Browse
Submit Data
Databases
API
Help

Dataset Information

5 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Prediction and experimental validation of a new salinity-responsive cis-regulatory element (CRE) in tilapia

ABSTRACT: Quantitative DIA proteomics in combination with the transcription inhibitor actinomycin D was performed on the tilapia OmB cell line to identify proteins that are upregulated by transcriptional regulation during hyperosmotic stress. This analysis revealed proteins that are transcriptionally up-regulated by hyperosmolality in these cells. The promoter regions of these proteins were compared and a novel hyperosmolality-induced cis-regulatory element (CRE) and corresponding transcription factor candidate were identified. The CRE was experimentlly validated by site-directed mutagenesis in combination with reporter assays.

ORGANISM(S): Oreochromis Mossambicus

SUBMITTER: Dietmar Kültz

PROVIDER: PXD032181 | panorama | Sun Sep 25 00:00:00 BST 2022

REPOSITORIES: PanoramaPublic

ACCESS DATA

Json Xml

Publications

Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line.

Kim Chanhee C Wang Xiaodan X Kültz Dietmar D

Life (Basel, Switzerland) 20220525 6

Transcriptional regulation is a major mechanism by which organisms integrate gene x environment interactions. It can be achieved by coordinated interplay between cis-regulatory elements (CREs) and transcription factors (TFs). Euryhaline tilapia (<i>Oreochromis mossambicus</i>) tolerate a wide range of salinity and thus are an appropriate model to examine transcriptional regulatory mechanisms during salinity stress in fish. Quantitative proteomics in combination with the transcription inhibitor a ...[more]

PMID: 35743818

Similar Datasets

Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish

Project description:Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit (LTL), namely the lower end of survival temperature, is an important trait delimiting the geographical distribution of a species, however, the genetic mechanisms are poorly understood. We investigated the inter-species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus, which were reared at a common temperature (28Â°C) but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia (8Â°C). Five KEGG pathways were found sequentially over-represented in the zebrafish/tilapia divergently expressed genes in the duration (12 hour) of 8Â°C exposure, forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently, we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia, corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis-related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.Â Examination of gene expressional divergence in gill between zebrafish and tilapia

2016-07-03 | E-GEOD-69965 | biostudies-arrayexpress

Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish

Project description:Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit (LTL), namely the lower end of survival temperature, is an important trait delimiting the geographical distribution of a species, however, the genetic mechanisms are poorly understood. We investigated the inter-species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus, which were reared at a common temperature (28°C) but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia (8°C). Five KEGG pathways were found sequentially over-represented in the zebrafish/tilapia divergently expressed genes in the duration (12 hour) of 8°C exposure, forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently, we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia, corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis-related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.

2016-07-03 | GSE69965 | GEO

Gene expression data of cancer cell lines treated with inhibitors of G9a and EZH2

Project description:Epigenetic modifications modulate gene expression and, when deregulated, contribute to the development and progression of cancer. G9a (EHMT2) and EZH2 are two histone methyltransferases commonly upregulated in several cancer types, leading to the silencing of tumor suppressor genes. We performed high throughput sequencing of a breast cancer cell line (MDA-MB-231), an ovarian cancer cell line (CAOV3) and a melanoma cell line (D14) treated with a G9a inhibitor (UNC0642), EZH2 inhibitor (GSK126) and their combination.

2022-02-20 | GSE168763 | GEO

Pharmacological inhibition of WIP1 sensitizes acute myeloid leukemia cells to MDM2 inhibitor Nutlin-3a

Project description:The wild-type p53-inducible protein phosphatase WIP1, encoded by the PPM1D gene, is a negative regulator of p53 and is involved in cell cycle control and DNA damage stress-response. In acute myeloid leukemia (AML), the restoration of p53 activity through MDM2 inhibition proved efficacy in a number of combination strategies. We investigated the therapeutic potential of its inhibition through the selective WIP1 inhibitor (WIP1i) GSK2830371, in association with the MDM2 inhibitor Nutlin-3a (Nut-3a) in a panel of AML cell lines and performed gene expression analysis of single agent and combined treatments. A p53-related signature was significantly upregulated in the TP53-wildtype MV-4-11 AML cell line. Moreover, drug-specific transcriptional changes likely contribute to the synergistic combination effect.

2021-05-06 | GSE156182 | GEO

Proteome alterations in MLL-rearranged leukemia cells following WIN Site inhibition

Project description:WIN Site inhibitors bind the WIN Site of WDR5 resulting in decreased transcription of WDR5 target genes, many of which encode components of the protein synthesis machinery. In this study, we determined proteome alterations in an MLL-rearranged leukemia cell line treated for either 24 or 72 hours with a WIN Site inhibitor. The data from these studies, along with Ribo-Seq, RNA-Seq, and CRISPR screen experiments, guided us in assembling a collection of compounds that, when combined with WIN Site inhibitor, synergistically inhibit growth of MLL-rearranged leukemia cells.

2023-07-04 | PXD035129 | Pride

Time-course effect of estradiol and ERa17p on Early Gene expression in T47D cells

Project description:ERα17p is a synthetic peptide corresponding to the sequence P295LMIKRSKKNSLALSLT311 of the estrogen receptor alpha (ERα) and initially synthesized to mimic its calmodulin binding site. ERα17p was subsequently found to elicit estrogenic responses in E2-deprived ERα-positive breast cancer cells, increasing proliferation and E2-dependent gene transcription. Surprisingly, in E2-supplemented media, ERα17p induced apoptosis and modified the actin network, influencing thereby cell motility. Here, we report that ERα17p induces a massive early (3h) transcriptional activity in breast cancer cell line T47D.

2012-07-31 | GSE39720 | GEO

Time-course effect of estradiol and ERa17p on Early Gene expression in MDA-MB-231 cells

2012-07-31 | GSE39718 | GEO

First Line Treatment of Metastatic Colorectal Cancer With mFOLFOX6 in Combination With Regorafenib

Project description:This is a study to evaluate the efficacy (effectiveness) and the safety of regorafenib when given in combination with chemotherapy mFOLFOX6 as first line therapy in patients with metastatic colorectal cancer (CRC). mFOLFOX6 is an approved chemotherapy. Regorafenib is an oral (i.e. taken by mouth) multi-targeted kinase inhibitor. A kinase inhibitor targets certain key proteins that are essential for the survival of the cancer cell. By specifically targeting these proteins, regorafenib may stop cancer growth. The growth of the tumor may be decreased by preventing these specific proteins from functioning. The primary endpoint (the most meaningful result to be tracked) of this study is based on the rate of response, i.e. the disease getting smaller. The aim is to show that the therapy of colorectal cancer with mFOLFOX6 in combination with regorafenib improves the response rate observed for the standard therapy only.

| 2101816 | ecrin-mdr-crc

FGF2 antiproliferative stimulus triggers proteomic and transcriptional changes associated with nucleolar disorganization in K-ras-driven mouse tumor cells (Nucleoli TMT)

Project description:Chromatin plays a crucial role in the intermediation between cell signaling and gene expression. The nucleolus is sensitive to stress and can orchestrate a chain of cellular events in response to stress signals. Despite being a growth factor, FGF2 has anti-proliferative and tumor-suppressive functions in some cellular contexts. In this work, we investigated how the antiproliferative effect of FGF2 modulates chromatin, nucleolus, and rDNA-associated proteins. The chromatin and nucleolar proteome indicated that FGF2 stimulation modulates proteins related to transcription regulation, particularly rRNA expression, and chromatin remodeling proteins. Upon 24 hrs of FGF2 stimulation, the global transcriptional rate and nucleolus area increased in associationalong with intense nucleolar disorganization detected by fibrillarin dispersion and electron microscopy analyses. We confirmed that FGF2 stimulation induced immature rRNA accumulation by increasing rRNA transcription regardless of changes in ribosome profiling. The rDNA-associated protein analysis reinforced that FGF2 stimulus interferes with transcription and rRNA processing/modification, since the proteins Nolc1 and Tcof1 are were upregulated after FGF2 stimulation. Changes in rRNA expression may be crucial for triggering the antiproliferative effect induced by FGF2 since inhibiting RNA Pol I, responsible for rRNA expression, partially reversed the growth arrest induced by FGF2. Taken together, we demonstrate that the antiproliferative FGF2 stimulus triggers significant transcriptional changes, and modulation modulates of the main cell transcription site, the nucleolus, directly modulating the proteome of the rDNA loci.

2022-10-12 | MSV000090518 | MassIVE

FGF2 antiproliferative stimulus triggers proteomic and transcriptional changes associated with nucleolar disorganization in K-ras-driven mouse tumor cells (CLASP MudPIT data)

2022-10-12 | MSV000090516 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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