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The Journal of Cell Biology Feb 2021Subcellular localization of RNAs has gained attention in recent years as a prevalent phenomenon that influences numerous cellular processes. This is also evident for the... (Review)
Review
Subcellular localization of RNAs has gained attention in recent years as a prevalent phenomenon that influences numerous cellular processes. This is also evident for the large and relatively novel class of long noncoding RNAs (lncRNAs). Because lncRNAs are defined as RNA transcripts >200 nucleotides that do not encode protein, they are themselves the functional units, making their subcellular localization critical to their function. The discovery of tens of thousands of lncRNAs and the cumulative evidence involving them in almost every cellular activity render assessment of their subcellular localization essential to fully understanding their biology. In this review, we summarize current knowledge of lncRNA subcellular localization, factors controlling their localization, emerging themes, including the role of lncRNA isoforms and the involvement of lncRNAs in phase separation bodies, and the implications of lncRNA localization on their function and on cellular behavior. We also discuss gaps in the current knowledge as well as opportunities that these provide for novel avenues of investigation.
Topics: Animals; Cell Membrane; Humans; Organelles; RNA Transport; RNA, Long Noncoding
PubMed: 33464299
DOI: 10.1083/jcb.202009045 -
Nature Reviews. Molecular Cell Biology Jul 2021Fine-tuning cellular physiology in response to intracellular and environmental cues requires precise temporal and spatial control of gene expression. High-resolution... (Review)
Review
Fine-tuning cellular physiology in response to intracellular and environmental cues requires precise temporal and spatial control of gene expression. High-resolution imaging technologies to detect mRNAs and their translation state have revealed that all living organisms localize mRNAs in subcellular compartments and create translation hotspots, enabling cells to tune gene expression locally. Therefore, mRNA localization is a conserved and integral part of gene expression regulation from prokaryotic to eukaryotic cells. In this Review, we discuss the mechanisms of mRNA transport and local mRNA translation across the kingdoms of life and at organellar, subcellular and multicellular resolution. We also discuss the properties of messenger ribonucleoprotein and higher order RNA granules and how they may influence mRNA transport and local protein synthesis. Finally, we summarize the technological developments that allow us to study mRNA localization and local translation through the simultaneous detection of mRNAs and proteins in single cells, mRNA and nascent protein single-molecule imaging, and bulk RNA and protein detection methods.
Topics: Animals; Cytoplasmic Granules; Gene Expression Regulation; Humans; Protein Biosynthesis; RNA Transport; RNA, Messenger; Ribonucleoproteins
PubMed: 33837370
DOI: 10.1038/s41580-021-00356-8 -
Molecular Cancer Oct 2018Exosomes, extracellular vesicles with diameters ranging from 30 to 150 nm, are widely present in various body fluids. Recently, microRNAs (miRNAs) have been identified... (Review)
Review
Exosomes, extracellular vesicles with diameters ranging from 30 to 150 nm, are widely present in various body fluids. Recently, microRNAs (miRNAs) have been identified in exosomes, the biogenesis, release, and uptake of which may involve the endosomal sorting complex required for transport (ESCRT complex) and relevant proteins. After release, exosomes are taken up by neighboring or distant cells, and the miRNAs contained within modulate such processes as interfering with tumor immunity and the microenvironment, possibly facilitating tumor growth, invasion, metastasis, angiogenesis and drug resistance. Therefore, exosomal miRNAs have a significant function in regulating cancer progression. Here, we briefly review recent findings regarding tumor-derived exosomes, including RNA sorting and delivering mechanism. We then describe the intercommunication occurring between different cells via exosomal miRNAs in tumor microenvironmnt, with impacts on tumor proliferation, vascularization, metastasis and other biological characteristics. Finally, we highlight the potential role of these molecules as biomarkers in cancer diagnosis and prognosis and tumor resistance to therapeutics.
Topics: Biomarkers; Cancer-Associated Fibroblasts; Exosomes; Extracellular Matrix; Humans; MicroRNAs; Neoplasms; Prognosis; RNA Transport; Signal Transduction
PubMed: 30309355
DOI: 10.1186/s12943-018-0897-7 -
Cell Dec 2020RNA viruses are among the most prevalent pathogens and are a major burden on society. Although RNA viruses have been studied extensively, little is known about the...
RNA viruses are among the most prevalent pathogens and are a major burden on society. Although RNA viruses have been studied extensively, little is known about the processes that occur during the first several hours of infection because of a lack of sensitive assays. Here we develop a single-molecule imaging assay, virus infection real-time imaging (VIRIM), to study translation and replication of individual RNA viruses in live cells. VIRIM uncovered a striking heterogeneity in replication dynamics between cells and revealed extensive coordination between translation and replication of single viral RNAs. Furthermore, using VIRIM, we identify the replication step of the incoming viral RNA as a major bottleneck of successful infection and identify host genes that are responsible for inhibition of early virus replication. Single-molecule imaging of virus infection is a powerful tool to study virus replication and virus-host interactions that may be broadly applicable to RNA viruses.
Topics: Cell Line, Tumor; Cell Survival; HEK293 Cells; Host-Pathogen Interactions; Humans; Interferons; Protein Biosynthesis; RNA Transport; RNA Viruses; RNA, Viral; Reproducibility of Results; Single Molecule Imaging; Time Factors; Virus Replication
PubMed: 33188777
DOI: 10.1016/j.cell.2020.10.019 -
Cell Research May 20175-methylcytosine (mC) is a post-transcriptional RNA modification identified in both stable and highly abundant tRNAs and rRNAs, and in mRNAs. However, its regulatory...
5-methylcytosine (mC) is a post-transcriptional RNA modification identified in both stable and highly abundant tRNAs and rRNAs, and in mRNAs. However, its regulatory role in mRNA metabolism is still largely unknown. Here, we reveal that mC modification is enriched in CG-rich regions and in regions immediately downstream of translation initiation sites and has conserved, tissue-specific and dynamic features across mammalian transcriptomes. Moreover, mC formation in mRNAs is mainly catalyzed by the RNA methyltransferase NSUN2, and mC is specifically recognized by the mRNA export adaptor ALYREF as shown by in vitro and in vivo studies. NSUN2 modulates ALYREF's nuclear-cytoplasmic shuttling, RNA-binding affinity and associated mRNA export. Dysregulation of ALYREF-mediated mRNA export upon NSUN2 depletion could be restored by reconstitution of wild-type but not methyltransferase-defective NSUN2. Our study provides comprehensive mC profiles of mammalian transcriptomes and suggests an essential role for mC modification in mRNA export and post-transcriptional regulation.
Topics: 5-Methylcytosine; Amino Acid Sequence; Base Sequence; HeLa Cells; Humans; Male; Methyltransferases; Models, Biological; Nuclear Proteins; Organ Specificity; Protein Binding; RNA Transport; RNA, Messenger; RNA-Binding Proteins; Testis; Transcription Factors
PubMed: 28418038
DOI: 10.1038/cr.2017.55 -
Neuron Mar 2023Localized mRNA translation regulates synapse function and axon maintenance, but how compartment-specific mRNA repertoires are regulated is largely unknown. We developed...
Localized mRNA translation regulates synapse function and axon maintenance, but how compartment-specific mRNA repertoires are regulated is largely unknown. We developed an axonal transcriptome capture method that allows deep sequencing of metabolically labeled mRNAs from retinal ganglion cell axon terminals in mouse. Comparing axonal-to-somal transcriptomes and axonal translatome-to-transcriptome enables genome-wide visualization of mRNA transport and translation and unveils potential regulators tuned to each process. FMRP and TDP-43 stand out as key regulators of transport, and experiments in Fmr1 knockout mice validate FMRP's role in the axonal transportation of synapse-related mRNAs. Pulse-and-chase experiments enable genome-wide assessment of mRNA stability in axons and reveal a strong coupling between mRNA translation and decay. Measuring the absolute mRNA abundance per axon terminal shows that the adult axonal transcriptome is stably maintained by persistent transport. Our datasets provide a rich resource for unique insights into RNA-based mechanisms in maintaining presynaptic structure and function in vivo.
Topics: Animals; Mice; Axons; Central Nervous System; Fragile X Mental Retardation Protein; Mammals; RNA; RNA Transport; RNA, Messenger
PubMed: 36584679
DOI: 10.1016/j.neuron.2022.12.015 -
Cell Dec 2020Cellular stress leads to reprogramming of mRNA translation and formation of stress granules (SGs), membraneless organelles consisting of mRNA and RNA-binding proteins....
Cellular stress leads to reprogramming of mRNA translation and formation of stress granules (SGs), membraneless organelles consisting of mRNA and RNA-binding proteins. Although the function of SGs remains largely unknown, it is widely assumed they contain exclusively non-translating mRNA. Here, we re-examine this hypothesis using single-molecule imaging of mRNA translation in living cells. Although we observe non-translating mRNAs are preferentially recruited to SGs, we find unequivocal evidence that mRNAs localized to SGs can undergo translation. Our data indicate that SG-associated translation is not rare, and the entire translation cycle (initiation, elongation, and termination) can occur on SG-localized transcripts. Furthermore, translating mRNAs can be observed transitioning between the cytosol and SGs without changing their translational status. Together, these results demonstrate that mRNA localization to SGs is compatible with translation and argue against a direct role for SGs in inhibition of protein synthesis.
Topics: Activating Transcription Factor 4; Cytoplasmic Granules; Cytosol; HeLa Cells; Humans; Open Reading Frames; Protein Biosynthesis; RNA Transport; RNA, Messenger; Single Molecule Imaging; Stress, Physiological
PubMed: 33308477
DOI: 10.1016/j.cell.2020.11.010 -
Nature Neuroscience May 2021Neurons decentralize protein synthesis from the cell body to support the active metabolism of remote dendritic and axonal compartments. The neuronal RNA transport... (Review)
Review
Neurons decentralize protein synthesis from the cell body to support the active metabolism of remote dendritic and axonal compartments. The neuronal RNA transport apparatus, composed of cis-acting RNA regulatory elements, neuronal transport granule proteins, and motor adaptor complexes, drives the long-distance RNA trafficking required for local protein synthesis. Over the past decade, advances in human genetics, subcellular biochemistry, and high-resolution imaging have implicated each member of the apparatus in several neurodegenerative diseases, establishing failed RNA transport and associated processes as a unifying pathomechanism. In this review, we deconstruct the RNA transport apparatus, exploring each constituent's role in RNA localization and illuminating their unique contributions to neurodegeneration.
Topics: Animals; Biological Transport; Brain; Humans; Neurodegenerative Diseases; Neurodevelopmental Disorders; Neurons; Protein Biosynthesis; RNA Transport
PubMed: 33510479
DOI: 10.1038/s41593-020-00785-2 -
Cell Research Mar 2021Dietary microRNAs have been shown to be absorbed by mammals and regulate host gene expression, but the absorption mechanism remains unknown. Here, we show that SIDT1...
Dietary microRNAs have been shown to be absorbed by mammals and regulate host gene expression, but the absorption mechanism remains unknown. Here, we show that SIDT1 expressed on gastric pit cells in the stomach is required for the absorption of dietary microRNAs. SIDT1-deficient mice show reduced basal levels and impaired dynamic absorption of dietary microRNAs. Notably, we identified the stomach as the primary site for dietary microRNA absorption, which is dramatically attenuated in the stomachs of SIDT1-deficient mice. Mechanistic analyses revealed that the uptake of exogenous microRNAs by gastric pit cells is SIDT1 and low-pH dependent. Furthermore, oral administration of plant-derived miR2911 retards liver fibrosis, and this protective effect was abolished in SIDT1-deficient mice. Our findings reveal a major mechanism underlying the absorption of dietary microRNAs, uncover an unexpected role of the stomach and shed light on developing small RNA therapeutics by oral delivery.
Topics: Administration, Oral; Animals; Diet; Female; Gastric Absorption; HEK293 Cells; Hep G2 Cells; Humans; Male; Membrane Transport Proteins; Mice; Mice, Inbred C57BL; Mice, Knockout; MicroRNAs; RNA Transport; RNA, Plant; Stomach
PubMed: 32801357
DOI: 10.1038/s41422-020-0389-3 -
Microbiology Spectrum Sep 2018Diverse mechanisms and functions of posttranscriptional regulation by small regulatory RNAs and RNA-binding proteins have been described in bacteria. In contrast, little... (Review)
Review
Diverse mechanisms and functions of posttranscriptional regulation by small regulatory RNAs and RNA-binding proteins have been described in bacteria. In contrast, little is known about the spatial organization of RNAs in bacterial cells. In eukaryotes, subcellular localization and transport of RNAs play important roles in diverse physiological processes, such as embryonic patterning, asymmetric cell division, epithelial polarity, and neuronal plasticity. It is now clear that bacterial RNAs also can accumulate at distinct sites in the cell. However, due to the small size of bacterial cells, RNA localization and localization-associated functions are more challenging to study in bacterial cells, and the underlying molecular mechanisms of transcript localization are less understood. Here, we review the emerging examples of RNAs localized to specific subcellular locations in bacteria, with indications that subcellular localization of transcripts might be important for gene expression and regulatory processes. Diverse mechanisms for bacterial RNA localization have been suggested, including close association to their genomic site of transcription, or to the localizations of their protein products in translation-dependent or -independent processes. We also provide an overview of the state of the art of technologies to visualize and track bacterial RNAs, ranging from hybridization-based approaches in fixed cells to imaging approaches using fluorescent protein reporters and/or RNA aptamers in single living bacterial cells. We conclude with a discussion of open questions in the field and ongoing technological developments regarding RNA imaging in eukaryotic systems that might likewise provide novel insights into RNA localization in bacteria.
Topics: Aptamers, Nucleotide; Bacteria; Bacterial Proteins; Fluorescent Dyes; Gene Expression Regulation, Bacterial; Green Fluorescent Proteins; In Situ Hybridization, Fluorescence; Microscopy, Fluorescence; Molecular Imaging; Protein Transport; RNA Transport; RNA, Bacterial; RNA-Binding Proteins; Recombinant Fusion Proteins; Ribonucleases; Staining and Labeling; Transcription, Genetic
PubMed: 30191804
DOI: 10.1128/microbiolspec.RWR-0024-2018