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Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics - human

ABSTRACT: Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics - human

PROVIDER: PRJNA494410 | ENA |

REPOSITORIES: ENA

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Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics - mouse

Project description:MicroRNAs (miRNAs) are highly conserved ∼22 nt small noncoding RNAs that bind partially complementary sequences in target transcripts. MicroRNAs regulate both translation and transcript stability, and play important roles in development, cellular homeostasis, and disease. There are limited approaches available to agnostically identify microRNA targets transcriptome-wide, and methods using miRNA mimics, which in principle identify direct miRNA:transcript pairs, have low sensitivity and specificity. Here, we describe a novel method to identify microRNA targets using miR-29b mimics containing 3cyanovinylcarbazole ( CNV K), a photolabile nucleoside analog. We demonstrate that biotin-tagged, CNV K-containing miR-29b ( CNV K-miR-29b) mimics are nontoxic in cell culture, associate with endogenous mammalian Argonaute2, arehighly sensitive for known targets and recapitulate endogenous transcript destabilization. Partnering CNV K-miR-29b with ultra-low-input RNA sequencing, we recover ∼40% of known miR-29b targets and findrobust conservation of the focal adhesion and apoptotic target pathways in mouse and mouse. We also identify hundreds of novel targets, including NRAS, HOXA10, and KLF11, with a validation rate of 71% for a subset of 73 novel target transcripts interrogated using a high-throughput luciferase assay. Consistent with previous reports, we show that both endogenous miR-29b and CNV K-miR-29b are trafficked to the nucleus, but find no evidence of nuclear-specific miR-29b transcript binding. This may indicate that miR-29b nuclear sequestration is a regulatory mechanism in itself. We suggest that CNV K-containing small RNA mimics may find applicability in other experimental models

2018-10-03 | GSE120764 | GEO

Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics - human

Project description:MicroRNAs (miRNAs) are highly conserved ∼22 nt small noncoding RNAs that bind partially complementary sequences in target transcripts. MicroRNAs regulate both translation and transcript stability, and play important roles in development, cellular homeostasis, and disease. There are limited approaches available to agnostically identify microRNA targets transcriptome-wide, and methods using miRNA mimics, which in principle identify direct miRNA:transcript pairs, have low sensitivity and specificity. Here, we describe a novel method to identify microRNA targets using miR-29b mimics containing 3cyanovinylcarbazole ( CNV K), a photolabile nucleoside analog. We demonstrate that biotin-tagged, CNV K-containing miR-29b ( CNV K-miR-29b) mimics are nontoxic in cell culture, associate with endogenous mammalian Argonaute2, arehighly sensitive for known targets and recapitulate endogenous transcript destabilization. Partnering CNV K-miR-29b with ultra-low-input RNA sequencing, we recover ∼40% of known miR-29b targets and findrobust conservation of the focal adhesion and apoptotic target pathways in mouse and human. We also identify hundreds of novel targets, including NRAS, HOXA10, and KLF11, with a validation rate of 71% for a subset of 73 novel target transcripts interrogated using a high-throughput luciferase assay. Consistent with previous reports, we show that both endogenous miR-29b and CNV K-miR-29b are trafficked to the nucleus, but find no evidence of nuclear-specific miR-29b transcript binding. This may indicate that miR-29b nuclear sequestration is a regulatory mechanism in itself. We suggest that CNV K-containing small RNA mimics may find applicability in other experimental models

2018-10-03 | GSE120763 | GEO

Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics

Project description:Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics

| PRJNA494408 | ENA

Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics - mouse

Project description:Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics - mouse

| PRJNA494409 | ENA

Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics.

Project description: Not available

| S-EPMC5855958 | biostudies-literature

Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-10-03 | GSE120765 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of miR-29b-1 and miR-29a targets in CHO-K1 cells

Project description:The goal of this experiment was to identify the putative mRNA targets of miR-29b-1 and miR-29a in CHO-K1 cells

2019-08-01 | GSE85710 | GEO

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2018-10-10 | GSE104831 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of miR-29b-1 and miR-29a targets in tamoxifen-sensitive and tamoxifen-resistant human breast cancer cells

Project description:The goal of this experiment was to identify the putative mRNA targets of miR-29b-1 and miR-29a in LCC9 tamoxifen-resistant breast cancer cell lines relative to parental MCF-7 tamoxifen-sensitive cells

2017-08-11 | GSE81620 | GEO

Transcriptomic profiling of HeLa cells treated with miR-29b-2-5p and control-miR

Project description:To have a global picture of the targets of the mir-29b-2-5p, we assessed transcriptome changes, by deep-sequencing, of HeLa cells transfected with this miRNA or a control miRNA (cel-miR-231).

2017-04-04 | GSE75747 | GEO

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