Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Intron-mediated induction of phenotypic heterogeneity

ABSTRACT: Intron-mediated induction of phenotypic heterogeneity

PROVIDER: PRJNA809314 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18098629_1.fastq.gz	Fastqsanger.gz
	SRR18098629_2.fastq.gz	Fastqsanger.gz
	SRR18098630_1.fastq.gz	Fastqsanger.gz
	SRR18098630_2.fastq.gz	Fastqsanger.gz
	SRR18098631_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 44

Similar Datasets

Intron-mediated induction of phenotypic heterogeneity

Project description:Introns are universally present in the nuclear genomes of eukaryotes. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein (RP) genes differing primarily in their introns. Despite recent findings on the role of RP introns under stress and starvation, understanding the contribution of introns to ribosome regulation remains challenging. Here, combining isogrowth profiling with single-cell protein measurements, we found that introns can mediate inducible phenotypic heterogeneity conferring a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low Rps22B protein levels resulted in prolonged survival under sustained starvation, while high Rps22B levels enabled cells to grow faster after transient starvation. Further, yeast growing at high sugar concentrations – similar to those in ripe grapes – exhibit bimodal Rps22B expression when approaching stationary phase. Differential intron-mediated regulation of RP genes thus provides a way to diversify the population when starvation looms in natural environments. Our findings reveal a new role for introns in inducing phenotypic heterogeneity in changing environments and suggest that duplicated RP genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness.

2022-02-23 | GSE197174 | GEO

Intron-mediated induction of phenotypic heterogeneity.

Project description:Intragenic regions that are removed during maturation of the RNA transcript-introns-are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein genes that differ primarily in their introns2,3. Although studies have shed light on the role of ribosomal protein introns under stress and starvation4-6, understanding the contribution of introns to ribosome regulation remains challenging. Here, by combining isogrowth profiling7 with single-cell protein measurements8, we show that introns can mediate inducible phenotypic heterogeneity that confers a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, which is mediated by an intron in the 5' untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low levels of Rps22B protein result in prolonged survival under sustained starvation, whereas high levels of Rps22B enable cells to grow faster after transient starvation. Furthermore, yeasts growing at high concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression of Rps22B when approaching the stationary phase. Differential intron-mediated regulation of ribosomal protein genes thus provides a way to diversify the population when starvation threatens in natural environments. Our findings reveal a role for introns in inducing phenotypic heterogeneity in changing environments, and suggest that duplicated ribosomal protein genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness9.

| S-EPMC9068511 | biostudies-literature

Alvarez2019 - A nonlinear mathematical model of cell-mediated immune response for tumor phenotypic heterogeneity

Project description:This is a non-linear mathematical model of cancer immunosurveillance that takes into account intratumoral phenotypic heterogeneity, such as differential expression of cell surface receptors and growth factors, according to cell-mediated immune responses. The model describes phenomena that have also been observed in vivo, such as tumor dormancy, cancer immunoediting, and a strong sensitivity to initial conditions.

2024-09-02 | BIOMD0000000790 | BioModels

Modeling Phenotypic Heterogeneity Towards Evolutionary Inspired Osteosarcoma Therapy

Project description:Modeling Phenotypic Heterogeneity Towards Evolutionary Inspired Osteosarcoma Therapy

| PRJNA1003084 | ENA

Modeling Phenotypic Heterogeneity Towards Evolutionary Inspired Osteosarcoma Therapy

Project description:Osteosarcoma is the most common bone sarcoma in children and young adults. While chemotherapy is universally delivered, benefit from chemotherapy is limited to roughly half of localized patients. Increasingly, intratumoral heterogeneity is being appreciated as a source of therapeutic resistance. In this study we developed and evaluated an in vitro model of osteosarcoma heterogeneity, characterizing phenotype (growth in varying environments, sensitivity to chemotherapy) and genotype. We present the genotypic and phenotypic characterization of an osteosarcoma cell line panel with a focus on coculture of the most phenotypically divergent cell lines, 143B and SAOS2. The extent of phenotypic heterogeneity can be altered with relatively modest environmental (pH, glutamine) or chemical perturbations. We demonstrate that in nutrient rich in vitro culture conditions 143B outcompetes SAOS2, but with selection pressure from nutrient variations or conventional chemotherapy, SAOS2 growth can be favored in spheroids. Importantly, perturbations that affect the faster growing cell line have only a modest effect on final spheroid size when the simplest heterogeneity state (a two-cell line coculture) is evaluated, and thus the only evaluated therapies to eliminate the spheroids were by switching therapies from a first strike to a second strike. This extensively characterized, widely available system can be modeled and scaled to allow for improved strategies to anticipate resistance in osteosarcoma due to phenotypic heterogeneity.

2023-11-22 | GSE240278 | GEO

The Host Modulates Transcriptional Profile and Phenotypic Heterogeneity in Symbionts

Project description:The Host Modulates Transcriptional Profile and Phenotypic Heterogeneity in Symbionts

| PRJNA972301 | ENA

Phenotypic heterogeneity in Stenotrophomonas maltophilia K279a colony morphotypes WGS study

Project description:Phenotypic heterogeneity in Stenotrophomonas maltophilia K279a colony morphotypes WGS study

| PRJEB9938 | ENA

The Host Modulates Transcriptional Profile and Phenotypic Heterogeneity in Symbionts.

Project description:The Host Modulates Transcriptional Profile and Phenotypic Heterogeneity in Symbionts.

| PRJNA971082 | ENA

Single seeds exhibit transcriptional heterogeneity during secondary dormancy induction

Project description:Single seeds exhibit transcriptional heterogeneity during secondary dormancy induction

| PRJNA767415 | ENA

Within patient Staphylococcus aureus phenotypic heterogeneity

Project description:Quantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations

| PRJEB48885 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data