Project description:Cells regulate the intracellular localization of proteins to adapt to different environmental conditions including DNA damage, but this form of regulation has not been analyzed systematically. The aim of this study was to investigate the protein distribution between nucleus and cytoplasm in response to cisplatin treatment. SKOV3 cells were treated or untreated with cisplatin in concentration 40 µM for 24 h followed by mass spectrometry-based proteomic analysis of extracts of cytoplasmic and nuclear fractions. To validate the quality of separation of the nuclear and cytoplasmic fractions, abundance of proteins, which are often used as markers of nuclear fraction (lamin B1 and RPA194), was evaluated using mass spectrometry. A total of 4,085 proteins were identified. Among them, 442 proteins were up-regulated, and 578 proteins were down-regulated in the nuclear fraction after cisplatin treatment. Interestingly, according to our data, after treatment of cells with cisplatin, spliceosomal proteins significantly increased in the cytoplasmic fraction. This indicates the relocalization of spliceosomal proteins from the nucleus into the cytoplasm under the influence of therapeutic stress.
Project description:The aim of this experiment was to develop new methods to extract pure fractions of nuclear and cytoplasmic RNA. We compared the results of nuclear and cytoplasmic RNA-sequencing to results of the total and polyA+ RNA-sequencing. Cytoplasmic, nuclear, total and polyA+ RNA was extracted from two human brain samples and sequenced on the SOLiD system. We analyzed the data to look for differences in levels of nascent transcription and mature mRNAs between the different samples.
Project description:Transcriptional profiling of Arabidopsis nuclear and cytoplasmic fractions using probes complementary to both sense and anti-sense transcripts.
Project description:CAGE sequencing of iPSC and Human dermal fibroblasts, total RNA and fractionated into nuclear, cytoplasmic and chromatin fractions.
Project description:HuH7 cells were grown under steady-state conditions or exposed 100 µM Na-arsenite for 1h. Subsequently, the cells were irradiated or not with 253 nm UV light (150 mJ/cm^2), processed to nuclear and cytoplasmic fractions, and subjected to eRIC for determining the nuclear and cytoplasmic RNA-binding proteins from the different conditions.
Project description:An LC-MS based discovery proteomics approach was used to measure the nuclear proteome fractions of Arabidopsis thaliana cell culture. An enrichment score based on the relative abundance of cytoplasmic, mitochondrial and golgi markers in the nuclear protein fraction allowed us to curate the nuclear proteome producing high quality catalogs of around 3,000 nuclear proteins under untreated and both PTI conditions (flg22 and nlp20). The measurements also covered low abundant proteins including more than 100 transcription factors and transcriptional co-activators. Here we sought to gain a broader impression of protein import to the nucleus upon stimulus with flg22 and nlp20. Furthermore, the abundance of 93 proteins changed significantly in the nucleus following elicitation of immunity. These results suggest promiscuous ribosome assembly and retrograde signaling from the mitochondrion to the nucleus including Prohibitins and Cytochrome C, in the two forms of PTI.
Project description:Drug-tolerant persister cells withstand treatments by adapting their identity through lineage-dependent plasticity during systemic anti-cancer therapies. This phenomenon is evident in small-cell lung carcinoma (SCLC), a lethal neuroendocrine cancer initially responsive (60-80%) to platinum-based chemotherapy but succumbing to resistance within 6 months in advanced stages. This resistance associates with the transdifferentiation of residual tumour cells into a non-neuroendocrine state, a process intricately tied to SCLC's chemotolerance, yet molecular mechanisms governing this lineage conversion remain completed understood. Here we use paired cytoplasmic RNA-seq and polysomal RNA-seq to compare gene expression between NE and non-NE SCLC cell lines on both transcriptional and translational level. We report that first-line chemotherapy induces translation initiation factor eIF6 in drug-tolerant persister-like cells in SCLC, correlating with the non-neuroendocrine state in SCLC. Intervening eIF6 inhibits non-neuroendocrine transdifferentiation, thus enhancing SCLC responsiveness to chemotherapy. This study sheds light on eIF6's potential therapeutic interventions to mitigate treatment resistance in SCLC.
