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MiRNA expression in response to LPS stimulus in macrophages

ABSTRACT: Our lab is currently using macrophages as a model system for understanding how genetic variation modulates the response to external environmental stimulus. We want to extend this beyond regular polyadenylated RNA to small RNAs such as miRNAs. This project would cover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed as part of a rotation project in the lab. We will require a small number of miRNA libraries and a single lane of MiSeq

PROVIDER: EGAS00001000691 | EGA |

REPOSITORIES: EGA

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EGAS00001000691-sc-20160615 - samples

Project description:Our lab is currently using macrophages as a model system for understanding how genetic variation modulates the response to external environmental stimulus. We want to extend this beyond regular polyadenylated RNA to small RNAs such as miRNAs. This project would cover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed as part of a rotation project in the lab. We will require a small number of miRNA libraries and a single lane of MiSeq

| EGAD00001002196 | EGA

miRNA regulation - Proteomic response of mammalian cells to miRNA treatment

Project description:Proteomic response of mammalian cells to miRNA treatment

2017-08-28 | PXD005569 | Pride

Coordinated miRNA activity mediates the cellular transition into dormancy during embryonic diapause

Project description:Dormancy is a key feature of stem cell function in adult tissues as well as embryonic cells in the context of diapause. The establishment of dormancy is an active process that involves extensive transcriptional, epigenetic, and metabolic rewiring. How these processes are coordinated to successfully transition cells to the resting dormant state is not known. Here we show that microRNA activity, which is normally dispensable for pre-implantation development, is essential for the adaptation of early mouse embryos to the dormant state of diapause. In particular, the pluripotent epiblast depends on miRNA activity, the absence of which results in loss of pluripotency and embryo collapse. Through tissue-specific small RNA profiling of single embryos and computational analyses of miRNA targets, we identified the miRNA-protein network of diapause. Individual miRNA function contributes to combinatorial regulation by the network of most notably RNA processing and chromatin modifier proteins. Without miRNAs, multiple nuclear and cytoplasmic bodies show aberrant expression and structure in normal ESCs and fail to reorganize in response to stress. We find extensive alternative splicing in wild-type, but not miRNA-deficient ESCs, of cell cycle and metabolic regulators. Our results reveal that miRNAs are critical for the transcriptional and structural rewiring of pluripotent cells in response to stress and to establish dormancy in the pluripotent state.

2024-03-26 | PXD044550 | Pride

miRNA overexpression modulates neutrophil migration

Project description:miRNA overexpression modulates neutrophil migration

| PRJNA704949 | ENA

HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing

Project description:HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing

| PRJEB42556 | ENA

Integrated small RNA, mRNA and protein omics reveal a miRNA network orchestrating metabolic maturation of the developing human heart

Project description:As the fetal heart develops, cardiomyocyte proliferation potential decreases while fatty acid oxidative capacity increases, a highly regulated transition known as cardiac maturation. Small noncoding RNAs, such as microRNAs (miRNAs), contribute to the establishment and control of tissue-specific transcriptional programs. However, small RNA expression dynamics and genome wide miRNA regulatory networks controlling maturation of the human fetal heart remain poorly understood. Transcriptome profiling of small RNAs revealed the temporal expression patterns of miRNA, piRNA, circRNA, snoRNA, snRNA and tRNA in the developing human heart between 8 and 19 weeks of gestation. Our analysis revealed that miRNAs were the most dynamically expressed small RNA species throughout mid-gestation. Cross-referencing differentially expressed miRNAs and mRNAs predicted 6,200 mRNA targets, 2134 of which were upregulated and 4066 downregulated as gestation progresses. Moreover, we found that downregulated targets of upregulated miRNAs predominantly control cell cycle progression, while upregulated targets of downregulated miRNAs are linked to energy sensing and oxidative metabolism. Furthermore, integration of miRNA and mRNA profiles with proteomes and reporter metabolites revealed that proteins encoded in mRNA targets, and their associated metabolites, mediate fatty acid oxidation and are enriched as the heart develops.This study revealed the small RNAome of the maturing human fetal heart. Furthermore, our findings suggest that coordinated activation and repression of miRNA expression throughout mid-gestation is essential to establish a dynamic miRNA-mRNA-protein network that decreases cardiomyocyte proliferation potential while increasing the oxidative capacity of the maturing human fetal heart.

2024-01-26 | PXD044936 | Pride

NTP4 modulates miRNA accumulation via asymmetric modification of miRNA-3p/5p duplex

Project description:NTP4 modulates miRNA accumulation via asymmetric modification of miRNA-3p/5p duplex

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Exosomal tumor miRNA modulates premetastatic organ cells

Project description:Exosomal tumor miRNA modulates premetastatic organ cells

| PRJNA150403 | ENA

Exosome miRNA protein interactions in brown adipocytes

Project description:We have identified several nucleotide motifs (caug, cgggag=S2) that promote exosome sorting of miRNA in different cell types including brown adipocytes. In order to identify which proteins might recognize and bind to these motifs, we have performed co-precipitations of proteins binding biotinylated forms of miRNAs containing the aforementioned motifs or none - using streptavidin beads incubated with brown adipocytes cell lysates. We have included two types of controls: negative poly-A control and a scramble miRNA.

2021-01-30 | MSV000086780 | MassIVE

METABRIC miRNA landscape

Project description:MicroRNAs (miRNAs) are key players in cancer pathogenesis1. They display differential expression across breast cancer subtypes, and play oncogenic and tumor-suppressive roles2-6. A systematic study of the global miRNA landscape in breast cancer and the factors shaping it has not been undertaken. Here we report the results of profiling miRNA expression in 1,302 breast tumors with detailed clinical annotation and long-term follow-up, and for which matching genomic and mRNA expression data were available7. This provides a comprehensive view of the quantity, distribution and variation of the miRNA population and dissects how much genomic, transcriptional and post-transcriptional events contribute to miRNA expression architecture. The key clinical parameters and cellular pathways related to the miRNA landscape are identified, exemplified by context-dependent interaction with cell adhesion and Wnt signaling. Strikingly, in breast cancer miRNAs appear to act as modulators of mRNA-mRNA interactions rather than molecular switches. We demonstrate an important modulatory role for miRNAs in the biology of breast tumors devoid of somatic copy number aberrations, a common subtype where immune response is prominent. Remarkably, prognostic miRNA signatures derived in this subtype are consistently prognostic across several other subtypes and validate in external cohorts. These findings represent a new framework to study the biology of miRNA in human cancer.

| EGAS00000000122 | EGA

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