Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Functional analysis of GATA2 synonymous mutations

ABSTRACT: The aim of the study is investigation of functional consequences of synonymous substitutions in the GATA2 gene in pediatric patients with myelodysplastic syndrome. Whole exome sequencing was performed in order to determine if other genetic conditions contributed to patients' phenotype.

PROVIDER: EGAS00001003817 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)

Project description:Illumina RNA-seq data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (Ks) between paralogous gene pairs were conducted to look for signals of large scale or genome-wide duplication events in each transcriptome. Raw data for four of the nice species studied are provided here. The data for the remaining species are provided elsewhere (see pape for details).

2018-03-05 | E-MTAB-4112 | biostudies-arrayexpress

Distinct and convergent consequences of splice factor mutations in myelodysplastic syndromes

Project description:Distinct and convergent consequences of splice factor mutations in myelodysplastic syndromes

| PRJNA527722 | ENA

Reannotation of cancer mutations based on expressed RNA transcripts reveals novel functional non-coding mutations in melanoma.

Project description:The role of synonymous mutations in cancer pathogenesis is currently underexplored. We developed a method to detect significant clusters of synonymous and missense mutations in public cancer genomics data. In melanoma, we show that 22% (11/50) of these mutation clusters are misannotated as coding mutations because the reference transcripts used for their annotation are not expressed. Instead, these mutations are actually non-coding. This, for instance, applies to the mutation clusters targeting known cancer genes kinetochore localized astrin (SPAG5) binding protein (KNSTRN) and BCL2 like 12 (BCL2L12), each affecting 4-5% of melanoma patients. For the latter, we show that these mutations are functional non-coding mutations that target the shared promoter region of the interferon regulatory factor 3 (IRF3) and BCL2L12 genes. This results in downregulation of IRF3, BCL2L12 and tumor protein p53 (TP53) expression in a CRISPR-Cas9 primary melanocyte model and in melanoma patients, in which these mutations are also associated to a worse response to immunotherapy. Finally, we propose a simple automated method to more accurately annotate cancer mutations based on expressed transcripts. This work shows the importance of integrating DNA- and RNA-sequencing data to properly annotate mutations, and identifies a number of previously overlooked and wrongly annotated functional non-coding mutations in melanoma.

2025-03-31 | GSE290597 | GEO

Compensating the fitness costs of synonymous mutations

Project description:Synonymous mutations do not change the sequence of the polypeptide but they may still influence fitness. We investigated in Salmonella enterica how four synonymous mutations in the rpsT gene (encoding ribosomal protein S20) reduce fitness (i.e. growth rate) and the mechanisms by which this cost can be genetically compensated. The reduced growth rates of the synonymous mutants were correlated with reduced levels of the rpsT transcript and S20 protein. In an adaptive evolution experiment these fitness impairments could be compensated by mutations that either caused up-regulation of S20 through increased gene dosage (due to duplications), increased transcription of the rpsT gene (due to an rpoD mutation or mutations in rpsT), or increased translation from the rpsT transcript (due to rpsT mutations). We suggest that the reduced levels of S20 in the synonymous mutants result in production of a defective subpopulation of 30S subunits lacking S20 that reduce protein synthesis and bacterial growth and that the compensatory mutations restore S20 levels and the number of functional ribosomes. Our results demonstrate how specific synonymous mutations can cause substantial fitness reductions and that many different types intra- and extragenic compensatory mutations can efficiently restore fitness. Furthermore, our study highlights that also synonymous sites can be under strong selection, which may have implications for the use of dN/dS ratios as signature for selection.

2016-03-11 | PXD003495 | Pride

FUNCTIONAL ANALYSIS OF SF3B1 K700E AND SRSF2 P95H MUTATIONS

Project description:Study of the consequences of expression of Sf3b1K700E in ES cells on splicing of messenger RNA and transcript levels

2014-10-28 | E-ERAD-224 | biostudies-arrayexpress

Project description:Genetic investigation in GATA2 deficiency

| PRJNA610566 | ENA

GATA2 tumor suppressive role revealed in ERG - AML mouse model, unveiling a preleukemic phenotype

Project description:The transcription factor (TF) GATA2, is crucial for the formation, and lifelong homeostasis of hematopoietic stem cells. Mono-Allelic germline disruptions of GATA2, result in haploinsufficiency syndromes. These disorders display variable manifestations, including immune deficiency, lymphedema, pulmonary proteinosis, and bone marrow failure. The later is presented by myelodysplastic changes (MDS), that subsequently evolve to leukemia (AML). MDS/AML are the most devastating, yet most consistent outcomes, designating GATA2 deficiency as one major predisposing condition to AML development.

2023-09-15 | GSE143308 | GEO

Functional and molecular characterization of mouse Gata2-independent hematopoietic progenitors

Project description:The Gata2 transcription factor is a pivotal regulator of hematopoietic stem cell (HSC) development and maintenance. Gata2 functions in the embryo during endothelial cell to hematopoietic cell transition (EHT) to affect hematopoietic cluster, HPC and HSC formation. Although previous studies of cell populations phenotypically enriched in HPCs and HSCs show expression of Gata2, there has been no direct study of Gata2 expressing cells during normal hematopoiesis. In this study we generate a Gata2 Venus reporter mouse model with unperturbed Gata2 expression to examine the hematopoietic function and transcriptome of Gata2 expressing and nonexpressing cells. Gata2Venus- HPCs 1 replicate, Gata2Venus+ HPCs 1 replicate

2015-12-22 | E-GEOD-76254 | biostudies-arrayexpress

Long-read sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations in cancer (SF3B1 & U2AF2 iCLIP)

Project description:Alternative splicing plays a critical role in generating transcriptome diversity, and aberrant splicing is frequently observed in cancer. Mutations in the splicing factor SF3B1 are particularly common in patients with chronic lymphocytic leukemia (CLL) and myelodysplastic syndromes (MDS), with different survival prognoses. We applied long-read sequencing for the investigation of the SF3B1 mutation effect on the transcriptome of MDS and CLL patients, as well as isogenic cell lines. Our results revealed that SF3B1 mutation effect was common across the different diseases and specifically altered the usage of 3’ alternative splice sites within short proximity to the canonical splice sites. Based on computational simulations, the most common K700E mutation led to destabilization of the SF3B1-mRNA binding. Furthermore, we combined the full isoform information with genome-wide SF3B1-RNA binding maps to predict the functional consequences of the aberrant splicing and gain mechanistic insights into the role of mutated SF3B1 in splicing.

2024-08-19 | GSE247658 | GEO

Escherichia coli REL606

Project description:Synonymous genetic variation in natural isolates of Escherichia coli does not predict where synonymous substitutions occur in a long-term experiment

| PRJNA288811 | 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