Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA173681 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes
2014-08-06 | GSE58734 | GEO
Project description:Background: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. Their abilyty to affect multiple gene pathways by targeting to various mRNAs makes them to an interesting class of regulators. The interplay between miRNA and mRNA has been proposed as an important process in cancer development and progression. In this study, we analyzed miRNA -mRNA interactions in bladder urothelial carcinoma. Methodology/Principal Findings: We have developed a new algorithm which is capable of identifying altered miRNA-mRNA regulation between tissues samples without preexisting stratification of groups. Microarray expression profiling of both miRNA and mRNA from the same sample were performed using a collective of 24 urothelial carcinoma and normal bladder tissue samples. Using our approach, normal and tumor tissue samples as well as different stages of tumor progression were successfully stratified. Also, we were able to analyzed individual miRNA-mRNA interactions from each patient, focusing on different miRNA families. Conclusions: Just recently, the need for tools that allow an integrative analysis of microRNA and mRNA expression data has been addressed. With this study, we provide an algorithm that considers the special nature of miRNA induced regulation and shows good specificities and sensitivities when applied to bladder cancer expression data. mRNA and microRNA expression data were analyzed together to identify bladder cancer specific micoRNA-mRNA interaction
2013-08-24 | E-GEOD-40355 | biostudies-arrayexpress
Project description:Bladder cancer (BCa) is one of the most common malignancy of the urinary tract. In order to improve the diagnosis, prevention and treatment of BCa, the details of molecular mechanisms underlying the tumorigenesis and development needs to be clarified. Results provide insight into molecular mechanisms underlying the mRNA and miRNA interactions in BCa. 3 human bladder cancer tissues and 3 normal bladder tissues were analyzed using microarray. The alteration of mRNA and miRNA expression between the 2 groups were detected.
2017-02-22 | GSE76211 | GEO
Project description:We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes Sequence library of miRNAs from a single sample of human foetal mesenchymal stem cells. Results tested and confirmed by northern blotting. Please note that only raw data files are available for the embryonic and neual samples and thus, directly submitted to SRA (SRX547311, SRX548700, respectively under SRP042115/PRJNA247767)
2014-08-06 | E-GEOD-58734 | biostudies-arrayexpress
Project description:Background: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. Their abilyty to affect multiple gene pathways by targeting to various mRNAs makes them to an interesting class of regulators. The interplay between miRNA and mRNA has been proposed as an important process in cancer development and progression. In this study, we analyzed miRNA -mRNA interactions in bladder urothelial carcinoma. Methodology/Principal Findings: We have developed a new algorithm which is capable of identifying altered miRNA-mRNA regulation between tissues samples without preexisting stratification of groups. Microarray expression profiling of both miRNA and mRNA from the same sample were performed using a collective of 24 urothelial carcinoma and normal bladder tissue samples. Using our approach, normal and tumor tissue samples as well as different stages of tumor progression were successfully stratified. Also, we were able to analyzed individual miRNA-mRNA interactions from each patient, focusing on different miRNA families. Conclusions: Just recently, the need for tools that allow an integrative analysis of microRNA and mRNA expression data has been addressed. With this study, we provide an algorithm that considers the special nature of miRNA induced regulation and shows good specificities and sensitivities when applied to bladder cancer expression data.
2013-08-24 | GSE40355 | GEO
Project description:mRNA Expression data from bladder cancer and normal bladder tissue
| PRJNA306651 | ENA
Project description:Genome-wide analysis of miRNA-mRNA interactions in the marrow microenvironment (HTS)
| PRJNA176418 | ENA
Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.
| S-EPMC2531291 | biostudies-literature
Project description:To identify miRNA-target interactions that are important in bladder cancer metastasis, we profiled miRNA and mRNA expression in poorly metastatic cell lines T24 and LUC, and their metastatic derivatives FL4 and LUL2, respectively. We reasoned that miRNAs and genes that expressed differently between parental and derivative cell lines could potentially contribute to their disparity in metastatic competence. We further hypothesized that interactions between these miRNAs and target genes may play an important role in metastatic competence. We have developed the multiMiR R pacakge and database for such integrated analysis of miRNA-target interactions. Here we demonstrate how multiMiR was used to generate testable hypotheses that could be pursued experimentally. The data set here is from the miRNA expression profiling experiment. Please see E-MTAB-2610 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2610/ ) for the mRNA profiling data set.
2014-07-25 | E-MTAB-2611 | biostudies-arrayexpress
Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2019-07-31 | GSE114179 | GEO