Dataset Information

Proteomic Analysis of RAP (RNA Antisense Purification) isolated RNPs (RiboNucleotide Particles) harboring the novel lncRNA mimi

ABSTRACT: In neurons, mRNAs and associated RNA-binding proteins assemble into ribonucleoprotein (RNP) granules essential to regulate mRNA trafficking, local translation, and turnover. Dysregulation of RNA-protein condensation can disturb synaptic plasticity. We report that the novel lncRNA mimi is a constitutive and essential component of large cytoplasmic condensates (RNP granules) in fly neurons. In order to identify direct mimi RNA binders we employ RAP assisted purification of mimi RNPs subsequent to UV-crosslinking of adult fly brain tissue (non UV irradiated samples serve as control). Applying relative Max Quant LFQ quantification (Max LFQ) we carry out a differential proteomic analysis of mimi RNP complexes in UV-irradiated versus non irradiated fly brains.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

TISSUE(S): Brain

SUBMITTER: Gerhard Mittler

LAB HEAD: Gerhard Mittler

PROVIDER: PXD034457 | Pride | 2022-10-12

REPOSITORIES: Pride

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Publications

The long noncoding RNA <i>mimi</i> scaffolds neuronal granules to maintain nervous system maturity.

Grzejda Dominika D Mach Jana J Schweizer Johanna Aurelia JA Hummel Barbara B Rezansoff Andrew Mischa AM Eggenhofer Florian F Panhale Amol A Lalioti Maria-Eleni ME Cabezas Wallscheid Nina N Backofen Rolf R Felsenberg Johannes J Hilgers Valérie V

Science advances 20220928 39

RNA binding proteins and messenger RNAs (mRNAs) assemble into ribonucleoprotein granules that regulate mRNA trafficking, local translation, and turnover. The dysregulation of RNA-protein condensation disturbs synaptic plasticity and neuron survival and has been widely associated with human neurological disease. Neuronal granules are thought to condense around particular proteins that dictate the identity and composition of each granule type. Here, we show in <i>Drosophila</i> that a previously u ...[more]

PMID: 36170367

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Project description:Ultraviolet (UV) wavebands in sunlight are immunomodulatory. About half the amount of UVA within a minimum erythemal dose of sunlight is systemically immunosuppressive, while higher doses protect from UVB immunosuppression in mice. We have previously shown that these responses to UVA are genetically restricted as they occur in C57BL/6 but not Balb/c mice. We used gene set enrichment analysis of microarray data and real-time RT-PCR confirmation to determine the molecular mechanisms associated with UVA immunomodulation. We found up-regulation of mRNA for the alternative complement pathway. The core-enriched genes complement component 3, properdin and complement factor B were all activated by the immunosuppressive dose of UVA only in UVA-responsive C57BL/6 but not unresponsive BALB/c mice. This therefore matched the genetic restriction and dose responsiveness of UVA immunosuppression. The immune-protective higher UVA dose prevented UVB from down regulating chemokine receptor 7 and IL-12B, and decreased IL-10, supporting previous identification of IL-12 and IL-10 in high dose UVA protection from UVB immunosuppression. Our study has identified activation of the alternative complement pathway as a trigger of UVA-induced systemic immunosuppression and suggests that this pathway is likely to be an important sensor of UVA-induced damage to the skin. 24 hours after UVA, UVB and ssUV irradiation, a 1 cm2 uniform section of skin was excised from the dorsal surface of irradiated and control mice. Total RNA was then extracted from the whole skin using TRIzol reagent (Gibco Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturerâ??s instructions, purified, DNase treated and reverse transcribed into cDNA. For the microarray study a direct incorporation of Cyanine 3-dCTP and Cyanine 5-dCTP fluorescent dyes (Perkin Elmer Life Sciences, Inc. Boston, MA, USA) was used for cDNA synthesis. For each UV dose, a reference design was used to compare an unirradiated control against an irradiated sample. Microarray experiments used compugen 22k mouse oligonucleotide microarray slides (The Clive and Vera Ramaciotti Centre for Gene Function Analysis, Sydney Australia (http://www.ramaciotti.unsw.edu.au). Lower and higher UVA doses were used. C57BL/6 mice were irradiated with lower UVA, higher UVA, UVB, or ssUV; Balb/C mice were irradiated with lower or higher UVA. Experiments were replicated 6 times for each UV dose. A fluorescent dye swap was done for each alternate hybridisation to reduce systematic dye bias of incorporated fluorescent dyes.

Dataset Information

Proteomic Analysis of RAP (RNA Antisense Purification) isolated RNPs (RiboNucleotide Particles) harboring the novel lncRNA mimi

Publications

The long noncoding RNA <i>mimi</i> scaffolds neuronal granules to maintain nervous system maturity.

Similar Datasets

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