Project description:We have performed parallel ribosome profiling and RNA sequencing to determine which mRNAs are being translated during exponential growth and following 24 hours of nutrient starvation in the human pathogen Mycobacterium tuberculosis.
Project description:In yeast, Hda1 histone deacetylase complex (Hda1C) plays an important role in transcriptional regulation by modulating histone acetylation. We here explored the dynamics of Hda1C binding in nutrient-rich and -starved conditions. Chromatin immunoprecipitation sequencing revealed that starvation alters RNA Pol II and Hda1C binding to coding genes in a highly correlated manner. Interestingly, we discovered RNA Pol II transcription-independent recruitment of Hda1C to intergenic regions, particularly the upstream regulatory sequences (URS) of ribosomal protein (RP) genes, which are enriched with Rap1 binding sites. Under nutrient starvation, Rap1 contributes to the recruitment of Hda1C to these URS regions, where Hda1C deacetylates histones, thereby fine-tuning basal gene expression and delaying RP gene reactivation. Furthermore, Hda1C is also required for RNA Pol I transcription of rRNAs and RNA Pol III transcription of tRNA genes, especially in nutrient-limited conditions. Significantly, Hda1C mutants are sensitive to translation inhibitors and display altered ribosome profiles. Thus, Hda1C may coordinate transcriptional regulation within the nucleus with translation control in the cytoplasm and could be a key regulator of gene expression responses to nutrient stress.
Project description:Transcriptional profiling of Mycobacterium tuberculosis H37Rv and Mycobacterium bovis Ravenel before (i.e., log-phase control) and at 24h and 96h after nutrient starvation. The transcriptional profile of the two strains were compared at log phase, and after 24h and 96h of starvation. In addition, the response of each strain to starvation was examined after 24h and 96h of starvation.
Project description:The variation of mRNA targets of mouse YTH N6-methyladenosine RNA binding protein 3 (Ythdf3) during nutrient starvation was determined by RNA immunoprecipitation and sequencing (RIP-seq).
Project description:Four Fe(II) concentrations (0.03, 0.09, 0.12 & 0.75 mM) were tested to investigate the stimulation and inhibition effects of ferrous iron on anammox bacterial activity. RNAs were extracted from the cultures, and the synthesized cDNAs by reverse transcription were used to carry out GeoChip analysis, by which the functional communities and expression level differences in functional genes under different Fe(II) concentrations conditions were obtained, and the response of anammox bacteria to Fe(II) stimulation and inhibition are speculated.
Project description:Here we sought to comprehensively characterize the role of the electron transport chain in yeast models of aging. Using a panel of ETC mutants, we observed that ETC mutants fail to survive starvation when grown to saturation in standard SD growth medium. This starvation lethality is associated with a significantly lower cytosolic pH and dysregulated gene expression compared to wild type cells. In an unbiased genetic suppressor screen, we found that loss of function mutations in major cellular nutrient sensing/signaling pathways (Ras/PKA, Tor, PP2A) along with a number of gene expression regulators can prevent starvation lethality in these mutants. Together our results suggest that the ETC plays a critical regulatory role in mounting an appropriate response to starvation through communication with major nutrient sensing/signaling pathways in the cell.
