The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites DOI Creative Commons
Joelle Lo, Katherine F. Vaeth, Gurprit Bhardwaj

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 26, 2024

ABSTRACT RNA molecules are localized to subcellular regions through interactions between localization-regulatory cis-elements and trans-acting binding proteins (RBPs). However, the identities of RNAs whose localization is regulated by a specific RBP as well impacts that on cell function have generally remained unknown. Here, we demonstrate HNRNPA2B1 acts keep out neuronal projections. Using fractionation, high-throughput sequencing, single molecule FISH, find hundreds markedly increased abundance in neurites knockout cells. These often encode motor enriched for known sites motifs their 3′ UTRs. The speed processivity microtubule-based transport impaired these cells, specifically neurites. point mutations increase its cytoplasmic relative wildtype lead stronger suppression mislocalization defects than seen with HNRNPA2B1. We further localizations target sensitive perturbations decay machinery, suggesting it HNRNPA2B1’s role regulating stability may explain observations. findings establish negative regulator neurite link activities them.

Language: Английский

Role of mRNA-binding proteins in retinal neovascularization DOI
Pei Lin, Wenye Cao, Xuemei Chen

et al.

Experimental Eye Research, Journal Year: 2024, Volume and Issue: 242, P. 109870 - 109870

Published: March 19, 2024

Language: Английский

Citations

3
Identification of putative baroreceptors in human aortic arch by histological and omics analyses DOI Creative Commons
Yankey Yundung, Jaroslav Pelisek,

Umberto Macciò

et al.

Hypertension Research, Journal Year: 2025, Volume and Issue: unknown

Published: May 7, 2025

Abstract Baroreflex regulates blood pressure and heartbeat through specific mechanosensitive baroreceptors. However, the current knowledge is derived only from animal experiments. No data about human aortic baroreceptors have been reported so far. Therefore, in this study, we performed extended histological, proteomics transcriptomics analyses of arch to identify potential Three healthy arches autopsies, six abdominal aneurysms four control tissue samples our vascular biobank were analysed. For histological analyses, antibodies against various neuronal markers used. Laser capture microdissection macrodissection selectively analyse nerves adventitia aorta using RNA sequencing. Histological analysis revealed a heterogeneous distribution along entire arch, predominantly ascending up left subclavian artery. Proteome identified three putative PIEZO1, TRPV2, TRPM4. Transcriptomics confirmed that these ion channels do not originate cells within wall but presumably cell body vagus nerve. Interestingly, also detected aneurysm without any significant differences their abundance. Our study identified, for first time, arch. Further studies are necessary validate results elucidate role

Language: Английский

Citations

0
Proximitomics by Reactive Species DOI Creative Commons
Shaoran Zhang, Qi Tang, Xu Zhang

et al.

ACS Central Science, Journal Year: 2024, Volume and Issue: 10(6), P. 1135 - 1147

Published: June 12, 2024

The proximitome is defined as the entire collection of biomolecules spatially in proximity a biomolecule interest. More broadly, concept can be extended to totality cells proximal specific cell type. Since spatial organization and essential for almost all biological processes, proximitomics has recently emerged an active area scientific research. One growing strategies leverages reactive species─which are generated situ confined, chemically tag capture systematic analysis. In this Outlook, we summarize different types species that have been exploited discuss their pros cons applications. addition, current challenges future directions exciting field.

Language: Английский

Citations

3
A KIF1C-CNBP motor-adaptor complex for trafficking mRNAs to cell protrusions DOI
Konstadinos Moissoglu, Tianhong Wang, Alexander N. Gasparski

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 27, 2024

Summary mRNA localization to subcellular compartments is a widely used mechanism that functionally contributes numerous processes. targeting can be achieved upon recognition of RNA cargo by molecular motors. However, our understanding how this accomplished limited, especially in higher organisms. We focus on pathway targets mRNAs peripheral protrusions mammalian cells and important for cell migration. Trafficking occurs through active transport microtubules, mediated the KIF1C kinesin. Here, we identify RNA-binding protein CNBP, as factor required protrusions. CNBP binds directly GA-rich sequences 3’UTR protrusion targeted mRNAs. also interacts with recruitment their trafficking microtubules periphery. This work provides reveals motor-adaptor complex

Language: Английский

Citations

1
Quantification of subcellular RNA localization through direct detection of RNA oxidation DOI Creative Commons
Hei‐Yong G. Lo, Raeann Goering, Agnese Kocere

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 12, 2024

Across cell types and organisms, thousands of RNAs display asymmetric subcellular distributions. The study this process often requires quantifying abundances specific at precise locations. To analyze transcriptomes, multiple proximity-based techniques have been developed in which near a localized bait protein are specifically labeled, facilitating their biotinylation purification. However, these complex methods laborious require expensive enrichment reagents. streamline the analysis RNA populations, we Oxidation-Induced Nucleotide Conversion sequencing (OINC-seq). In OINC-seq, genetically encoded, oxidized photo-controllable manner. These oxidation events then directly detected quantified using high-throughput our software package, PIGPEN, without need for biotin-mediated enrichment. We demonstrate that OINC-seq can induce quantify with high specificity dose- light-dependent further show spatial by it to transcriptomes associated cytoplasm, ER, nucleus, inner outer membranes mitochondria. Finally, transgenic zebrafish, allows proximity-mediated labeling live animals. sum, together PIGPEN provide an accessible workflow across different biological systems.

Language: Английский

Citations

1
Intracellular polarization of RNAs and proteins in the human small intestinal epithelium DOI Creative Commons
Roy Novoselsky, Yotam Harnik, Oran Yakubovsky

et al.

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(12), P. e3002942 - e3002942

Published: Dec. 2, 2024

The intestinal epithelium is a polarized monolayer of cells, with an apical side facing the lumen and basal blood stream. In mice, both proteins mRNAs have been shown to exhibit global basal-apical polarization; however, polarization in human intestine has not systematically explored. Here, we employed laser-capture microdissection isolate epithelial segments from tissues 8 individuals performed RNA sequencing mass-spectrometry proteomics. We find substantial mRNA molecules that largely overlaps patterns observed mice. This remains consistent across different zones villi generally correlated proteins. Our protein analysis exposes streamlined intracellular nutrient transport processing reveals mitochondria ribosomes are less humans compared study provides resource for understanding biology.

Language: Английский

Citations

1
Enhanced binding of guanylated poly(A) RNA by the LaM domain of LARP1 DOI Creative Commons
Guennadi Kozlov,

Jianning Jiang,

Tyler Rutherford

et al.

RNA Biology, Journal Year: 2024, Volume and Issue: 21(1), P. 7 - 16

Published: July 17, 2024

La-related proteins (LARPs) are a family of RNA-binding that share conserved La motif (LaM) domain. LARP1 plays role in regulating ribosomal protein synthesis and stabilizing mRNAs has unique structure without an RNA binding RRM domain adjoining the LaM In this study, we investigated physical basis for specificity poly(A) sequences observed unexpected bias with single guanines. Multiple guanine substitutions did not increase affinity, demonstrating preferential recognition singly guanylated sequences. We also cyclic di-nucleotides cCAS/STING pathway, cyclic-di-GMP 3',3'-cGAMP, bound sub-micromolar affinity. Isothermal titration measurements were complemented by high-resolution crystal structures six different ligands, including two stereoisomers phosphorothioate linkage. The selectivity substituted suggests may play effect tail guanylation.

Language: Английский

Citations

1
Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5′TOP mRNAs DOI Creative Commons

Tobias Hochstoeger,

Panagiotis Papasaikas, Ewa Piskadlo

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 22, 2023

Abstract A central mechanism of mTOR complex 1 (mTORC1) signaling is the coordinated translation ribosomal protein and factor mRNAs mediated by 5′-terminal oligopyrimidine motif (5′TOP). Recently, La-related (LARP1) has been proposed to be specific regulator 5′TOP mRNA downstream mTORC1, while eIF4E-binding proteins (4EBP1/2) were suggested have a general role in repression. Here, we employ single-molecule site imaging canonical study translational dynamics single living cells. Our data reveals that 4EBP1/2 dominant repression both during pharmacological inhibition mTOR. In contrast, find LARP1 selectively protects from degradation transcriptome-wide analysis half-lives. results clarify roles regulating provides framework further how these factors control cell growth development disease.

Language: Английский

Citations

3
Small-molecule Ro-08-2750 interacts with many RNA-binding proteins and elicits MUSASHI2-independent phenotypes DOI Open Access
Kathryn Walters, Marcin Piotr Sajek, Elisabeth Murphy

et al.

RNA, Journal Year: 2023, Volume and Issue: 29(10), P. 1458 - 1470

Published: June 27, 2023

RNA-binding proteins (RBPs) are key regulators of gene expression. Small molecules targeting these RBP–RNA interactions a rapidly emerging class therapeutics for treating variety diseases. Ro-08-2750 (Ro) is small molecule identified as competitive inhibitor Musashi (MSI)–RNA interactions. Here, we show that multiple Ro-dependent cellular phenotypes, specifically adrenocortical steroid production and cell viability, Musashi-2 (MSI2)-independent. Using an unbiased proteome-wide approach, discovered Ro broadly interacts with RBPs, many containing RRM domains. To confirm this finding, leveraged the large-scale ENCODE data to identify subset RBPs whose depletion phenocopies inhibition, indicating promiscuous RBPs. Consistent broad disruption ribonucleoprotein complexes, treatment leads stress granule formation. This strategy represents generalizable framework validating specificity identifying targets RBP inhibitors in context.

Language: Английский

Citations

3
Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs DOI Creative Commons
Evgenia Ntini,

Stefan Budach,

Ulf Andersson Ørom

et al.

Cell Systems, Journal Year: 2023, Volume and Issue: 14(10), P. 906 - 922.e6

Published: Oct. 1, 2023

Language: Английский

Citations

2