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Global transcriptomic analysis of Drosophila Hinfp mutant and wild-type gut to understand their role in genome stability

ABSTRACT: Global transcriptomic analysis of Drosophila Hinfp mutant and wild-type gut to understand their role in genome stability

PROVIDER: PRJNA575851 | ENA |

REPOSITORIES: ENA

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Global transcriptomic analysis of Drosophila Hinfp mutant and wild-type gut to understand their role in genome stability

Project description:Drosophila hinfp mutant is lethal. They are unble to ecolose from the pupal case and died. To investigate the molecular function of Hinfp in Drosophila gut, we isolated RNA from mutant and wild type adult pharate gut and performed RNA-seq analysis. The comparison of mutant and control samples revealed significantly changed expression of over more than thousand Drosophila genes. Among the down regulated genes were many Histone genes. Further validation of RNA-seq data of Histone genes divulged that His1 is significantly down-regulated lead to genome instability through de-repression of menay of the retrotransposon. We also rescued the all phenotypes by overexpression of UAS-Hinfp and UAS-His1 gene.

2021-08-16 | GSE138430 | GEO

ADAR1 role on transcriptome stability

Project description:ADAR1 role on transcriptome stability

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Quantitative Analysis of Global Protein Stability Rates in Tissues

Project description:We have developed QUAD (Quantification of Azidohomoalanine Degradation), a technique to quantitate global protein degradation using mass spectrometry. Azidohomoalanine (AHA) is pulsed into mouse tissues through their diet. The mice are then returned to a normal diet and the decrease of AHA abundance can be quantitated in the proteome. QUAD analysis reveals that protein stability varied within tissues, but discernible trends in the data suggest that cellular environment is a major factor dictating stability. Within a tissue, different organelles, post-translation modifications, and protein functions were enriched with different stability patterns. Surprisingly, subunits of the TRIC molecular chaperonin possessed markedly distinct stability trajectories in the brain. Further investigation revealed that these subunits also possessed different subcellular localization indicating a potential non-canonical chaperonin. Finally, QUAD analysis demonstrated that protein stability is enhanced with age in the brain but not in the liver. Overall, QUAD allows the first global quantitation of protein stability rates in tissues, which may lead to new insights and hypotheses in basic and translational research.

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Global RNA stability profiling during selective chemical inhibition of human Dcp2

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Global RNA stability profiling in human NBDY knockout using TimeLapse-seq

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DHX36 is the missing link to understand RNA G-quadruplex structures, mRNA stability, and translation [RNA-seq]

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Global RNA stability profiling in HEK293T cells under EGF treatment using TimeLapse-seq

Project description:We discovered through LC-MS/MS followed by biochemical assays and immunofluorescence that human microprotein NoBody/NBDY can be phosphorylated during EGF signaling transduction, and that this single post-translational modification of the smallest decapping complex component known to date is necessary to the observed disappearance of P-bodies under EGF treatment. RNA stability measurement of a known hDcp2 substrate, RRP41, showed decreased RNA life-time under EGF treatment. We hence wish to investigate the effect of this phospho-NBDY mediated P-body disassembly on global RNA turnover. Here we present a global profile of RNA stability in human HEK293 cells under EGF treatment via TimeLapse-seq. By comparing this dataset to our previous and current work done in DCP2 KO and in NBDY KO cells, respectively, we demonstrate that P-body dissociation observed during EGF signaling does not cause RNA stability change globally except for a few known EGF regulated transcripts.

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Transcriptomic dataset of wild type and phoP mutant Pectobacterium versatile.

Project description: Not available

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To understand the effects of global Cyp27a1 and Cyp3a4 gene deletions on bile acid synthesis

Project description:To understand the effects of global Cyp27a1 and Cyp3a4 gene deletions on bile acid synthesis

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Global RNA stability profiling in human NBDY knockout using TimeLapse-seq

Project description:We previously identified a conserved human microprotein NoBody/NBDY that can interact with the mRNA decapping complex through EDC4 and affects the expression of an NMD (nonsense-mediated decay) substrate. However, it remains unclear the exact mechanism of NBDY-regulated RNA stability change and whether this is the direct cause/consequence of its modulation of P-body structure/numbers. Here we present a global profile of RNA stability in human NBDY knockout cells via TimeLapse-seq. By comparing this dataset to our previous work done in DCP2 KO cells, we demonstrate that NBDY is a specificity factor of the 5'-3' RNA decay. In addition, these data indicate a role of NBDY in cell cycle and other signaling transduction processes as well.

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