mRNA secondary structure, which we find to be conserved through primate evolution. We provide evidence for secondary structure-based regulatory pathways, which impact on gene expression through associations with translational machinery and RNA-binding proteins, including components of the microprocessor complex. Our results lend support to an unexpected, conserved mechanism by which highly structured regions of mRNAs serve as processing sites for small RNAs, resulting in subsequent turnover. Global mRNA secondary structure analysis in primate transcriptomes using high-throughput, nuclease-mediated, structure mappinng approaches of dsRNA-seq and ssRNA-seq, also with polyA+ mRNA-seq, smRNA-seq (small RNA), and genome-wide mapping of uncapped and cleaved transcripts (GMUCT); these NGS-seq experiments were carried out in three primate brains as well as three different cell lines, both in in vitro and in vivo.
2017-05-01 | E-GEOD-57295 | biostudies-arrayexpress
Project description:The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale. RNA sample was treated with one of two structure-specific enzymes (RNase V1 or RNase S1). Four independent V1 experiments and three independent S1 experiments were carried out. Processed data file linked below. Data processing involves merging (or rather log-ratio-ing) the 7 lanes of SOLiD sequencing data against each other. Also linked below are the genome and transcriptome FASTA files used for mapping, and the annotation file having the format: gene_ID, chromosome, start, end, feature. Start and end are 1-based; feature is "Transcript" for the entire transcript (including introns), "Intron", "Exon", "5UTR" or "3UTR". Genome-wide measurement of RNA secondary structure in yeast, Kertesz et al., Nature Volume:467, Pages:103-107, Date published:(02 September 2010) http://www.nature.com/nature/journal/v467/n7311/abs/nature09322.html
2010-08-24 | E-GEOD-22393 | biostudies-arrayexpress
Project description:The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale.
2010-08-24 | GSE22393 | GEO
Project description:Shoot zinc (Zn) in Brassica oleracea is affected by soil Zn and phosphorus (P) concentrations. Most problematic is the negative impact of P fertilizers on Zn concentrations in crops, which makes balancing yield and mineral quality challenging. To evaluate molecular mechanisms involved in the accumulation of large shoot Zn concentrations regardless of the P supply, two B. oleracea accessions were grown hydroponically for two weeks with different combination of P and Zn supply. Ionome profiling and deep RNA sequencing of roots revealed interactions of P and Zn in planta, without apparent phenotypic effects. In addition, increasing P supply did not reduce tissue Zn concentration. Substantial changes in gene expression in roots of both accessions ensured nutritionally sufficient P and Zn uptake. Numerous genes were differentially expressed after changing Zn or P supply and most of them were unique to only one accession, highlighting different strategies in achieving nutrient sufficiency. Thus, different gene networks responded to the changing P and Zn supply in the two accessions. Additionally, enrichment analysis of gene ontology classes revealed that genes involved in lipid metabolism, response to starvation, and anion transport mechanisms were most responsive to the contrasting P and Zn supply in both accessions. The results agreed with previously studies demonstrating alterations in P transport and phospholipid metabolism in response to reduced P supply. Knowledge of genes responsive to P or Zn supply will help illuminate the interactions between these elements in their uptake and accumulation by plants and might highlight candidate genes for breeding high-yield-high-Zn crops.
2019-03-01 | GSE127467 | GEO