Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ICLIP-Seq analyses of DDX46-bound RNAs

ABSTRACT: DDX46 is identified to be required at the early step of pre-spliceosome assembly,but the potential roles of DDX46 in RNA editing and whether DDX46 could regulate antiviral innate immunity by editing antiviral transcripts in the nucleus remain elusive.

ORGANISM(S): Mus musculus

PROVIDER: GSE81386 | GEO | 2016/05/13

SECONDARY ACCESSION(S): PRJNA321425

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

iCLIP-Seq analyses of DDX46-bound RNAs

Project description:DDX46 is identified to be required at the early step of pre-spliceosome assembly,but the potential roles of DDX46 in RNA editing and whether DDX46 could regulate antiviral innate immunity by editing antiviral transcripts in the nucleus remain elusive. iCLIP-Seq analyses of DDX46-bound RNAs from uninfected and VSV-infected RAW264.7 cells

2016-05-13 | E-GEOD-81386 | biostudies-arrayexpress

Transcriptome sequencing analyses of WT and DDX46+/- macrophages

Project description:DDX46 is identified to be required at the early step of pre-spliceosome assembly,but whether DDX46 could regulate antiviral transcripts isoform splicing in the nucleus remain elusive.

2017-08-28 | GSE98359 | GEO

iCLIP-Seq analyses of YTHDF3-bound RNAs

Project description:We found that YTHDF3 work as m1A reader,but the potential substrate RNA remain elusive.

2020-03-24 | GSE135642 | GEO

iCLIP-Seq analyses of NSP12-bound RNAs

Project description:We known that NSP12 as an important RNA binding protein, but the potential substrate RNA of host cells remain elusive.

2024-08-22 | GSE182750 | GEO

iCLIP-Seq analyses of NSP12-bound RNAs

Project description:iCLIP-Seq analyses of NSP12-bound RNAs

| PRJNA757705 | ENA

iCLIP-Seq analyses of YTHDF3-bound RNAs

Project description:iCLIP-Seq analyses of YTHDF3-bound RNAs

| PRJNA559536 | ENA

Spliceosome iCLIP

Project description:Spliceosome iCLIP

| PRJEB27592 | ENA

CDK11 phosphorylates SF3B1 and is essential for constitutive splicing (iCLIP)

Project description:Pre-mRNA splicing is a highly regulated process catalyzing intron excision by spliceosome. Spliceosome activation is a major control step requiring dramatic protein and RNA rearrangements leading to a catalytically active complex. Prior research has linked hyperphosphorylation of SF3B1, a subunit of U2 snRNP, with spliceosome activation and catalytically active spliceosome, rendering a relevant kinase a key player for pre-mRNA splicing. Here we use OTS964, the first potent inhibitor of cyclin-dependent kinase 11 (CDK11), to show rapid and selective dephosphorylation of SF3B1 on threonines required for spliceosome activation. CDK11 associates with SF3B1 and its inhibition causes massive intron retention, block in precatalytic spliceosome complex B to activated spliceosome complex Bact transition and accumulation of non-functional spliceosomes on pre-mRNA and chromatin. These studies reveal crucial regulatory role of CDK11 in human pre-mRNA splicing and define the compound OTS964 as a quality chemical biology probe for CDK11.

2022-07-09 | GSE185811 | GEO

Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach

Project description:We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions.

2024-06-19 | MODEL2406180001 | BioModels

Spliceosome iCLIP

Project description:The studies of spliceosomal interactions are challenging due to their dynamic nature. Here we developed spliceosome iCLIP, which immunoprecipitates SmB along with snRNPs and auxiliary RNA binding proteins (RBPs) to simultaneously map the spliceosomal binding to human snRNAs and pre-mRNAs. This identified 9 distinct regions on pre-mRNAs, which overlap with position-dependent binding patterns of 15 RBPs. Using spliceosome iCLIP, we additionally identified >50,000 branchpoints (BPs) that have canonical features, unlike those identified by RNA-seq. The iCLIP BPs generally overlap with the computationally predicted BPs, and alternative BPs are associated with extended regions of structurally accessible RNA. We find that the position and strength of BPs defines the binding patterns of SF3 and U2AF complexes, whereas the RNA structure around BPs affects the sensitivity of exons to perturbation of these complexes. Our findings introduce spliceosome iCLIP as a new method for transcriptomic studies of BPs and splicing mechanisms.

2019-08-30 | E-MTAB-6950 | biostudies-arrayexpress

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