CoLoC-seq probes the global topology of organelle transcriptomes DOI Creative Commons

Damien Jeandard,

Anna Smirnova, Akinyemi M. Fasemore

et al.

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(3), P. e16 - e16

Published: Dec. 20, 2022

Abstract Proper RNA localisation is essential for physiological gene expression. Various kinds of genome-wide approaches permit to comprehensively profile subcellular transcriptomes. Among them, cell fractionation methods, that couple RNase treatment isolated organelles the sequencing protected transcripts, remain most widely used, mainly because they do not require genetic modification studied system and can be easily implemented in any cells or tissues, including non-model species. However, suffer from numerous false-positives since incompletely digested contaminant RNAs still captured erroneously identified as resident transcripts. Here we introduce Controlled Level Contamination coupled deep (CoLoC-seq) a new transcriptomics approach efficiently bypasses this caveat. CoLoC-seq leverages classical enzymatic kinetics tracks depletion dynamics transcripts gradient an exogenously added RNase, with without organellar membranes. By means straightforward mathematical modelling, infers topology robustly distinguishes between genuinely resident, luminal merely abundant surface-attached contaminants. Our generic performed well on human mitochondria principle applicable other membrane-bounded organelles, plastids, compartments vacuolar system, extracellular vesicles, viral particles.

Language: Английский

Subcytoplasmic location of translation controls protein output DOI Creative Commons

Ellen L. Horste,

Mervin M. Fansler, Ting Cai

et al.

Molecular Cell, Journal Year: 2023, Volume and Issue: 83(24), P. 4509 - 4523.e11

Published: Dec. 1, 2023

The cytoplasm is highly compartmentalized, but the extent and consequences of subcytoplasmic mRNA localization in non-polarized cells are largely unknown. We determined enrichment TIS granules (TGs) rough endoplasmic reticulum (ER) through particle sorting isolated cytosolic mRNAs by digitonin extraction. When focusing on genes that encode non-membrane proteins, we observed 52% have transcripts enriched specific compartments. Compartment correlates with a combinatorial code based length, exon 3′ UTR-bound RNA-binding proteins. Compartment-biased differ functional classes their encoded proteins: TG-enriched low-abundance proteins strong transcription factors, whereas ER-enriched large expressed an important determinant protein abundance, which supported reporter experiments showing redirecting to ER increases expression. In summary, functionally compartmentalized local translation environments.

Language: Английский

Citations

29
Regulation and outcomes of localized RNA translation DOI Creative Commons
Alexander N. Gasparski, Devon E. Mason, Konstadinos Moissoglu

et al.

Wiley Interdisciplinary Reviews - RNA, Journal Year: 2022, Volume and Issue: 13(6)

Published: Feb. 14, 2022

Spatial segregation of mRNAs in the cytoplasm cells is a well-known biological phenomenon that widely observed diverse species spanning different kingdoms life. In mammalian cells, localization has been documented and studied quite extensively highly polarized most notably neurons, where localized function to direct protein production at sites are distant from soma. Recent studies have strikingly revealed large proportion cellular transcriptome exhibits distributions even lack an obvious need for long-range transport, such as fibroblasts or epithelial cells. This review focuses on emerging concepts regarding functional outcomes mRNA targeting We also discuss regulatory mechanisms controlling these events, with emphasis role cell mechanics organization cytoskeleton. article categorized under: Translation > Regulation RNA Export Localization Localization.

Language: Английский

Citations

30
The kinesin-3 KIF1C undergoes liquid-liquid phase separation for accumulation of specific transcripts at the cell periphery DOI Creative Commons
Qi Geng, Jakia Jannat Keya, Takashi Hotta

et al.

The EMBO Journal, Journal Year: 2024, Volume and Issue: 43(15), P. 3192 - 3213

Published: June 19, 2024

Language: Английский

Citations

7
Quantifying 3′UTR length from scRNA-seq data reveals changes independent of gene expression DOI Creative Commons
Mervin M. Fansler, Sibylle Mitschka, Christine Mayr

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 14, 2024

Abstract Although more than half of all genes generate transcripts that differ in 3′UTR length, current analysis pipelines only quantify the amount but not length mRNA transcripts. is determined by 3′ end cleavage sites (CS). We map CS 200 primary human and mouse cell types increase annotations relative to GENCODE database 40%. Approximately are used few types, revealing most have one or two major ends. incorporate into a computational pipeline, called scUTRquant, for rapid, accurate, simultaneous quantification gene isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant data 474 2134 perturbations, we discover extensive changes across as widespread coordinately regulated affect mostly different genes. Our indicate abundance largely independent axes regulation together determine spatial organization protein synthesis.

Language: Английский

Citations

6
mRNA location and translation rate determine protein targeting to dual destinations DOI Creative Commons
Alexander N. Gasparski, Konstadinos Moissoglu, Sandeep Pallikkuth

et al.

Molecular Cell, Journal Year: 2023, Volume and Issue: 83(15), P. 2726 - 2738.e9

Published: July 27, 2023

Numerous proteins are targeted to two or multiple subcellular destinations where they exert distinct functional consequences. The balance between such differential targeting is thought be determined post-translationally, relying on protein sorting mechanisms. Here, we show that mRNA location and translation rate can also determine by modulating binding specific interacting partners. Peripheral localization of the NET1 fast lead higher cytosolic retention promoting its membrane-associated scaffold CASK. By contrast, perinuclear and/or slower favor nuclear importins. This location-dependent mechanism modulated physiological stimuli profoundly impacts function in cell motility. These results reveal synthesis elongation act coordination as a "partner-selection" robustly influences distribution function.

Language: Английский

Citations

14
In situ visualization of m6A sites in cellular mRNAs DOI Creative Commons
Charles J. Sheehan,

Bahjat Fadi Marayati,

Janvi Bhatia

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(20), P. e101 - e101

Published: Oct. 9, 2023

N 6-methyladenosine (m6A) is an abundant RNA modification which plays critical roles in function and cellular physiology. However, our understanding of how m6A spatially regulated remains limited due to a lack methods for visualizing methylated transcripts interest cells. Here, we develop DART-FISH, method situ visualization specific sites target RNAs enables simultaneous detection both m6A-modified unmodified transcript copies. We demonstrate the ability DART-FISH visualize variety mRNAs across diverse cell types provide information on location stoichiometry at single-cell resolution. Finally, use reveal that not sufficient mRNA localization stress granules during oxidative stress. This technique provides powerful tool examining dynamics investigating individual

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
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
Local mRNA translation and cytoskeletal reorganization: Mechanisms that tune neuronal responses DOI Creative Commons
Nikoletta Triantopoulou, Marina Vidaki

Frontiers in Molecular Neuroscience, Journal Year: 2022, Volume and Issue: 15

Published: Aug. 1, 2022

Neurons are highly polarized cells with significantly long axonal and dendritic extensions that can reach distances up to hundreds of centimeters away from the cell bodies in higher vertebrates. Their successful formation, maintenance, proper function depend on coordination intricate molecular networks allow axons dendrites quickly process information, respond a continuous diverse cascade environmental stimuli, often without enough time for communication soma. Two seemingly unrelated processes, essential these rapid responses, thus neuronal homeostasis plasticity, local mRNA translation cytoskeletal reorganization. The cytoskeleton is characterized by high stability great plasticity; two contradictory attributes emerge powerful rearrangement dynamics. Cytoskeletal reorganization crucial during nervous system development adulthood, ensuring establishment shape polarity, as well regulating intracellular transport synaptic functions. Local another mechanism well-established role developing adult system. It pivotal guidance arborization, seems be key player processes activated after damage. Perturbations regulatory pathways contribute various pathologies clinical manifestations, ranging intellectual disabilities (ID) autism spectrum disorders (ASD) schizophrenia (SCZ). Despite fact both orchestration critical function, interplay between them remains elusive. Here we review our current knowledge mechanisms specific interaction regulate potentially coordinate interconnected processes.

Language: Английский

Citations

11
Analgesic targets identified in mouse sensory neuron somata and terminal pain translatomes DOI Creative Commons
Muhammad Bangash, Cankut Çubuk, Federico Iseppon

et al.

Cell Reports, Journal Year: 2024, Volume and Issue: 43(8), P. 114614 - 114614

Published: Aug. 1, 2024

The relationship between transcription and protein expression is complex. We identified polysome-associated RNA transcripts in the somata central terminals of mouse sensory neurons control, painful (plus nerve growth factor), pain-free conditions (Nav1.7-null mice). majority (98%) translated are shared male female mice both terminals. Some highly enriched or Changes translatome include novel known regulators pain pathways. Antisense knockdown selected somatic terminal that correlate with states diminished behavior. Terminal-enriched included those encoding synaptic proteins (e.g., synaptotagmin), non-coding RNAs, factors Znf431), associated transsynaptic trafficking (HoxC9), GABA-generating enzymes (Gad1 Gad2), neuropeptides (Penk). Thus, translation may well be a significant regulatory locus for peripheral input from neurons.

Language: Английский

Citations

2