Global identification of functional microRNA-mRNA interactions in Drosophila
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PROVIDER: PRJNA432508 | ENA |
REPOSITORIES: ENA
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Project description:MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. To close this gap, we generated the first transcriptome-wide in vivo map of miRNA-mRNA interactions in Drosophila melanogaster, making use of single nucleotide resolution in Argonaute1 (AGO1) crosslinking and immunoprecipitation (CLIP) data. Absolute quantification of cellular miRNA levels presents the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two CLIP approaches, we identify a similar predictive potential to unambiguously assign thousands of miRNA-mRNA pairs from AGO1 interaction data at unprecedented depth, achieving higher signal-to-noise ratios than with computational methods alone. Quantitative RNA-Seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites and their quantitative functional impact in Drosophila.
2019-02-11 | GSE109980 | GEO
Project description:MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. Here, we generated a transcriptome-wide in vivo map of miRNA-mRNA interactions in Drosophila melanogaster, making use of single nucleotide resolution in Argonaute1 (AGO1) crosslinking and immunoprecipitation (CLIP) data. Absolute quantification of cellular miRNA levels presents the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two CLIP approaches, we identify a similar predictive potential to unambiguously assign thousands of miRNA-mRNA pairs from AGO1 interaction data at unprecedented depth, achieving higher signal-to-noise ratios than with computational methods alone. Quantitative RNA-seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites and their quantitative functional impact in Drosophila.
| S-EPMC6456604 | biostudies-literature
Project description:MicroRNAs contribute to metastatic progression in many cancers by modulation of phenotypic reprogramming processes such as epithelial-mesenchymal plasticity. However, it remains challenging to identify microRNA-mRNA interactions of functional significance at endogenous expression levels. The LM-MEL cell line panel comprises a large set of unique melanoma cell lines derived from largely metastatic melanoma tumours, as described in Behren et al, PCMR 2013 26(4):597-600 (PMID 23527996). For this study, 57 of the cell lines underwent matched gene expression (Illumina HT12v4 microarray) and small RNASeq (Illumina HiSeq) profiling in unperturbed conditions, generating a large dataset of matched gene and microRNA abundance data which was integrated with available phenotypic annotations covering several conditions of biological interest. We developed a novel systems analysis workflow to identify putative regulatory interactions suitable for subsequent validation.
2016-11-03 | GSE89438 | GEO
Project description:BackgroundCellular senescence can be induced by a variety of extrinsic stimuli, and sustained exposure to sunlight is a key factor in photoaging of the skin. Accordingly, irradiation of skin fibroblasts by UVB light triggers cellular senescence, which is thought to contribute to extrinsic skin aging, although molecular mechanisms are incompletely understood. Here, we addressed molecular mechanisms underlying UVB induced senescence of human diploid fibroblasts.ResultsWe observed a parallel activation of the p53/p21(WAF1) and p16(INK4a)/pRb pathways. Using genome-wide transcriptome analysis, we identified a transcriptional signature of UVB-induced senescence that was conserved in three independent strains of human diploid fibroblasts (HDF) from skin. In parallel, a comprehensive screen for microRNAs regulated during UVB-induced senescence was performed which identified five microRNAs that are significantly regulated during the process. Bioinformatic analysis of miRNA-mRNA networks was performed to identify new functional mRNA targets with high confidence for miR-15a, miR-20a, miR-20b, miR-93, and miR-101. Already known targets of these miRNAs were identified in each case, validating the approach. Several new targets were identified for all of these miRNAs, with the potential to provide new insight in the process of UVB-induced senescence at a genome-wide level. Subsequent analysis was focused on miR-101 and its putative target gene Ezh2. We confirmed that Ezh2 is regulated by miR-101 in human fibroblasts, and found that both overexpression of miR-101 and downregulation of Ezh2 independently induce senescence in the absence of UVB irradiation. However, the downregulation of miR-101 was not sufficient to block the phenotype of UVB-induced senescence, suggesting that other UVB-induced processes induce the senescence response in a pathway redundant with upregulation of miR-101.ConclusionWe performed a comprehensive screen for UVB-regulated microRNAs in human diploid fibroblasts, and identified a network of miRNA-mRNA interactions mediating UVB-induced senescence. In addition, miR-101 and Ezh2 were identified as key players in UVB-induced senescence of HDF.
| S-EPMC4008267 | biostudies-literature
Project description:The objective of this study was to determine the global chromosomal interaction map for exponentially growing Saccharomyces cerevisiae cells using Genome Conformation Capture. Interactions between chromosomes were identified within a population of yeast cells growing exponentially in a semi-defined medium containing glucose. The series contains the sequences of the ligated restriction fragments that identified the interactions.
2009-07-21 | GSE13648 | GEO
Project description:Identification of new microRNA-22-5p and -199a-5p/MMP1 functional interactions in stress-induced senescent human dermal fibroblasts
| PRJNA310229 | ENA
Project description:MicroRNAs play important roles in physiology and pathology by repressing target gene expression, but it remains challenging to identify targets and regulatory networks on a global scale. MicroRNAs often pair with targets complementary to nucleotide 2 to 7, but such complementarity is not always found within targets. Here we show global views of microRNA-target interactions with unparalleled resolution and confidence by conducting a series of UV-crosslinking and immunoprecipitation experiments for AGO2. Our data indicate that direct interactions are mainly guided by seed complementarity. However, we find that different microRNAs recognize atypical sites with varying tolerance to mismatches. Pathway enrichment analyses reveal that many target genes encoding constituents of the same pathways such as Hippo and Wnt, yet unexpectedly, both positive and negative components are targeted by identical and/or different microRNAs from a same polycistronic cluster. The prevalence of incoherent feedforward loops epitomizes the complexity of microRNA-target networks and the pitfalls of reductionistic inference of miRNA functions. Our results illuminate target sites of miRNAs and regulatory networks that facilitate a deeper understanding of miRNA functions.
2018-09-19 | GSE112006 | GEO
Project description:The objective of this study was to determine the global chromosomal interaction map for exponentially growing Saccharomyces cerevisiae cells using Genome Conformation Capture. Interactions between chromosomes were identified within a population of yeast cells growing exponentially in a semi-defined medium containing glucose. The series contains the sequences of the ligated restriction fragments that identified the interactions. A GCC library was prepared, using MspI, from 1.5 x 10^5 cells and sequenced. Data was processed using the Flp_spin_man program suite in conjunction with SOAP (Rodley C.D., Bertels F., Jones B., and O'Sullivan J.M., submitted). The software package initially sorted sequences according to the presence or absence of the MspI restriction site. Sequences containing the restriction site were broken, in silico, and their positions mapped onto the yeast genome (using SOAP). Thus regions of the genome that were in close enough proximity to be cross-linked and subsequently ligated together were identified.
2009-07-21 | E-GEOD-13648 | biostudies-arrayexpress
Project description:MicroRNAs (miRs) function primarily as post-transcriptional negative regulators of gene expression through binding to their mRNA targets. Reliable prediction of a miR’s targets is a considerable bioinformatic challenge of great importance for inferring the miR’s function. Sequence-based prediction algorithms have high false-positive rates, are not in agreement, and are not biological context specific. Here we introduce CoSMic (Context-Specific MicroRNA analysis), an algorithm that combines sequence-based prediction with miR and mRNA expression data. CoSMic differs from existing methods—it identifies miRs that play active roles in the specific biological system of interest and predicts with less false positives their functional targets. We applied CoSMic to search for miRs that regulate the migratory response of human mammary cells to epidermal growth factor (EGF) stimulation. Several such miRs, whose putative targets were significantly enriched by migration processes were identified. We tested three of these miRs experimentally, and showed that they indeed affected the migratory phenotype; we also tested three negative controls. In comparison to other algorithms CoSMic indeed filters out false positives and allows improved identification of context-specific targets. CoSMic can greatly facilitate miR research in general and, in particular, advance our understanding of individual miRs’ function in a specific context.
2012-09-19 | GSE33538 | GEO
Project description:We mapped CstF64-RNA interactions at the transcriptome level and studied CstF64-mediated regulation of global mRNA alternative polyadenylation by using iCLIP-seq and direct RNA sequencing analyses.
2012-10-01 | GSE40859 | GEO