Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of the intrinsically disordered region (IDR) within the CLK2 (T343A) mutant in the regulation of intron retention

ABSTRACT: Effect of the intrinsically disordered region (IDR) within the CLK2 (T343A) mutant in the regulation of intron retention

PROVIDER: PRJNA1037522 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR26779293_1.fastq.gz	Fastqsanger.gz
	SRR26779293_2.fastq.gz	Fastqsanger.gz
	SRR26779294_1.fastq.gz	Fastqsanger.gz
	SRR26779294_2.fastq.gz	Fastqsanger.gz
	SRR26779295_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Effect of the intrinsically disordered region (IDR) within the CLK2 (T343A) mutant in the regulation of intron retention

Project description:We established the HeLa cells expressing the GFP (control) or CLK2 (T343A) with deletion of the IDR [T343A (dIDR)]. These cells were subjected to RNA-seq for the alternative splicing analysis.

2023-11-09 | GSE247419 | GEO

Effect of CLK2 expression in the regulation of intron retention during heat shock [RNA-seq]

Project description:Intron retention (IR) constitutes a less explored form of alternative splicing, wherein introns are retained within mature mRNA transcripts. Our investigation demonstrates that the CDC-like kinase 2 (CLK2) undergoes liquid-liquid phase separation (LLPS) within nuclear speckles in response to heat shock (HS). The formation of CLK2 condensates depends on the intrinsically disordered region (IDR) located within the N-terminal amino acids 1-148. Phosphorylation at residue T343 sustains CLK2 kinase activity and facilitates autophosphorylation, thus inhibiting the LLPS activity of the IDR. These CLK2 condensates initiate the reorganization of nuclear speckles, transforming them into larger, rounded structures. Moreover, these condensates facilitate the recruitment of splicing factors into these compartments, potentially restricting their access to mRNA for intron splicing. Consequently, the formation of CLK2 condensates promotes the IR.

2024-07-15 | GSE271918 | GEO

Effect of CLK2 expression in the regulation of intron retention during heat shock

Project description:We established the HeLa cells expressing the GFP (control) or CLK2 (WT) and subjected them to heat shock. These cells were subjected to RNA-seq for the alternative splicing analysis.

2023-11-09 | GSE247417 | GEO

Sequence and chemical specificity define the functional landscape of intrinsically disordered regions [ONT]

Project description:Intrinsically disordered regions (IDRs) pervasively engage in essential molecular functions, yet they are often poorly conserved as assessed by sequence alignment. To explore the seeming paradox of how sequence variability is compatible with persistent function, we examined the functional determinants for a poorly conserved but essential IDR. We show that IDR function depends on two distinct but related properties: sequence and chemical specificity. While sequence-specificity operates via binding motifs and depends on the precise order and identity of residues, chemical specificity reflects the sequence-encoded chemistry of multivalent interactions across an IDR and depends on local and global chemical properties. Unexpectedly, a binding motif essential in the wild- type IDR can be removed when compensatory changes to the sequence chemistry are introduced, highlighting the orthogonality and interoperability of these properties and expanding the sequence space compatible with function. Our results provide a general framework for the functional constraints on IDR evolution.

2025-12-17 | GSE314049 | GEO

Sequence and chemical specificity define the functional landscape of intrinsically disordered regions [RNA-seq]

2025-12-17 | GSE314051 | GEO

Sequence and chemical specificity define the functional landscape of intrinsically disordered regions [MNase-seq]

2025-12-17 | GSE314050 | GEO

Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [Histone_LCD_RNA]

Project description:Intrinsically disordered regions (IDRs) are well-known facilitators of chromatin regulation, but their role as regulatory restraints remains underexplored. Here, we reveal that the C-terminal IDR of mammalian ALKBH5 anchors its main activity to mRNA, limiting chromatin engagement in mouse embryonic stem cells (mESCs). IDR deletion redirects ALKBH5 to chromatin-associated non-coding RNAs, driving widespread chromatin opening and transcriptional activation. This mechanism extends to histone demethylases, where IDR deletion also results in broad removal of repressive histone marks, leading to increased chromatin accessibility and activation of transposable elements. Leveraging these insights, we engineered ALKBH5 and its plant homologs with IDR deletion. Overexpression of these IDR-deleted ALKBH5 demethylases could promote Arabidopsis root growth and increase rice yield. Our findings uncover a conserved role for IDRs in restraining chromatin access by RNA and histone demethylases and establish a new strategy of chromatin programming for crop engineering using plant proteins.

2026-03-09 | GSE286064 | GEO

Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [m6a]

2026-03-09 | GSE286065 | GEO

Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [Histone_ALKBH]

2026-03-09 | GSE286063 | GEO

Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [YY1]

2026-03-09 | GSE286066 | GEO