Genome binding/occupancy profiling of methylated Pontin under glucose starvation
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ABSTRACT:
PROVIDER: PRJNA663492 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To determine where methylated Pontin is recruited, we performed ChIP-sequencing (ChIP-seq) in WT MEFs after glucose starvation.
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Project description:For cells to grow and proliferate both a growth signal and available nutrients are required. Several lines of evidence suggest that there is recriprocal regulation of nutrients by growth signals and growth signals by nutrients. Since microRNAs are regulated by growth signals, we sought to determine if microRNAs could also be regulated by nutrient availability. We found that several microRNAs change expression following glucose starvation and that their Ago2 occupancy remains constant. Immortalized Bax/Bak double-knockout mouse embryonic fibroblasts were deprived of glucose for 5 days and then re-fed glucose for 2 days. Cells were collected at the beginning of the starvation period (d0), following five days of glucose deprivation (d5), and following two days of glucose re-feed (d7). Total RNA was isolated from half of the collected cells using Trizol and the remaining cells were used to perform Ago2 immunoprecipitation followed by isolation of bound RNA.
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2015-08-24 | PXD002140 | Pride
Project description:For cells to grow and proliferate both a growth signal and available nutrients are required. Several lines of evidence suggest that there is recriprocal regulation of nutrients by growth signals and growth signals by nutrients. Since microRNAs are regulated by growth signals, we sought to determine if microRNAs could also be regulated by nutrient availability. We found that several microRNAs change expression following glucose starvation and that their Ago2 occupancy remains constant.
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Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions.
2014-07-28 | GSE56622 | GEO
Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions. Examination of mRNA translation in S. cerevisiae upon glucose starvation.
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