Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulation by the RNA-binding protein Unkempt at its effector interface [RNA]

ABSTRACT: How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP–effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of ‘dual-purpose’ peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP–effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP–effector interface.

ORGANISM(S): Homo sapiens

PROVIDER: GSE240565 | GEO | 2024/03/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Regulation by the RNA-binding protein Unkempt at its effector interface [iCLIP]

Project description:How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP–effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of ‘dual-purpose’ peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP–effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP–effector interface.

2024-03-17 | GSE240562 | GEO

Regulation by the RNA-binding protein Unkempt at its effector interface [Ribo]

2024-03-17 | GSE240563 | GEO

Regulation by the RNA-binding protein Unkempt at its effector interface [Tail seq]

2024-03-17 | GSE240568 | GEO

Regulation by the RNA-binding protein Unkempt at its effector interface

2024-04-11 | PXD050601 | Pride

Transcriptional profiling upon knockdown of the RNA-binding protein Unkempt

Project description:RNAseq to assess changes in transcript abundance upon knockdown of the RNA-binding protein Unkempt in human SH-SY5Y cell lines.

2015-01-15 | E-MTAB-2277 | biostudies-arrayexpress

Ribosome profiling upon overexpression of the RNA-binding protein Unkempt

Project description:Ribosome profiling to assess changes in ribosome occpancy upon overexpression of the RNA-binding protein Unkempt (most likely acts as a translational regulator) in human HeLa cell lines.

2015-03-09 | E-MTAB-2278 | biostudies-arrayexpress

Transcriptional profiling upon knockdown of the RNA-binding protein Unkempt

Project description:Transcriptional profiling upon knockdown of the RNA-binding protein Unkempt

| PRJEB5284 | ENA

Ribosome profiling upon overexpression of the RNA-binding protein Unkempt

Project description:Ribosome profiling upon overexpression of the RNA-binding protein Unkempt

| PRJEB5285 | ENA

Genome-wide maps of nuclear lamina interactions in single human cells. (Hi-C, KBM7 haploid)

Project description:Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, single-cell gene expression and chromatin accessibility analysis shows that loci with consistent NL contacts are expressed at lower levels and are more consistently inaccessible than loci with lower contact frequencies. These results highlight fundamental principles of single cell chromatin organization. Hi-C Data

2015-09-24 | E-GEOD-69841 | biostudies-arrayexpress

Transcriptome-wide mapping of RNA binding sites of the RNA-binding protein Unkempt using iCLIP-seq

Project description:iCLIP experiments tomap the RNA binding sites of the RNA-binding protein Unkempt across the transcriptome in SH-SY5Y cells, HeLa cells with ectopic Unk expression and mouse E15 embryonic brain samples. Expression of Unk is normally largely restricted to the nervous system. We therefore mapped the binding sites in human SH-SY5Y and mouse E15 brain to detect its physiological binding sites (in SH-SY5Y, we also performed the RNAseq experiment upon Unk knockdown). HeLa cells on the other hand normally don't express Unk, but convert to neuron-like shape when the protein is ectopically expressed. So, here we hoped to identify those binding events (and hence target transcripts) that are critical for this morphological transformation.

2015-03-09 | E-MTAB-2279 | 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