miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

An, Jiyuan; Lai, John; Lehman, Melanie; Nelson, Colleen C.

doi:10.1093/nar/gks1187

Cited by 211 publications

(158 citation statements)

References 44 publications

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“…This workflow provides comprehensive analysis of miRNA sequencing data, including read preprocessing, alignment, mature/precursor/novel miRNA quantification, and variant detection in the miRNA coding region. In particular, CAP-miRSeq utilizes miRDeep2 (47) to classify and quantify the expressions of known and novel miRNAs, based on the annotations from miRBase version 19 (48). Normalization and differential analysis were performed FIGURE 1.…”

Section: Construction Of Vdr Pegfp Expression Vectors and Transfectiomentioning

confidence: 99%

1α,25-Dihydroxyvitamin D3 Regulates Mitochondrial Oxygen Consumption and Dynamics in Human Skeletal Muscle Cells

Ryan¹,

Craig²,

Folmes³

et al. 2016

Journal of Biological Chemistry

189

163

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Previous reports have shown that in avian and rodent isolated skeletal muscle cells and cultured myoblast cell lines, vitamin D 3 metabolites, such as 25-hydroxyvitamin D 3 (25(OH)D 3 ) and 1␣,25(OH) 2 D 3 , influence cellular calcium and phosphorus uptake, cellular growth, differentiation, and the expression of a limited number of genes (14 -19). Many reports suggest that the vitamin D receptor (VDR) is expressed in skeletal muscle (20 -24), and VDR deletion in mice results in alterations in muscle function and strength (25,26). Treatment of vitamin D-deficient humans with cholecalciferol improves muscle phosphocreatine recovery after exercise (27), suggesting that vitamin D 3 or its metabolites alter skeletal muscle oxidative capacity.To assess the mechanism of action of the active metabolite of vitamin D 3 , 1␣,25(OH) 2 D 3 , in human skeletal muscle cells, we examined changes in mitochondrial oxygen consumption (OCR), mitochondrial dynamics, mitochondrial OXPHOS proteins, pyruvate dehydrogenase phosphorylation, and nuclear gene expression using whole transcriptome shotgun sequencing (WTSS, RNA-seq) of messenger RNAs and micro-RNAs Tables 1 and 2

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Section: Construction Of Vdr Pegfp Expression Vectors and Transfectiomentioning

confidence: 99%

1α,25-Dihydroxyvitamin D3 Regulates Mitochondrial Oxygen Consumption and Dynamics in Human Skeletal Muscle Cells

Ryan¹,

Craig²,

Folmes³

et al. 2016

Journal of Biological Chemistry

189

163

View full text Add to dashboard Cite

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“…The resulting files were processed individually using miRDeep* [21] alignment (operating in Java  mode) against the hg19 human genome. Known miRNA's from each of the CTL and AD samples were manually curated to align expression (as number of reads of each mature miRNA) across both groups.…”

Section: Resultsmentioning

confidence: 99%

“…Single-end sequencing files were aligned against the hg19 version of the human genome using miRDeep* [21]. Total reads for known miRNA's were manually aligned for each CTL and AD sample.…”

Section: Microrna'smentioning

confidence: 99%

Micro RNA’s (mirna’s) may help explain expression of multiple genes in Alzheimer’s Frontal Cortex

Bennett¹,

Keeney²

2017

J Syst Integr Neurosci

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MicroRNA's (miRNA's) are non-coding RNA's that can regulate gene expression. miRNA's are small (~22 nt) and can bind by complementation to mRNA's resulting in direct degradation and/or interference with translation. We used paired-end RNAseq and small RNAseq to examine expression of mRNA's and miRNA's, respectively, in total RNA's isolated from frontal cortex of Alzheimer's disease (AD) and control (CTL) subjects. mRNA's were aligned to the hg38 human genome using Tophat2/Bowtie2 and relative expression levels determined by Cufflinks as FPKM (fragments per kilobase of exon per million mapped reads). miRNA's were aligned to the hg19 human genome and quantitated as number of mature known miRNA reads with miRDeep*. Using a false-discovery rate (FDR) of 10% (FDR ≤ 0.10) applied to 11,794 genes with FPKM > 2.0, we identified 55 genes upregulated in AD and 191 genes downregulated in AD. The top 145 miRNA's with the highest mean expression were mostly under-expressed in AD (132/145 miRNAs had AD/CTL < 1.0)). AD samples had increased coefficients of variation for miRNA and mRNA expression, implying greater heterogeneity. miRTAR analysis showed that 32 (58%) of the mRNA genes upregulated in AD could be controlled by one or more of 60 miRNA's under-expressed >1.5-fold in AD (AD/CTL < 0.67). AD frontal cortex gene expression analysis showed extensive regulation by miRNAs that appear to interact with the majority of overexpressed protein coding genes. The temporal sequence of appearance in AD brain and etiologies of this extensive, heterogeneous regulation by miRNA's are unknown. (243 words)

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“…miRNA-Seq libraries were sequenced with SE36 using an Illumina HiSeq2500. To analyze the differentially expressed miRNAs (DEmiRs), we performed miRDeep to obtain the RPM of each transcript [36]. Then, miRNAs with greater than or equal to one RPM were defined as expressed.…”

Section: High-throughput Sequencing Data Analysismentioning

confidence: 99%

Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro

Sheng

Zhang

Chen

et al. 2014

Sci. China Life Sci.

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Ebola virus (EBOV) causes a highly lethal hemorrhagic fever syndrome in humans and has been associated with mortality rates of up to 91% in Zaire, the most lethal strain. Though the viral envelope glycoprotein (GP) mediates widespread inflammation and cellular damage, these changes have mainly focused on alterations at the protein level, the role of microRNAs (miRNAs) in the molecular pathogenesis underlying this lethal disease is not fully understood. Here, we report that the miRNAs hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p were induced in human umbilical vein endothelial cells (HUVECs) following expression of EBOV GP. Among the proteins encoded by predicted targets of these miRNAs, the adhesion-related molecules tissue factor pathway inhibitor (TFPI), dystroglycan1 (DAG1) and the caspase 8 and FADD-like apoptosis regulator (CFLAR) were significantly downregulated in EBOV GP-expressing HUVECs. Moreover, inhibition of hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p, or overexpression of TFPI, DAG1 and CFLAR rescued the cell viability that was induced by EBOV GP. Our results provide a novel molecular basis for EBOV pathogenesis and may contribute to the development of strategies to protect against future EBOV pandemics. Ebola virus, glycoprotein, microRNAs, cytotoxicity Citation:Sheng MM, Zhong Y, Chen Y, Du JC, Ju XW, Zhao C, Zhang GG, Zhang LF, Liu KT, Yang N, Xie P, Li DS, Zhang MQ, Jiang CY. Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro. Sci China Life Sci, 2014, 57: 959 -972,

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miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

Cited by 211 publications

References 44 publications

1α,25-Dihydroxyvitamin D3 Regulates Mitochondrial Oxygen Consumption and Dynamics in Human Skeletal Muscle Cells

1α,25-Dihydroxyvitamin D3 Regulates Mitochondrial Oxygen Consumption and Dynamics in Human Skeletal Muscle Cells

Micro RNA’s (mirna’s) may help explain expression of multiple genes in Alzheimer’s Frontal Cortex

Hsa-miR-1246, hsa-miR-320a and hsa-miR-196b-5p inhibitors can reduce the cytotoxicity of Ebola virus glycoprotein in vitro

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