Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Loc1 RIP-chip; Niedner et al.

ABSTRACT: Loc1 RIP-chip Experimental procedure: C-terminally TAP-tagged Loc1p from yeast S. cerevisiae was purified from 1 L of cells grown in YPD medium as previously described (Gerber et al. 2004, PLoS Biol. 2, E79). Untagged control cells (BY4741) cells served as a negative control. cDNA was synthesized from 3 μg of total RNA derived from the extract and 500 ng of affinity-isolated RNA and labeled with Cy3 and Cy5 fluorescent dyes, respectively. Samples were mixed and hybridized to cDNA microarrays. Publication: Niedner-Boblenz A. et al. 2024, Nucleic Acids Res, in press. Title: Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation Abstract: RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro- and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA- and DNA-related processes by concentrating them in membrane-less organelles. The general function and wide distribution of PUN motifs across species suggests that in an ancient “RNA world” PUN-like motifs may have supported the correct folding of early ribozymes.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE273374 | GEO | 2024/10/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Molecular basis for the interaction of intrinsically disordered proteins with nuclear PIP2 compartments

Project description:Phosphatidylinositol 4,5 bisphosphate (PIP2) is the most abundant eukaryotic nuclear phosphoinositide. PIP2 is found in the nuclear speckles (NS), nucleoli (NL), and nuclear lipid islets (NLIs) and participates in the RNA polymerase II (Pol2) transcription. The formation of phase-separated nuclear sub-compartments, such as NS and NL, as well as PIP2 localization, depends on RNA. Thus, we studied if the PIP2 and RNA cooperate in the establishment of nuclear architecture. We identified the RNA-dependent PIP2-associated (RDPA) nuclear proteome in human cells. RDPA proteome participates in all steps of gene expression, and typical RDPA protein possesses RNA binding and phase separation capacity. RDPA proteins associate with PIP2 by electrostatic interactions, which depend on intact RNA and the phase separation capacity of the participating proteins. Moreover, we identified that intrinsically disordered regions (IDRs) with polybasic PIP2-binding K/R-motifs are common structural features of RDPA proteins and confirmed that manipulation of the PIP2 level changes the nuclear localization of RDPA proteins. We showed that PIP2 spatiotemporally orchestrates nuclear processes through association with RNA and RDPA proteins and their capacity to phase separate, which is the first evidence that PIP2 is crucial for establishment of functional nuclear architecture competent for gene expression.

2024-09-30 | PXD045745 | Pride

Defining the mechanisms and properties of post-transcriptional regulatory disordered regions by high-throughput functional profiling

Project description:Disordered regions within RNA binding proteins are required to control mRNA decay and protein synthesis. To understand how these disordered regions modulate gene expression, we surveyed regulatory activity across the entire disordered proteome using a high-throughput functional assay. We identified hundreds of regulatory sequences within intrinsically disordered regions and demonstrate how these elements cooperate with core mRNA decay machinery to promote transcript turnover. Coupling high-throughput functional profiling with mutational scanning revealed diverse molecular features, ranging from defined motifs to overall sequence composition, underlying the regulatory effects of disordered peptides. Machine learning analysis implicated aromatic residues in particular contexts as critical determinants of repressor activity, consistent with their roles in forming protein-protein interactions with downstream effectors. Our results define the molecular principles and biochemical mechanisms that govern post-transcriptional gene regulation by disordered regions and exemplify the encoding of diverse yet specific functions in the absence of well-defined structure.

2024-02-02 | GSE254492 | GEO

Aberrant phase separation of transcription factors in human developmental disorders

Project description:Components of the transcription machinery can undergo liquid-liquid phase separation, but the functional importance of phase-separated condensates in transcriptional control is not well understood. Here we report that disease-causing mutations in several transcription factors (TFs) alter the phase separation capacity of those TFs. We first demonstrate that the Hoxd13 TF, and its intrinsically disordered N-terminus form phase-separated condensates. Expansions of a polyalanine repeat, which cause hereditary synpolydactyly in humans, facilitate phase separation of Hoxd13, and alter the transcriptional program of several cell types in a cell-specific manner in vivo. Disease-associated expansions of aminoacid repeats in intrinsically disordered regions of other TFs were similarly found to alter phase separation. These results suggest that aberrant phase separation of transcriptional regulators may underlie a spectrum of human pathologies. The paper is available at https://doi.org/10.1016/j.cell.2020.04.018

2020-05-07 | GSE128818 | GEO

Synthetic biomolecular condensates enhance translation from a target mRNA in living cells

Project description:Biomolecular condensates composed of proteins and RNA are one approach by which cells regulate post-transcriptional gene expression. Their formation typically involves the phase separation of intrinsically disordered proteins with a target mRNA, sequestering the mRNA into a liquid condensate. This sequestration regulates gene expression by modulating translation or facilitating RNA processing. Here, we engineer synthetic condensates using a fusion of an RNA-binding protein, the human Pumilio2 homology domain, and a synthetic intrinsically disordered protein, an elastin-like polypeptide, that can bind and sequester a target mRNA transcript. In protocells, sequestration of a target mRNA largely limits its translation. Conversely, in E. Coli, sequestration of the same target mRNA increases its translation. We characterize the Pum2-ELP condensate system using microscopy, biophysical and biochemical assays, and RNA-seq. This approach enables modulation of cell function via the formation of synthetic biomolecular condensates that upregulate the expression of a target protein.

2024-11-30 | GSE277409 | GEO

The intrinsically disordered region of SPIN1 regulates its function by phase separation [RNA-seq]

Project description:The intrinsically disordered region of SPIN1 regulates its function by phase separation [RNA-seq]

| PRJNA890210 | ENA

mRNA binding - Insights into RNA biology from an atlas of mammalian mRNA-binding proteins

Project description:RNA-binding proteins (RBPs) determine RNA fate from synthesis to decay. Employing two complementary protocols for covalent UV crosslinking of RBPs to RNA, we describe a systematic, unbiased, and comprehensive approach, termed "interactome capture," to define the mRNA interactome of proliferating human HeLa cells. We identify 860 proteins that qualify as RBPs by biochemical and statistical criteria, adding more than 300 RBPs to those previously known and shedding light on RBPs in disease, RNA-binding enzymes of intermediary metabolism, RNA-binding kinases, and RNA-binding architectures. Unexpectedly, we find that many proteins of the HeLa mRNA interactome are highly intrinsically disordered and enriched in short repetitive amino acid motifs. Interactome capture is broadly applicable to study mRNA interactome composition and dynamics in varied biological settings.

2015-09-11 | PXD002880 | Pride

The intrinsically disordered region of SPIN1 regulates its function by phase separation.

Project description:The intrinsically disordered region of SPIN1 regulates its function by phase separation.

| PRJNA890202 | ENA

Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association [RNA-Seq]

Project description:Bombyx Vasa (BmVasa) assembles non-membranous organelle, nuage or Vasa bodies, in germ cells, known as the center for Siwi-dependent transposon silencing and concomitant Ago3-piRISC biogenesis. However, details of the body assembly remain unclear. Here, we show that the N-terminal intrinsically disordered region (N-IDR) and RNA helicase domain of BmVasa are responsible for self-association and RNA binding, respectively, but N-IDR is also required for full RNA-binding activity. Both domains are essential for Vasa body assembly in vivo and droplet formation in vitro via phase separation. FAST-iCLIP reveals that BmVasa preferentially binds transposon mRNAs. Loss of Siwi function derepresses transposons but has marginal effects on BmVasa-RNA binding. This study shows that BmVasa assembles nuage by phase separation via its ability to self-associate and bind newly exported transposon mRNAs. This unique property of BmVasa allows transposon mRNAs to be sequestered and enriched in nuage, resulting in effective Siwi-dependent transposon repression and Ago3-piRISC biogenesis.

2023-03-06 | GSE213915 | GEO

Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association [RIP-Seq]

2023-03-06 | GSE213914 | GEO

Regulation of zebrafish dorsoventral patterning by phase separation of RNA-binding protein rbm14

Project description:RNA-binding proteins with intrinsically disordered regions (IDRs) such as Rbm14 can phase separate in vitro. To what extent the phase separation contributes to their physiological functions is however unclear. Here we show that zebrafish rbm14 regulates embryonic dorsoventral patterning through phase separation. Zebrafish rbm14 morphants displayed dorsalized phenotypes associated with attenuated BMP signaling. Consistently, depletion of mammalian Rbm14 downregulated BMP regulators and effectors Nanog, Smad4/5, and Id1/2, whereas overexpression of the BMP-related proteins in the morphants significantly restored the developmental defects. Importantly, rbm14's IDR demixed into liquid droplets in vitro despite poor sequence conservation with its mammalian counterpart. While its phase separation mutants or IDR failed to rescue the morphants, its chimeric proteins containing an IDR from other phase-separation proteins were effective. Rbm14 complexed with proteins involved in RNA metabolism and phase separated into cellular ribonucleoprotein compartments. Consistently, RNA deep sequencing analysis on the morphant embryos revealed increased alternative splicing events as well as largescale transcriptomic downregulations. Our results suggest that Rbm14 functions in ribonucleoprotein compartments through phase separation to modulate multiple aspects of RNA metabolism. Furthermore, IDRs conserve in phase separation ability but not primary sequence and can be functionally interchangeable.

2019-08-05 | GSE128984 | 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