Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A network of DZF proteins controls alternative splicing regulation and fidelity [eCLIP-seq]

ABSTRACT: A network of DZF proteins controls alternative splicing regulation and fidelity [eCLIP-seq]

PROVIDER: PRJNA848990 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19646428_1.fastq.gz	Fastqsanger.gz
	SRR19646428_2.fastq.gz	Fastqsanger.gz
	SRR19646429_1.fastq.gz	Fastqsanger.gz
	SRR19646429_2.fastq.gz	Fastqsanger.gz
	SRR19646430_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

A network of DZF proteins controls alternative splicing regulation and fidelity [eCLIP-seq]

Project description:Proteins containing DZF (domain associated with zinc fingers) modules play important roles throughout gene expression, from transcription to translation. Derived from nucleotidyltransferases but lacking catalytic residues, DZF domains serve as heterodimerization surfaces between DZF protein pairs. Three DZF proteins are widely expressed in mammalian tissues, ILF2, ILF3, and ZFR, which form mutually exclusive ILF2-ILF3 and ILF2-ZFR heterodimers. Using eCLIP-Seq, we find that ZFR binds across broad intronic regions to regulate the alternative splicing of cassette and mutually exclusive exons. ZFR preferentially binds dsRNA in vitro and is enriched on introns containing conserved dsRNA elements in cells. Many splicing events are similarly altered upon depletion of any of the three DZF proteins; however, we also identify independent and opposing roles for ZFR and ILF3 in alternative splicing regulation. Along with widespread involvement in cassette exon splicing, the DZF proteins control the fidelity and regulation of over a dozen highly validated mutually exclusive splicing events. Our findings indicate that the DZF protein complexes form a complex regulatory network that leverages dsRNA binding by ILF3 and ZFR to modulate splicing regulation and fidelity.

2023-05-09 | GSE206059 | GEO

A network of DZF proteins controls alternative splicing regulation and fidelity [RNA-seq]

2023-05-09 | GSE206058 | GEO

A network of DZF proteins controls alternative splicing regulation and fidelity [RNA Bind-n-Seq]

2023-05-09 | GSE206060 | GEO

A network of DZF proteins controls alternative splicing regulation and fidelity.

Project description:A network of DZF proteins controls alternative splicing regulation and fidelity.

| PRJNA848988 | ENA

A network of DZF proteins controls alternative splicing regulation and fidelity [RNA-seq]

Project description:A network of DZF proteins controls alternative splicing regulation and fidelity [RNA-seq]

| PRJNA848991 | ENA

A network of DZF proteins controls alternative splicing regulation and fidelity [RNA Bind-n-Seq]

Project description:A network of DZF proteins controls alternative splicing regulation and fidelity [RNA Bind-n-Seq]

| PRJNA848989 | ENA

A network of DZF proteins controls alternative splicing regulation and fidelity.

Project description:This SuperSeries is composed of the SubSeries listed below. GSE206058: Paired-end total RNA-seq of triplicate biological replicate treatments of HEK-293 cells with negative control siRNAs or siRNAs targeting ZFR, ILF2, or ILF3. GSE206059: eCLIP analysis of FLAG-ZFR binding in HEK-293 Flp-In TREx cell lines, with size-matched input control. GSE206060: RNA Bind-n-Seq of recombinantly expressed and purified ZFR-ILF2 complexes, with PTBP1 as a positive control for successful library generation.

2023-05-09 | GSE206061 | GEO

QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5’splice sites [eCLIP HEK293xT]

Project description:During organogenesis, the establishment of tissue architecture requires precise RNA processing. Many developmentally essential exons bear weak 5′ splice sites (5′SS) yet are spliced with high precision, implying unknown yet active splicing fidelity mechanisms. Combining transcriptome and alternative splicing profiling and with temporal eCLIP mapping of RNA interactions across development, we identify the RNA-binding protein QKI as an essential direct regulator of splicing fidelity in key cardiac transcripts. Although QKI is dispensable for cardiac lineage specification, its loss disrupts sarcomere assembly despite intact expression of sarcomere mRNAs through exon skipping and intron retention in key sarcomeric mRNAs. QKI-dependent exons in essential cardiac genes have weak 5′SS and frequently show poor complementarity with U6 snRNA; we show that QKI directly interacts with U6 snRNA using an overlapping interface to its traditional intronic binding activity, securing U4/U6·U5 tri-snRNP recruitment to ensure exon inclusion. Thus, QKI exemplifies how context-aware RBPs enforce splicing fidelity at structurally vulnerable splice sites by coupling local intronic cues to spliceosome engagement, thereby securing accurate exon inclusion during organogenesis.

2025-09-17 | GSE306688 | GEO

QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5’splice sites [eCLIP Hues6]

2025-09-17 | GSE306579 | GEO

A network of DZF proteins controls alternative splicing regulation and fidelity.

Project description:Proteins containing DZF (domain associated with zinc fingers) modules play important roles throughout gene expression, from transcription to translation. Derived from nucleotidyltransferases but lacking catalytic residues, DZF domains serve as heterodimerization surfaces between DZF protein pairs. Three DZF proteins are widely expressed in mammalian tissues, ILF2, ILF3 and ZFR, which form mutually exclusive ILF2-ILF3 and ILF2-ZFR heterodimers. Using eCLIP-Seq, we find that ZFR binds across broad intronic regions to regulate the alternative splicing of cassette and mutually exclusive exons. ZFR preferentially binds dsRNA in vitro and is enriched on introns containing conserved dsRNA elements in cells. Many splicing events are similarly altered upon depletion of any of the three DZF proteins; however, we also identify independent and opposing roles for ZFR and ILF3 in alternative splicing regulation. Along with widespread involvement in cassette exon splicing, the DZF proteins control the fidelity and regulation of over a dozen highly validated mutually exclusive splicing events. Our findings indicate that the DZF proteins form a complex regulatory network that leverages dsRNA binding by ILF3 and ZFR to modulate splicing regulation and fidelity.

| S-EPMC10325889 | biostudies-literature

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