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MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Illumina expression beadchip)

ABSTRACT: Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. We isolated polyribosome-associated mRNA, and captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs. Together, these results find isomiRs to be biologically relevant and functionally synergistic partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur with predominantly non-specific miRNA-mRNA interactions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE29043 | GEO | 2011/12/21

SECONDARY ACCESSION(S): PRJNA142907

REPOSITORIES: GEO

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MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Agilent miRNA array)

Project description:This data set is part of a larger study: Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. We isolated polyribosome-associated mRNA, and captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs. Together, these results find isomiRs to be biologically relevant and functionally synergistic partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur with predominantly non-specific miRNA-mRNA interactions. 6 samples submitted, all replicates of Human Placenta total RNA, Ambion The miRNA-Seq data have been submitted to the short read archive under SRA number SRP006043: http://www.ncbi.nlm.nih.gov/sra?term= SRP006043

2011-12-21 | E-GEOD-29100 | biostudies-arrayexpress

MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Agilent miRNA array)

2011-12-21 | GSE29100 | GEO

MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Illumina expression beadchip)

Project description:Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. We isolated polyribosome-associated mRNA, and captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs. Together, these results find isomiRs to be biologically relevant and functionally synergistic partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur with predominantly non-specific miRNA-mRNA interactions. HEK293T cells were transfected with biotinylated miRNAs (either mir-10a-iso, mir-10a, mir-10b-iso or mir-10b) or a mock control. The miRNAs and target mRNA were pulled down with streptavidin. The pulled down RNA was hybridised to Illumina microarrays. The miRNA-Seq data have been submitted to the short read archive under SRA number SRP006043: http://www.ncbi.nlm.nih.gov/sra?term= SRP006043

2011-12-21 | E-GEOD-29043 | biostudies-arrayexpress

IsomiRage: from functional classification to differential expression of miRNAs and their isoforms

Project description:Characterization and analysis of miRNAs and their variants (called "IsomiRs") in next-generation sequencing datasets in breast epithelium. Our pipeline, called IsomiRage, allows distinguishing canonical miRNAs from templated and non-templated isomiRs by alignment to a custom database, which comprises all possible 3’-, 5’- and trimmed variants. Functionally equivalent isomiRs can be grouped together according to the type of modification (e.g. uridylation, adenylation, trimming...) to assess which miRNAs are more intensively modified in a given biological context. When applied to the analysis of primary epithelial breast cancer cells, our methodology provided a 40% increase in the number of detected miRNA species and allowed to easily identify and classify more than 1000 variants. Most modifications were compatible with templated IsomiRs, as a consequence of imprecise Drosha or Dicer cleavage. However, some non-templated variants were consistently found either in the normal or in the cancer cells, with the 3’-end adenylation and uridylation as the most frequent events, suggesting that miRNA post- transcriptional modification frequently occurs. Our analytical tool permits the deconvolution of miRNA heterogeneity and could be used to explore the functional role of miRNA isoforms. A matched normal/tumor primary culture from breast epithelium

2014-09-05 | E-GEOD-61165 | biostudies-arrayexpress

IsomiRage: from functional classification to differential expression of miRNAs and their isoforms

2014-09-05 | GSE61165 | GEO

Deep sequencing analysis of miRNAs and isomiRs modulated by long-term exposure of human endothelial cells to metformin

Project description:Increasing evidence suggest anti-senescence and geroprotective roles for the glucose-lowering drug metformin. In this framework, the ability of metformin to affect the biogenesis of selected microRNAs (miRNAs) was recently suggested. IsomiRs are distinct variations of miRNA sequences, such as addition or deletion of one or more nucleotides at the 5’ and/or 3’ ends of the canonical miRNA sequence. Since no study has comprehensively assessed the miRNA signatures, including isomiR variants, affected by metformin treatment during cellular senescence, we analysed miRNA and isomiR expression in human umbilical vein endothelial cells (HUVECs) undergoing replicative senescence in presence of metformin.

2020-12-03 | GSE149771 | GEO

MicroRNAs and their isomiRs function cooperatively to target common biological pathways

Project description:This SuperSeries is composed of the following subset Series: GSE29043: MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Illumina expression beadchip) GSE29100: MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Agilent miRNA array) Refer to individual Series This represents the miRNA placenta samples and mRNA + miRNA pulldown only The miRNA-Seq data have been submitted to the short read archive under SRA number SRP006043: http://www.ncbi.nlm.nih.gov/sra?term= SRP006043

2011-12-21 | E-GEOD-29101 | biostudies-arrayexpress

microRNAs and isomiRs repertoire in poricne endometrium revealed by Illumina sequencing

Project description:Recently, microRNAs (miRNAs), known to modulate gene expression through post-transcriptional mechanisms, were implied in regulation of early pregnancy events including maternal recognition of pregnancy and implantation. To characterize complex transcriptomic changes in expression of miRNAs in pregnant and cyclic endometria collected on days 12, 16 and 20 was analyzed using Illumina deep sequencing. This research showed repertoire of pregnancy-related miRNAs in porcine endometrium during initial stages of conceptus implantation and during the estrous cycle and sheds light on miRNA-mediated gene expression regulation mechanism at the maternal-conceptus interface. miRNAs and isomiRs expression profiles were analyzed in samples collected from porcine endometrium on Days 12, 16 and 20 of pregnancy and estrous cycle. Each group was represented by 4 to 6 samples. Generated libraries were run in multiplex using specific barcodes to differentiate samples. Illumina sequencing was performed in duplicate (two runs) and after demultiplexing, the same samples from two independent runs were concatenated.

2015-11-06 | E-GEOD-64863 | biostudies-arrayexpress

Circulating miRNAs. isomiRs and small RNA clusters in human plasma and breast milk

Project description:Circulating small RNAs. including miRNAs but also isomiRs and other RNA species. have the potential to be used as non-invasive biomarkers for communicable and non-communicable diseases. This study aims to characterize miRNAs. isomiRs and small RNA clusters in biofluids. to compare their profiles. and to help in the establishment of standard guidelines. For this purpose. RNA from plasma and breast milk samples from 15 healthy postpartum mothers was extracted. Small RNA libraries were prepared with the NEBNext® small RNA library preparation kit and sequenced in an Illumina HiSeq2000 platform. After an initial quality control. miRNAs. isomiRs and clusters of small RNAs were annotated using seqBuster/seqCluster framework. The average amount of extracted RNA was 81 ng/mL [standard deviation (SD): 41] and 3985 ng/mL (SD: 3767) for plasma and breast milk. respectively. Mean number of good quality reads was 4.04 million (M) (40.01% of the reads) in plasma and 12.5M (89.6%) in breast milk. One thousand one hundred eighty two miRNAs. 74.317 isomiRs and 1.053 small RNA clusters that included piwi-interfering RNAs (piRNAs). tRNAs. small nucleolar RNAs (snoRNA) and small nuclear RNAs (snRNAs) were detected. Samples grouped by biofluid. with 308 miRNAs. 4.737 isomiRs and 778 small RNA clusters differentially detected. In summary. plasma and milk showed a completely different small RNA profile. In both. miRNAs. piRNAs. tRNAs. snRNAs. and snoRNAs were identified. confirming the presence of non-miRNA species in biofluids

2018-03-14 | GSE107524 | GEO

shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [DU-145 cells]

Project description:miRNA overexpression strategy based on RNA Polymerase (Pol) III mediated expression of short hairpin RNA (shRNA) coding particular miRNA is widely used for miRNA functional studies. For some miRNAs, e.g., encoded in the genome as a part of a polycistronic miRNA cluster, it is most likely the only way for their individual stable overexpression. Here we have revealed that extra \texttt{U} residues (up to five) added Pol III at the 3$'$-end of the transcribed shRNA associated with a shift in the Dicer cleavage position of the shRNA. This results in the undesirable formation of 5$'$-end miRNA isoforms (5$'$-isomiRs), which have a significantly altered seed region compared to the initially encoded canonical hsa-miR-93-5p. The predominant expression of 5$'$-isomiRs without three or four first nucleotides instead of the canonical isoform could be disclosed based on miRNA-Seq analysis. Moreover, mRNA sequencing data showed that the 5$'$-isomiRs of hsa-miR-93-5p presumably regulate their own mRNA targets. Thus, omitting miRNA-Seq analysis may lead to erroneous conclusions regarding revealed mRNA targets and possible molecular mechanisms in which studied miRNA is involved.

2023-11-17 | GSE247987 | GEO

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