Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A massively parallel reporter assay reveals novel features and players of RNA localization in neurons

ABSTRACT: This experiment aims to identify the RNA-binding proteome that is pulled-down from a cellular lysate with biotinylated RNA probes.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Andreas Moor

LAB HEAD: Andreas Moor

PROVIDER: PXD025492 | Pride | 2021-04-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	1864460.zip	Other
	20201127_C23444_005_S276596_CAD_UTR_ctrls_3_CAD_Ctrl.raw	Raw
	20201127_C23444_013_S276595_CAD_UTR_probe_3_CAD_probe.raw	Raw
	20201127_C23444_017_S276590_N2A_UTR_ctrls_1_N2A_Ctrl.raw	Raw
	20201127_C23444_019_S276594_N2A_UTR_ctrls_2_N2A_Ctrl.raw	Raw

Items per page:

1 - 5 of 9

Similar Datasets

High-throughput identification of RNA localization elements reveals a regulatory role for A/G rich sequences

Project description:This experiment aims to identify the RNA-binding proteome that is pulled-down from a cellular lysate with biotinylated RNA probes.

2022-09-21 | PXD030720 | Pride

Identification the proteins interacted with SNHG26 in human keratinocytes

Project description:The cell transition from an inflammatory phase to a subsequent proliferative phase is crucial for wound healing, yet the driving mechanism remains unclear. By profiling lncRNA expression changes during human skin wound healing and screening lncRNA functions, we identified SNHG26 as a pivotal regulator in keratinocyte progenitors underpinning this phase transition. To study the proteins interact with SNHG26, we performed RNA pull-down assay in human keratinocyte progenitors. The mass spectrometry (MS) analysis was performed to identify the proteins interacted with SNHG26.

2024-08-28 | PXD055231 | Pride

Transcription profiling of mouse CAD cells transfected with miR-124a-2 reveals the microRNA miR-124 Promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing

Project description:Both microRNAs and alternative pre-mRNA splicing have been implicated in the development of the nervous system (NS), but functional interactions between these two pathways are poorly understood. We demonstrate that the neuron-specific microRNA miR-124a directly targets PTBP1/PTB/hnRNPI mRNA, which encodes a global repressor of alternative pre-mRNA splicing in non-neuronal cells. Among the targets of PTBP1 is a critical cassette exon in the pre-mRNA of PTBP2/nPTB/brPTB, an NS-enriched PTBP1 homolog. When this exon is skipped, PTBP2 mRNA is subject to nonsense-mediated decay. During neuronal differentiation, miR-124a reduces PTBP1 levels leading to the accumulation of correctly spliced PTBP2 mRNA and a dramatic increase in PTBP2 protein. These events culminate in the transition from non-NS to NS-specific alternative splicing patterns. We also present evidence that miR-124a plays a key role in the differentiation of progenitor cells to mature neurons. Thus, miR-124a promotes NS development at least in part by regulating an intricate network of NS-specific alternative splicing. We used microarrays to detail the global programme of gene expression of CAD cells over-expressing miR-124a-2. Experiment Overall Design: Expression data from CAD cells transfected with plasmid expressing miR-124a-2.

2008-06-16 | E-GEOD-8498 | biostudies-arrayexpress

The conserved 3’ UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration

Project description:In pursuit of a biological role of Salmonella 3' UTR derived sRNA NarS ,we sought to determine potential target mRNAs of NarS under anaerobic conditions. To this end, we compared gene expression in NarS-deficient and NarS overexpression (from plasmid pPL-NarS) strains following a 30-minute anaerobic shock by RNA-seq.

2019-08-22 | E-MTAB-8244 | biostudies-arrayexpress

LETR1 (LINC01197) RNA pull-down in human LECs followed by LC-MSMS

Project description:Recent studies have revealed the importance of long noncoding RNAs (lncRNAs) as tissue-specific regulators of gene expression. There is ample evidence that distinct types of vasculature undergo tight transcriptional control to preserve their structure, identity, and functions. We determined, for the first time, the global lineage-specific lncRNAome of human dermal blood and lymphatic endothelial cells (BECs and LECs), combining RNA-Seq and CAGE-Seq. A subsequent genome-wide antisense oligonucleotide-knockdown profiling of two BEC- and two LEC-specific lncRNAs identified LETR1 as a critical gatekeeper of the global LEC transcriptome. Deep RNA-DNA and RNA-protein interaction studies, and phenotype rescue analyses revealed that LETR1 is a nuclear trans-acting lncRNA modulating, via key epigenetic factors, the expression of essential target genes governing the growth and migratory ability of LECs. Together, our study provides new evidence supporting the intriguing concept that every cell type expresses precise lncRNA signatures to control lineage-specific regulatory programs.

2020-12-21 | PXD018578 | Pride

Effect of diet and association with fertility outcomes in semen proteome and transcriptome from wild and captive Black-footed ferrets

Project description:The black-footed ferret (Mustela nigripes) is a star example of the efforts of conservation programs in bringing endangered species back from the brink of extinction. As one of the world’s most endangered mammals, the vast majority of black-footed ferrets living in the wild today are the offspring of a founding captive population. The success of this ongoing breeding program, however, is threatened by inbreeding depression and the observed decline in pregnancy rates since its founding. As the wild and modern captive populations share a genetic history, the greatest difference between the two groups is the captive environment of the breeding program. In this study, we used RNA sequencing and proteomics for the first time in black-footed ferrets to explore whether the diet of wild ferrets versus captive diet variants could explain the differences in fertility and sperm characteristics observed between each population. We find that changes in both the transcriptional and proteomic profile of black-footed ferret ejaculate are strongly associated with differences in fertility, especially in pathways associated with innate immunity and metabolism; that transcriptional changes are further exacerbated by diet. Overall, our results support the hypothesis of ongoing environmental-dependent inbreeding depression in the black-footed ferret, with a need to re-evaluate dietary and environmental parameters of the conservation program; and also illustrates the value of multi-level genomics for conservation management programs.

2023-09-20 | PXD044152 | Pride

Acetyl-CoA metabolism by ACSS2 regulates neuronal histone acetylation and long-term memory [ChIP-seq]

Project description:Metabolic production of acetyl-CoA has been linked to histone acetylation and gene regulation, however the mechanisms are largely unknown. We show that the metabolic enzyme acetyl-CoA synthetase 2 (ACSS2) is a critical and directchum regulator of histone acetylation in neurons and of long-term mammalian memory. We observe increased nuclear ACSS2 in differentiating neurons in vitro. Genome-wide, ACSS2 binding corresponds with increased histone acetylation and gene expression of key neuronal genes. These data indicate that ACSS2 functions as a chromatin-bound co-activator to increase local concentrations of acetyl-CoA and to locally promote histone acetylation for transcription of neuron-specific genes. Remarkably, in vivo attenuation of hippocampal ACSS2 expression in adult mice impairs long-term spatial memory, a cognitive process reliant on histone acetylation. ACSS2 reduction in hippocampus also leads to a defect in upregulation of key neuronal genes involved in memory. These results reveal a unique connection between cellular metabolism and neural plasticity, and establish a link between generation of acetyl-CoA and neuronal chromatin regulation. Genome-wide examination of histone H3 and H4 acetylation, as well as ACSS2 binding, in undifferentiated CAD cells and differentiated CAD neurons; background adjusted by H3 ChIP or Input.

2017-05-01 | E-GEOD-76850 | biostudies-arrayexpress

DIA analysis of paired primary and recurrent breast cancers

Project description:Molecular profiling of breast cancer has achieved great depth in defining the mutational landscapes and molecular profiles of primary tumors, though little is still known regarding cancer evolution into a recurrence. Proteogenomic workflows are particularly useful in defining the multi-layered biology of complex diseases by combining genomic, transcriptomic, and proteomic technologies so to inform not only on mutational processes, but also on their repercussion at the effector level, proteins. We employed our recently developed proteogenomic workflow to analyze a cohort of 27 primary breast cancers and their matched loco-regional recurrences by whole genome sequencing, RNA sequencing, and mass spectrometry.

2023-02-03 | PXD032266 | Pride

Structural elucidation of a novel mechanism for bacteriophage-based inhibition of the RNA degradosome

Project description:In all domains of life, the catalysed degradation of RNA facilitates rapid adaption to changing environmental conditions. We identified a virus-encoded protein that directly binds and inhibits the RNA degradation machinery of its bacterial host, allowing efficient accumulation of viral RNA in the infected cell. Encoded by the giant phage фKZ, KZ37/Dip associates with two RNA binding sites of the RNase E component of the Pseudomonas aeruginosa RNA degradosome. Thereby, KZ37/Dip competes with the binding of RNA substrates, resulting in effective inhibition of RNA degradation. The crystal structure of KZ37/Dip (2.2 Å) reveals an unprecedented fold for which there are no identified structural homologues. The protein forms a homo-dimer that resembles a partially opened scroll and binds RNase E through exposed acidic patches on its convex outer surface. Through the activity of KZ37/Dip, фKZ has evolved a unique mechanism to down regulate a key process of its host.

2016-07-27 | PXD003285 | Pride

Trypanosoma cruzi infection changes the chromatin proteome profile of infected human cells

Project description:Chagas disease is endemic in 22 Latin American countries, with approximately 8 million individuals infected worldwide and 10,000 deaths per year. Trypanosoma cruzi, the etiologic agent from Chagas disease, presents an intracellular life cycle in mammalian hosts to sustain infection. Parasite infection activates host cell responses, promoting an unbalance in reactive oxygen species (ROS) in the intracellular environment inducing genomic DNA lesions in the host cell during the early and late stages of infection. To further understand changes in host cell chromatin induced by parasite infection, we investigated proteomic alterations in chromatin caused by parasite infection at early and late infection phases by performing a quantitative proteomic analysis. Interestingly, we identified DNA Damage Repair (DDR) proteins recruited to the chromatin and changes in chromatin remodeling enzymes, suggesting that parasite infection may shape the epigenome of the host cells. Furthermore, the presence of Poly-ADP-ribose Polymerase 1 (PARP-1) and 8-oxoG Glycosylase (OGG1) in the host nucleus confirm the damaged cellular genome. Moreover, we observed that at 6 h post-infection, PARP-1 and X-Ray Repair Cross Complementing 6 (XRRC6) were upregulated in the chromatin of infected cells. Interestingly, mitochondrial proteins involved in oxidative phosphorylation and vesicle-mediated transport proteins were upregulated in the host chromatin at the final stages of infection. Additionally, we have observed that Apoptosis-inducing Factor (AIF) is translocated to the host cell nucleus upon infection, suggesting that cells enter parthanatos type of death. Finally, we also observed that T. cruzi induces changes in chromatin-modifying enzymes. Altogether, this work provides novel data reveals how parasites interfere in the host cells' responses at the chromatin level and important crosstalks that support and disseminate infection.

2024-09-28 | PXD033862 | Pride