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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Screening and validation of lncRNAs and circRNAs as miRNA sponges

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Shizuka Uchida

PROVIDER: E-GEOD-73691 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Screening and validation of lncRNAs and circRNAs as miRNA sponges.

Militello Giuseppe G Weirick Tyler T John David D Döring Claudia C Dimmeler Stefanie S Uchida Shizuka S

Briefings in bioinformatics 20170901 5

Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the rol ...[more]

PMID: 27373735

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Screening and validation of lncRNAs and circRNAs as miRNA sponges [cell lines, miRNA-2_0]

Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments. The expressions of miRs were examined in HEK-293, HUVEC and Hs68 cells.

2016-07-06 | E-GEOD-73690 | biostudies-arrayexpress

Screening and validation of lncRNAs and circRNAs as miRNA sponges [siRNA, miRNA-2_0]

2016-07-06 | E-GEOD-73689 | biostudies-arrayexpress

Screening and validation of lncRNAs and circRNAs as miRNA sponges [siRNA, HuGene-1_0-st]

Project description:Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments. Using HEK-293 cells, we performed microarray experiments (n=2) for siRNA-mediated silencing of LINC00324 and LOC40043.

2016-07-06 | E-GEOD-73683 | biostudies-arrayexpress

Transcriptome sequencing of nasopharyngeal carcinoma model system (mRNA)

Project description:Nasopharyngeal carcinoma (NPC) is a prevalent malignancyt disease in Southeast Asia among the Chinese population. Aberrant regulation of transcripts has been implicated in many types of cancers including NPC. Herein, we characterized mRNA and miRNA transcriptomes by RNA sequencing (RNASeq) of NPC model systems. Matched total mRNA and small RNA of undifferentiated Epstein-Barr virus (EBV)-positive NPC xenograft X666 and its derived cell line C666, well-differentiated NPC cell line HK1, and the immortalized nasopharyngeal epithelial cell line NP460 have been sequenced by Solexa technology.

2014-02-05 | E-GEOD-54159 | biostudies-arrayexpress

Transcriptome sequencing of nasopharyngeal carcinoma model system (miRNA)

2014-02-05 | E-GEOD-54161 | biostudies-arrayexpress

Quantitation of microRNAs in seminal fluid from men with and without prostate cancer

Project description:The objective of this study was to determine whether prostate cancer-associated miRNAs are present in seminal fluid and, if so, evaluate their diagnostic potential. Small RNA sequencing was used to profile and compare miRNAs in the non-sperm cellular fraction of seminal fluid from men with biopsy-proven cancer (one pooled sample from 6 men) and men with elevated serum PSA but negative biopsy results (one pooled sample from 6 men).

2014-04-15 | E-GEOD-56686 | biostudies-arrayexpress

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance (HTS)

Project description:LIN28 is a conserved RNA binding protein implicated in pluripotency, reprogramming and oncogenesis. Previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) targets. Through cross-linking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in human embryonic stem cells and somatic cells expressing exogenous LIN28, we have defined discrete LIN28 binding sites in a quarter of human transcripts. These sites revealed that LIN28 binds to GGAGA sequences enriched within loop structures in mRNAs, reminiscent of its interaction with let-7 miRNA precursors. Among LIN28 mRNA targets, we found evidence for LIN28 autoregulation and also direct but differing effects on the protein abundance of splicing regulators in somatic and pluripotent stem cells. Splicing-sensitive microarrays demonstrated that exogenous LIN28 expression causes widespread downstream alternative splicing changes. These findings identify important regulatory functions of LIN28 via direct mRNA interactions. CLIP-seq for LIN28-V5 in stable human Flp-In-293 cells, and LIN28 in hES cells; strand-specific mRNA-seq for uninfected, control KD, and LIN28 KD human H9 ES cells; and strand-specific smallRNA-seq for uninfected, control KD, and LIN28 KD human H9 ES cells.

2012-09-10 | E-GEOD-39872 | biostudies-arrayexpress

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance

Project description:This SuperSeries is composed of the following subset Series: GSE39855: LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance (splicing array) GSE39872: LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance (HTS) Refer to individual Series

2012-09-10 | E-GEOD-39873 | biostudies-arrayexpress

microRNA-like RNAs exploring and expression profile in plant pathogenic fungus Fusarium oxysporum f. sp. niveum

Project description:To explore the presence of milRNA in Fusarium oxysporum f. sp. niveum (Fon) and evaluate their expression at different propagules, two categories of sRNAs were identified from Fon hyphae and microconidia by using illumina sequencing. A total of 650,960 and 561,114 unique sRNAs were obtained from the hyphae and microconidia samples. With a previously constructed pipeline to search for microRNA, we then identified 74 and 56 miRNA-like small RNAs (milRNAs) candidates in hyphae and microconidia based on the short hairpin structure analysis, respectively. Global expression analysis showed an extensively differential expression of sRNAs between two propagules. Altogether, 78 significantly differently expressed milRNAs were identified in two libraries. Target prediction revealed 2 interesting genes involved in trichothecene and necrosis and ethylene-inducing peptide 1 (NEP1) biosynthesis predicted to be down regulated by Fon-miR7696a-3p and Fon-miR6108a. These two milRNAs were further validated by qRT-PCR and showed a well consistency with sequencing. The negative correlation expression levels between these two milRNAs and their targets genes imply that they might play a role in trichothecene and NEP1 biosynthesis, and this negative regulation for toxin related gene expression are more specific in microconidia. The present study provides the firstly large-scale characterization of milRNAs in Fon and the comparison between hyphae and microconidia propagules gives a clue on how milRNAs involves in toxin biosynthesis. microRNA-like RNAs in hyphae and microconidia were identified and compared

2016-07-15 | E-GEOD-84384 | biostudies-arrayexpress

microRNA profiling of female and male mouse pituitary gland across pubertal transition

Project description:The pituitary gland exhibits sex differences in its function. Diseases associated with dysregulation of the pituitary are also sex-biased in prevalence. Previous qPCR profiling of puberty-related genes in the pituitary gland revealed increasingly sex-biased expression of genes profiled across pubertal transition. Here, we performed small RNA-seq on total RNA extracted from C57BL/6J mouse pituitary gland of both sexes mice at 4 ages spanning pubertal transition (postnatal days 12, 22, 27, 32) (6 replicates per sex at each age) to examine microRNA (miRNA) regulation of sex differences in gene expression observed. Total RNA was sent to SickKids TCAG core to construct small RNA-seq libraries using NEBNext Small RNA Library Prep Kit according to manufacterer’s protocol. Resulting single-end libraries were sequenced at TCAG core on the Illumina HiSeq 2500 v4 flow cell with SR50 bp. Data obtained was processed using miRDeep2 pipeline to align small RNA-seq reads to the mouse genome (mm10) and to filter for miRNAs.

2022-10-12 | E-MTAB-9460 | biostudies-arrayexpress

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