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

The Roles of Drug Metabolism-Related ADH1B in Immune Regulation and Therapeutic Response of Ovarian Cancer DOI Creative Commons
Zhijie Xu, Bi Peng,

Fanhua Kang

et al.

Frontiers in Cell and Developmental Biology, Journal Year: 2022, Volume and Issue: 10

Published: June 9, 2022

Background: The different pharmacological effects of drugs in people can be explained by the polymorphisms drug metabolism-related genes. Emerging studies have realized importance genes treatment and prognosis cancers, including ovarian cancer (OV). In this study, using comprehensive bioinformatics western blot, we identified that gene, ADH1B, was significantly down-regulated OV cells tissues. patients with a high level ADH1B presented good prognosis. We also found negative correlation between expression activity chemotherapeutic agents, such as cyclophosphamide. addition, positive correlations were observed multiple immune checkpoints, LAG3 HAVCR2. infiltration analysis further indicated aberrantly expressed might important roles regulating macrophages neutrophils Then, co-expression conducted top three enriched KEGG pathways spliceosome, RNA transport, DNA replication. conclusion, gene its interactive network play an essential role regulation therapeutic response maybe promising targets for patients.

Language: Английский

Citations

11
Identifying mRNAs Residing in Myelinating Oligodendrocyte Processes as a Basis for Understanding Internode Autonomy DOI Creative Commons
Robert M. Gould, Scott T. Brady

Life, Journal Year: 2023, Volume and Issue: 13(4), P. 945 - 945

Published: April 4, 2023

In elaborating and maintaining myelin sheaths on multiple axons/segments, oligodendrocytes distribute translation of some proteins, including basic protein (MBP), to sites sheath assembly, or MSAS. As mRNAs located at these are selectively trapped in vesicles during tissue homogenization, we performed a screen identify mRNAs. To confirm locations, used real-time quantitative polymerase chain reaction (RT-qPCR), measure mRNA levels (M) 'non-myelin' pellet (P) fractions, found that five (

Language: Английский

Citations

4
Advances and opportunities in methods to study protein translation - A review DOI

Dejiu Zhang,

Yanyan Gao, Lei Zhu

et al.

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: 259, P. 129150 - 129150

Published: Jan. 1, 2024

Language: Английский

Citations

1
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
Orchestrated centers for the production of proteins or “translation factories” DOI Creative Commons
Robert A. Crawford, Matthew Eastham, Martin Pool

et al.

Wiley Interdisciplinary Reviews - RNA, Journal Year: 2024, Volume and Issue: 15(4)

Published: July 1, 2024

The mechanics of how proteins are generated from mRNA is increasingly well understood. However, much less known about protein production coordinated and orchestrated within the crowded intracellular environment, especially in eukaryotic cells. Recent studies suggest that localized sites exist for specific proteins. These have been termed "translation factories" roles complex formation, localization, inheritance, translation regulation postulated. In this article, we review evidence supporting at these sites, details their mechanism likely functional significance. Finally, consider key uncertainties regarding elusive structures This article categorized under: Translation > Mechanisms RNA Export Localization Regulation.

Language: Английский

Citations

1
Centrocortin potentiates co-translational localization of its mRNA to the centrosome via dynein DOI Creative Commons

Hala Zein-Sabatto,

Jovan S. Brockett, Li Jin

et al.

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

Published: Aug. 9, 2024

Abstract Centrosomes rely upon proteins within the pericentriolar material to nucleate and organize microtubules. Several mRNAs also reside at centrosomes, although less is known about how why they accumulate there. We previously showed that local Centrocortin ( Cen ) mRNA supports centrosome separation, microtubule organization, viability in Drosophila embryos. Here, using as a model, we examine mechanisms of centrosomal localization. find while N’-terminus sufficient for protein enrichment multiple domains cooperate concentrate this location. further identify an N’-terminal motif conserved among dynein cargo adaptor test its contribution RNA Our results support model whereby enables accumulation own centrosomes through mechanism requiring active translation, microtubules, motor complex. Taken together, our data uncover basis translation-dependent localization required mitotic integrity. Summary Enrichment fidelity. This study describes underlying co-translational targeting involving motor, highly binding coding sequence.

Language: Английский

Citations

1
Detection and Automated Quantification of Nucleocytoplasmic RNA Fractions in Arabidopsis Using smFISH DOI
Alejandro Fonseca, Stefanie Rosa

Methods in molecular biology, Journal Year: 2024, Volume and Issue: unknown, P. 187 - 203

Published: Nov. 22, 2024

Language: Английский

Citations

1
Vasa, a regulator of localized mRNA translation on the spindle DOI Creative Commons

Paola Alejandra Sundaram Buitrago,

Kavya Rao, Mamiko Yajima

et al.

BioEssays, Journal Year: 2023, Volume and Issue: 45(4)

Published: Feb. 24, 2023

Localized mRNA translation is a biological process that allows to be translated on-site, which proposed provide fine control in protein regulation, both spatially and temporally within cell. We recently reported Vasa, an RNA-helicase, promising factor appears regulate this on the spindle during embryonic development of sea urchin, yet detailed roles functional mechanisms Vasa are still largely unknown. In review article, elucidate these remaining questions, we first summarize prior knowledge our recent findings area research further discuss how may function localized translation, contributing efficient regulation rapid embryogenesis cancer cell regulation.

Language: Английский

Citations

3
Is there a localized role for translational quality control? DOI Open Access

Sezen Meydan,

Nicholas R. Guydosh

RNA, Journal Year: 2023, Volume and Issue: 29(11), P. 1623 - 1643

Published: Aug. 15, 2023

It is known that mRNAs and the machinery translates them are not uniformly distributed throughout cytoplasm. As a result, expression of some genes localized to particular parts cell this makes it possible carry out important activities, such as growth signaling, in three-dimensional space. However, functions gene fully understood, underlying mechanisms enable have been determined many cases. One consideration could help addressing these challenges role quality control (QC) monitor translating ribosomes. On global level, QC pathways critical for detecting aberrant translation events, ribosome stalls while translating, responding by activating stress resolving problematic ribosomes at molecular level. unclear how pathways, even when active cell, affect local translation. Importantly, themselves reported be enriched proximity organelles, but extent activity remains largely unknown. Here, we describe major review studies begun explore their roles Given limited data area, also pose broad questions about possibilities limitations facilitate with goal offering ideas future experimentation.

Language: Английский

Citations

3
mRNA Location and Translation Rate Determine Protein Targeting to Dual Destinations DOI Open Access
Alexander N. Gasparski, Konstadinos Moissoglu, Sandeep Pallikkuth

et al.

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

Published: April 26, 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 can additionally by mRNA location and translation rate, through modulating binding specific interacting partners. Peripheral localization of the

Language: Английский

Citations

2