Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA secondary structome of different retrotransposons with DNA/protein binding

ABSTRACT: RNA secondary structome of different retrotransposons with DNA/protein binding

PROVIDER: PRJNA941794 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23723400.fastq.gz	Fastqsanger.gz
	SRR23723401.fastq.gz	Fastqsanger.gz
	SRR23723402.fastq.gz	Fastqsanger.gz
	SRR23723403.fastq.gz	Fastqsanger.gz
	SRR23723404.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

RNA secondary structome of different retrotransposons with DNA/protein binding

Project description:We determined the RNA secondary structure of different retrotransposon by icSHAPE. The retrotransposon has differnet states including protein bound, DNA and protein bound.

2023-05-11 | GSE226783 | GEO

Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex

Project description:Production of secondary metabolites is controlled by a complicated regulatory network in eukaryotic cells. Several layers of regulators are involved in this process, ranging from pathway-specific regulation, to epigenetic control, to global regulation. Unprecedentedly, we have discovered that interaction of an RNA-binding protein CsdA with a regulator RsdA coordinates fungal secondary metabolism. Employing a genetic deletion approach and transcriptome analysis as well as metabolomics analysis, we revealed that CsdA and RsdA synergistically regulate fungal secondary metabolism comprehensively. Mechanistically, comprehensive genetic and biochemical studies proved that RsdA and CsdA co-localize in the nucleus and physically interact to achieve their function. In particular, we have demonstrated that CsdA mediates rsdA expression by binding specific motif “GUCGGUAU” of its pre-mRNA at a post-transcriptional level. We thus uncover a general mechanism in which RNA-binding protein physically interacts with, and controls the expression level of, the RsdA to coordinate fungal secondary metabolism.

2023-10-23 | GSE241019 | GEO

Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex

Project description:Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex

| PRJNA1006056 | ENA

GNPS - Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex, A eukaryotic functionally conserved RNA-binding protein CsdA with a global regulator RsdA coordinates fungal secondary metabolism

2023-02-08 | MSV000091220 | GNPS

RNA G-quadruplex secondary structure promotes alternative splicing via the RNA binding protein hnRNPF

Project description:RNA G-quadruplex secondary structure promotes alternative splicing via the RNA binding protein hnRNPF

| PRJNA420499 | ENA

Assessment of the Diagnostic Role of Serum Insulin-like Growth Factor Binding Protein-3 as a Potential Biomarker for Colorectal Cancer (CRC) in Egypt

Project description:1. evaluation of diagnostic importance of insulin like growth factor binding protein3 in patient with recently diagnosed as Colorectal cancer 2. correlation between the diagnostic efficacy of insulin like growth factor binding protein 3 with routine marker carcinoembryonic antigen.

| 59449 | ecrin-mdr-crc

RNA secondary structome of different cell lines

Project description:RNA secondary structome of different cell lines

| PRJNA608297 | ENA

RNA secondary structome of different cell lines

Project description:we resolved the RNA secondary structure of human (HEK293, HeLa, K562, HepG2, H9) and mouse (mES) cells based on optimized in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). we describe a deep discriminative neural network (PrismNet) that integrates big data of RBP binding and RNA secondary structure from matched living cells and accurately models the RNA sequence and structural preferences of protein-RNA interactions in vivo, enabling precise prediction of the perturbation effects of genetic variants.

2021-02-05 | GSE145805 | GEO

Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex, A eukaryotic functionally conserved RNA-binding protein CsdA with a global regulator RsdA coordinates fungal secondary metabolism

2023-02-08 | MSV000091220 | MassIVE

RBFOX2 alter splicing outcome in distinct binding modes with multiple protein partners

Project description:RBFOX2 controls the splicing of a large number of transcripts implicated in cell differentiation and development. Parsing RNA-binding protein datasets, we uncover that RBFOX2 can interact with hnRNPC, hnRNPM and SRSF1 to regulate splicing of a broad range of splicing events using different sequence motifs and binding modes. Using immunoprecipitation, specific RBP knockdown, RNA-seq and splice-sensitive PCR, we show that RBFOX2 can target splice sites using three binding configurations: single, multiple or secondary modes. In the single binding mode RBFOX2 is recruited to its target splice sites through a single canonical binding motif, while in the multiple binding mode RBFOX2 binding sites include the adjacent binding of at least one other RNA binding protein partner. Finally, in the secondary binding mode RBFOX2 likely does not bind the RNA directly but is recruited to splice sites lacking its canonical binding motif through the binding of one of its protein partners. These dynamic modes bind distinct sets of transcripts at different positions and distances relative to alternative splice sites explaining the heterogeneity of RBFOX2 targets and splicing outcomes.

2021-06-23 | GSE140679 | GEO

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