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Transcriptional heterogeneity shapes stress-adaptive responses in yeast

ABSTRACT: Transcriptional heterogeneity shapes stress-adaptive responses in yeast

PROVIDER: PRJNA1147604 | ENA |

REPOSITORIES: ENA

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Transcriptional heterogeneity shapes stress-adaptive responses in yeast

Project description:In response to stress, cells activate signaling pathways that coordinate broad changes in gene expression to enhance cell survival. Remarkably, complex variations in gene expression occur even in isogenic populations and in response to similar signaling inputs. However, the molecular mechanisms underlying this variability and their influence on adaptive cell fate decisions are not fully understood. Here, we use scRNA-seq to longitudinally assess transcriptional dynamics during osmoadaptation in yeast. Our findings reveal highly heterogeneous expression of the osmoresponsive program, which organizes into combinatorial patterns that generate distinct cellular programs. The induction of these programs is favored by global transcriptome repression upon stress. Cells displaying basal expression of the osmoresponsive program are hyper-responsive and resistant to stress. Through a transcription-focused analysis of more than 300 RNA-barcoded deletion mutants, we identify genetic factors that shape the heterogeneity of the osmostress-induced transcriptome, define regulators of stress-related subpopulations and find a link between transcriptional heterogeneity and increased cell fitness. Our findings provide a regulatory map of the complex transcriptional phenotypes underlying osmoadaptation in yeast and highlight the importance of transcriptional heterogeneity in generating distinct adaptive strategies.

2025-02-04 | GSE274661 | GEO

Post-transcriptional regulation shapes the transcriptome of quiescent yeast

Project description:Post-transcriptional regulation shapes the transcriptome of quiescent yeast

| PRJNA999709 | ENA

Single-cell RNA-seq reveals early heterogeneity during aging in yeast

Project description:we carried out a systematic and quantitative investigation of yeast aging with single-cell resolution through transcriptomic sequencing. We optimized a single-cell RNA sequencing (scRNA-seq) protocol to quantitatively study the whole transcriptome profiles of single yeast cells at different ages, finding increased cell-to-cell transcriptional variability during aging. The single-cell transcriptome analysis also highlighted key biological processes or cellular components, including oxidation-reduction process, oxidative stress response (OSR), translation, ribosome biogenesis and mitochondrion that underlie aging in yeast. We uncovered a molecular marker of FIT3, indicating the early heterogeneity during aging in yeast. We also analyzed the regulation of transcription factors and further characterized the distinctive temporal regulation of the OSR by YAP1 and proteasome activity by RPN4 during aging in yeast. Overall, our data profoundly reveal early heterogeneity during aging in yeast and shed light on the aging dynamics at the single cell level.

2022-08-01 | GSE210032 | GEO

An alternative transcriptome shapes cell fate transitions in yeast (TES-seq)

Project description:An alternative transcriptome shapes cell fate transitions in yeast (TES-seq)

| PRJNA566361 | ENA

An alternative transcriptome shapes cell fate transitions in yeast (mRNA-seq)

Project description:An alternative transcriptome shapes cell fate transitions in yeast (mRNA-seq)

| PRJNA566360 | ENA

An alternative transcriptome shapes cell fate transitions in yeast (TSS-seq)

Project description:An alternative transcriptome shapes cell fate transitions in yeast (TSS-seq)

| PRJNA566359 | ENA

An alternative transcriptome shapes cell fate transitions in yeast (TIF-seq)

Project description:An alternative transcriptome shapes cell fate transitions in yeast (TIF-seq)

| PRJNA592981 | ENA

An alternative transcriptome shapes cell fate transitions in yeast (MNase-seq)

Project description:An alternative transcriptome shapes cell fate transitions in yeast (MNase-seq)

| PRJNA566362 | ENA

QUILT-2.025 NANT Neoepitope Yeast Vaccine (YE-NEO-001): Adjuvant Immunotherapy Using a Personalized Neoepitope Yeast-Based Vaccine To Induce T-Cell Responses In Subjects W/ Previously Treated Cancers.

Project description:This is a phase 1 study to evaluate the safety, the Recommended Phase 2 Dose (RP2D), and preliminary efficacy of a personalized neoepitope yeast-based vaccine, YE-NEO-001, in subjects who have completed potentially curative therapy for their solid cancer and who would otherwise be entering a period of surveillance for recurrent disease.

| 2275044 | ecrin-mdr-crc

Molecular Evolution of the Activating Transcription Factors Shapes the Adaptive Cellular Responses to Oxidative Stress.

Project description:Reactive oxygen species (ROS) play an essential part in physiology of individual cell. ROS can cause damage to various biomolecules, including DNA. The systems that have developed to harness the impacts of ROS are antique evolutionary adaptations that are intricately linked to almost every aspect of cellular function. This research reveals the idea that during evolution, rather than being largely conserved, the molecular pathways reacting to oxidative stress have intrinsic flexibility. The coding sequences of the ATF2, ATF3, ATF4, and ATF6 genes were aligned to examine selection pressure on the genes, which were shown to be very highly conserved among vertebrate species. A total of 33 branches were explicitly evaluated for their capacity to diversify selection. After accounting for multiple testing, significance was determined using the likelihood ratio test with a threshold of p ≤ 0.05. Positive selection signs in these genes were detected across vertebrate lineages. In the selected test branches of our phylogeny, the synonymous rate variation revealed evidence (LRT, p value = 0.011 ≤ 0.05) of gene-wide episodic diversifying selection. As a result, there is evidence that diversifying selection occurred at least once on at least one test branch. These findings indicate that the activities of ROS-responsive systems are also theoretically flexible and may be altered by environmental selection pressure. By determining where the genes encoding these processes are "targeted" during evolution, we may better understand the mechanism of adaptation to oxidative stress during evolution.

| S-EPMC9300285 | biostudies-literature

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