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

mRNA stability and m6A are major determinants of subcellular mRNA localization in neurons DOI Creative Commons
Inga Loedige, Artem Baranovskii, Samantha Mendonsa

et al.

Molecular Cell, Journal Year: 2023, Volume and Issue: 83(15), P. 2709 - 2725.e10

Published: July 13, 2023

For cells to perform their biological functions, they need adopt specific shapes and form functionally distinct subcellular compartments. This is achieved in part via an asymmetric distribution of mRNAs within cells. Currently, the main model mRNA localization involves sequences called "zipcodes" that direct proper locations. However, while thousands localize cells, only a few zipcodes have been identified, suggesting additional mechanisms contribute localization. Here, we assess role stability by combining isolation soma neurites mouse primary cortical mESC-derived neurons, SLAM-seq, m6A-RIP-seq, perturbation destabilization mechanisms, analysis multiple datasets. We show depletion elements, such as m6A, AU-rich suboptimal codons, functions mechanism mediates associated with housekeeping several types neurons.

Language: Английский

Citations

45
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.

Science Advances, Journal Year: 2024, Volume and Issue: 10(7)

Published: Feb. 16, 2024

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) was proposed to be specific regulator 5′TOP mRNA downstream mTORC1, while eIF4E-binding proteins (4EBP1/2) were suggested have a general role in translational repression all transcripts. Here, we use single-molecule site imaging canonical study single living cells. Our data reveal that 4EBP1/2 has dominant both during pharmacological inhibition mTOR. In contrast, find LARP1 selectively protects from degradation transcriptome-wide analysis half-lives. results clarify roles regulating provide framework further how these factors control cell growth development disease.

Language: Английский

Citations

10
G3BP1 ribonucleoprotein complexes regulate focal adhesion protein mobility and cell migration DOI Creative Commons
Liana C. Boraas, Mengwei Hu, Pieter Martino

et al.

Cell Reports, Journal Year: 2025, Volume and Issue: 44(2), P. 115237 - 115237

Published: Feb. 1, 2025

The subcellular localization of mRNAs plays a pivotal role in biological processes, including cell migration. For instance, β-actin mRNA and its associated RNA-binding protein (RBP), ZBP1/IGF2BP1, are recruited to focal adhesions (FAs) support localized synthesis, crucial for However, whether other RBPs also localize at FAs remains unclear. Here, we identify hundreds that enriched (FA-mRNAs). FA-mRNAs share characteristics with stress granule (SG) found ribonucleoprotein (RNP) complexes the SG RBP. Mechanistically, G3BP1 binds FA proteins an RNA-dependent manner, dimerization domains, essential form RNPs SG, required We find promote speed by enhancing mobility size. These findings suggest previously unappreciated regulating function under non-stress conditions.

Language: Английский

Citations

1
Mechanistic insights into the basis of widespread RNA localization DOI
Marina Chekulaeva

Nature Cell Biology, Journal Year: 2024, Volume and Issue: 26(7), P. 1037 - 1046

Published: July 1, 2024

Language: Английский

Citations

8
RNA trafficking and subcellular localization—a review of mechanisms, experimental and predictive methodologies DOI Creative Commons
Jun Wang, Marc Horlacher, Lixin Cheng

et al.

Briefings in Bioinformatics, Journal Year: 2023, Volume and Issue: 24(5)

Published: June 27, 2023

Abstract RNA localization is essential for regulating spatial translation, where RNAs are trafficked to their target locations via various biological mechanisms. In this review, we discuss in the context of molecular mechanisms, experimental techniques and machine learning-based prediction tools. Three main types mechanisms that control distinct cellular compartments reviewed, including directed transport, protection from mRNA degradation, as well diffusion local entrapment. Advances methods, both image sequence based, provide substantial data resources, which allow design powerful learning models predict localizations. We review publicly available predictive tools serve a guide users inspire developers build more effective models. Finally, an overview multimodal learning, may new avenue localization.

Language: Английский

Citations

14
Localization ofKif1cmRNA to cell protrusions dictates binding partner specificity of the encoded protein DOI Open Access
Megan L. Norris, Joshua T. Mendell

Genes & Development, Journal Year: 2023, Volume and Issue: 37(5-6), P. 191 - 203

Published: March 1, 2023

Subcellular localization of messenger RNA (mRNA) is a widespread phenomenon that can impact the regulation and function encoded protein. In nonneuronal cells, specific mRNAs localize to cell protrusions, proper mRNA required for migration. However, mechanisms by which regulates protein in this setting remain unclear. Here, we examined functional consequences encoding KIF1C. KIF1C kinesin motor migration trafficking, including trafficking its own mRNA. We show Kif1c does not regulate KIF1C's abundance, distribution, or ability traffic other mRNAs. Conversely, protrusions directed used mass spectrometry identify binding partners endogenous KIF1C, revealed dramatic dysregulation number identity interactors response mislocalization. These results therefore uncovered mechanistic connection between specificity protein–protein interactions. anticipate mechanism limited likely be general principle impacts functions proteins protrusion-enriched cells.

Language: Английский

Citations

12
The role of midbody-associated mRNAs in regulating abscission DOI Creative Commons
Trey Farmer, Katherine F. Vaeth,

Ke-Jun Han

et al.

The Journal of Cell Biology, Journal Year: 2023, Volume and Issue: 222(12)

Published: Nov. 3, 2023

Midbodies function during telophase to regulate the abscission step of cytokinesis. Until recently, it was thought that abscission-regulating proteins, such as ESCRT-III complex subunits, accumulate at MB by directly or indirectly binding resident protein, CEP55. However, recent studies have shown depletion CEP55 does not fully block targeting MB. Here, we show MBs contain mRNAs and these MB-associated can be locally translated, resulting in accumulation proteins. We demonstrate localized translation CHMP4B is required for its site 3′ UTR-dependent mRNA successful completion Finally, identify regulatory cis-elements within RNAs are necessary sufficient trafficking propose a novel method regulating cytokinesis selective mRNAs.

Language: Английский

Citations

11
A KIF1C-CNBP motor-adaptor complex for trafficking mRNAs to cell protrusions DOI Creative Commons
Konstadinos Moissoglu, Tianhong Wang, Alexander N. Gasparski

et al.

Cell Reports, Journal Year: 2025, Volume and Issue: 44(3), P. 115346 - 115346

Published: Feb. 20, 2025

Language: Английский

Citations

0
Pumilio differentially binds to mRNA 3′ UTR isoforms to regulate localization of synaptic proteins DOI Creative Commons
Dominika Grzejda, Andreas Heß,

Andrew Rezansoff

et al.

EMBO Reports, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 21, 2025

Language: Английский

Citations

0
Quantification of subcellular RNA localization through direct detection of RNA oxidation DOI Creative Commons
Hei‐Yong G. Lo, Raeann Goering, Agnese Kocere

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(5)

Published: Feb. 12, 2025

Across cell types and organisms, thousands of RNAs display asymmetric subcellular distributions. Studying this process 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 often 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 analyzing across different biological systems.

Language: Английский

Citations

0