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Analysis of HeLa cells after transfection with miR-1 or miR-155, by microarray profiling

ABSTRACT: MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.

ORGANISM(S): Homo sapiens

PROVIDER: GSE22002 | GEO | 2010/08/03

SECONDARY ACCESSION(S): PRJNA129165

REPOSITORIES: GEO

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Analysis of HeLa cells after transfection with miR-1 or miR-155, by microarray profiling

Project description:MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output. Examine mRNA expression levels in HeLa cells transfected with miR-1 or miR-155, versus mock-transfected cells, at two different time points post-transfection.

2010-08-03 | E-GEOD-22002 | biostudies-arrayexpress

Analysis of mir-223 knockout cultured neutrophils versus wild-type cultured neutrophils, by microarray profiling

Project description:MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output. Examine mRNA expression levels in mir-223 knockout cultured neutrophils, versus wild-type cultured neutrophils.

2010-08-03 | E-GEOD-22003 | biostudies-arrayexpress

Analysis of HeLa cells after transfection with miR-1 or miR-155, by ribosome profiling and mRNA-Seq

2010-08-03 | GSE21992 | GEO

Analysis of HeLa cells after transfection with miR-1 or miR-155, by ribosome profiling and mRNA-Seq

Project description:MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output. Examine ribosome footprints and mRNA abundance of HeLa cells transfected with miR-1 or miR-155, versus mock-transfected cells, at two different time points post-transfection. Supplementary processed data files linked below. mir155_summaryTable.txt: log2 fold changes (miR-155-transfected versus mock-transfected HeLa cells, 32hr). mir1_summaryTable.txt: log2 fold changes (miR-1-transfected versus mock-transfected HeLa cells, 32hr).

2010-08-03 | E-GEOD-21992 | biostudies-arrayexpress

Analysis of mir-223 knockout cultured neutrophils versus wild-type cultured neutrophils, by microarray profiling

2010-08-03 | GSE22003 | GEO

Analysis of mir-223 knockout cultured neutrophils versus wild-type cultured neutrophils, by ribosome profiling and mRNA-Seq

Project description:MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output. Examine ribosome footprints and mRNA abundance of mir-223 knockout cultured neutrophils, versus wild-type cultured neutrophils Supplementary processed data file linked below. mir223_summaryTable.txt: log2 fold changes (miR-223-knockout versus wild-type neutrophils).

2010-08-03 | E-GEOD-22001 | biostudies-arrayexpress

Analysis of mir-223 knockout cultured neutrophils versus wild-type cultured neutrophils, by ribosome profiling and mRNA-Seq

2010-08-03 | GSE22001 | GEO

Mammalian microRNAs predominantly act to decrease target mRNA levels

Project description:MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output. This SuperSeries is composed of the SubSeries listed below.

2010-08-03 | GSE22004 | GEO

Transcription profiling of mouse embryonic stem cells transfected with miR-10a or miR-10a-MUT shows that miR-10a interacts with the 5 prime untranslated region of mRNAs encoding ribosomal proteins and enhances their translation

Project description:MicroRNAs (miRNAs) are small RNAs that function as post-transcriptional regulators of gene expression. miRNAs affect a variety of signaling pathways and impaired miRNA regulation may contribute to the development of cancer and other diseases. We show that miRNA miR-10a interacts with the 5' untranslated region of mRNAs encoding ribosomal proteins and enhances their translation. miR-10a alleviates translational repression of the ribosomal protein mRNAs during amino acid starvation and is required for their stress-mediated activation following anisomycin treatment. miR-10a binds immediately downstream of the regulatory 5' TOP motif and the 5Â´TOP is necessary for miR-10a translational enhancement. The results indicate that miR-10a may positively control global protein synthesis via stimulation of ribosomal protein mRNA translation and that the 5' TOP regulatory complex and miR-10a are functionally interconnected.

2008-11-08 | E-MEXP-1375 | biostudies-arrayexpress

p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses

Project description:We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino acids in cell culture, pSILAC) in combination with mRNA and non-coding RNA expression analyses by next generation sequencing (RNA-, miR-Seq) in the colorectal cancer (CRC) cell line SW480. Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down), lncRNAs (270 up, 123 down) and proteins (542 up, 569 down). Changes in mRNA and protein expression levels showed a positive correlation (r = 0.50, p < 0.0001). More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the downregulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3â??-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed upregulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibited proliferation in SW480 cells. Furthermore, HMGB1, KLF12 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of HMGB1, KLF12 and CIT was detected in advanced stages of cancer. This study provides new insights and a comprehensive catalogue of p53-mediated regulations and p53 DNA binding in CRC cells.

2016-05-24 | MSV000079767 | MassIVE

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