Project description:In this study, we aim to understand how the fates of stress-activated mRNAs are determined under stress conditions by isolating individual osmostress-activated mRNA species, quantitating the proteins associated in vivo with each of them, and analyzing how deletion of these proteins impact on the expression of stress-activated genes. By comparison with the proteome associated with individual not stress-related mRNA species, we show specific proteins to be preferentially binding to osmostress-activated mRNAs, notably members of the cytoplasmic Pat1 / Lsm1 – 7 complex. We evaluated the impact of this complex on the stress response by analyzing expression of osmostress-activated genes, production of osmo-protein and, mapping ribosome transit at single nucleotide resolution using 5’-phosphate sequencing of mRNAs in lsm1 and pat1 mutants. We conclude that our biochemical co-purification approach has successfully identified RNA-binding proteins with a particular role in regulating post-transcriptional expression of stress-activated mRNAs.
Project description:We present ribosome profiling(for activaly translated RNA) and RNA-seq (for total RNA) data for human corneal epithelial cells exposed to mild osmotic stress (500 mOsm) for 1h and 6h (additionally torin1 (mTOR inhibitor) or MeAIB (SNAT2 inhibitor were added for the last hour of treatment.
Project description:To determine whether osmotic pressure affects the translation efficiency of Lactobacillus rhamnosus, the ribosome profiling assay was performed to analyze the changes in translation efficiency in L. rhamnosus ATCC 53103. Under osmotic stress, differentially expressed genes (DEGs) involved in fatty acid biosynthesis and metabolism, ribosome, and purine metabolism pathways were co-regulated with consistent expression direction at translation and transcription levels. DEGs involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan, and the phosphotransferase system pathways also were co-regulated at translation and transcription levels, while they showed opposite expression direction at two levels. Moreover, DEGs involved in the two-component system, amino acid metabolism, and pyruvate metabolism pathways were only regulated at the transcription level. And DEGs involved in fructose and mannose metabolism were only regulated at the translation level. The translation efficiency of DEGs involved in the biosynthesis of amino acids was downregulated while in quorum sensing and PTS pathways was upregulated. In addition, the ribosome footprints accumulated in open reading frame regions resulted in impaired translation initiation and elongation under osmotic stress. In summary, L. rhamnosus ATCC 53103 could respond to osmotic stress by translation regulation and control the balance between survival and growth of cells by transcription and translation.
Project description:To investigate ribosome localization and gene expression dynamics during starvation in cancer cells, we performed RNA sequencing and ribosome profiling in RKO cells under fed and starved (12.5 uM arginine) conditions.
Project description:Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multiple myeloma cells exposed to bortezomib, a first-line chemotherapy and proteasome inhibitor. In the absence of drug effects, we found that direct measurement of protein synthesis by pSILAC correlated well with indirect measurement of synthesis from ribosome footprint density. This correlation, however, broke down under bortezomib-induced stress. By developing a statistical model integrating longitudinal proteomic and mRNA-seq measurements, we found that proteomics could directly detect global alterations in translational rate caused by bortezomib; these changes are not detectable by ribosomal profiling alone. Further, by incorporating pSILAC data into a gene expression model, we predict cell-stress specific proteome remodeling events. These results demonstrate that pSILAC provides an important complement to ribosome profiling in measuring proteome dynamics. Timecourse experiment with six points over 48hr after bortezomib exposure in MM.1S myeloma cells. mRNA-seq and ribosome profiling data at each time point.
Project description:To identifiy osmotic stress responsive smRNAs, we used a deep-sequencing technique to profile small RNA populations in leaf and root tissues of plants under high osmotic stress and control conditions.
Project description:Purpose:to identify the response of Frankia sp.strain CcI6 to salt and osmotic stress. Frankia sp.strain CcI6 was exposed to salt and osmotic stress for seven days. RNAseq analysis was carried out to ge an insight into the response of the bacterium under salt and osmotic stress conditons
Project description:To identifiy osmotic stress responsive smRNAs, we used a deep-sequencing technique to profile small RNA populations in leaf and root tissues of plants under high osmotic stress and control conditions. We treated 30day-old plants with high osmotic stress and sampled leaves and roots from the same plant with 3 biologial replicates. Then, 3 replicates were pooled and total RNA was extracted and prepared for smRNA deep sequencing. After normalization and annotation, we selected potential osmotic stress responsive smRNAs.
Project description:RNA polymerase (RNAP) is the key transcription machinery and its interaction with genomic DNA orchestrates gene expression in response to environmental cues. Dynamic interaction and localization between RNAP and nucleoid were observed before and after osmotic stress. Chromatin immunoprecipitation (ChIP) of RNAP β’ subunit together with chromatin profiling by ChIP-on-chip analysis demonstrated the dynamics of genome-wide RNAP-DNA interactions during osmotic stress.