-
Clinical Epigenetics Oct 2023Multiple mechanisms are involved in kidney damage, among which the role of epigenetic modifications in the occurrence and development of kidney diseases is constantly... (Review)
Review
Multiple mechanisms are involved in kidney damage, among which the role of epigenetic modifications in the occurrence and development of kidney diseases is constantly being revealed. However, N6-methyladenosine (M6A), a well-known post-transcriptional modification, has been regarded as the most prevalent epigenetic modifications in higher eukaryotic, which is involved in various biological processes of cells such as maintaining the stability of mRNA. The role of M6A modification in the mechanism of kidney damage has attracted widespread attention. In this review, we mainly summarize the role of M6A modification in the progression of kidney diseases from the following aspects: the regulatory pattern of N6-methyladenosine, the critical roles of N6-methyladenosine in chronic kidney disease, acute kidney injury and renal cell carcinoma, and then reveal its potential significance in the diagnosis and treatment of various kidney diseases. A better understanding of this field will be helpful for future research and clinical treatment of kidney diseases.
Topics: Humans; DNA Methylation; RNA, Messenger; Kidney; Kidney Diseases
PubMed: 37865763
DOI: 10.1186/s13148-023-01586-7 -
Science (New York, N.Y.) Jun 2023A new method maps the location of thousands of translating RNAs in cells and tissues.
A new method maps the location of thousands of translating RNAs in cells and tissues.
Topics: Gene Expression Regulation; Protein Biosynthesis; RNA, Messenger; Gene Expression Profiling
PubMed: 37384700
DOI: 10.1126/science.adi6844 -
Small (Weinheim An Der Bergstrasse,... Oct 2023Lipid nanoparticles (LNPs) and ribonucleic acid (RNA) technology are highly versatile tools that can be deployed for diagnostic, prophylactic, and therapeutic...
Lipid nanoparticles (LNPs) and ribonucleic acid (RNA) technology are highly versatile tools that can be deployed for diagnostic, prophylactic, and therapeutic applications. In this report, supramolecular chemistry concepts are incorporated into the rational design of a new ionizable lipid, C3-K2-E14, for systemic administration. This lipid incorporates a cone-shaped structure intended to facilitate cell bilayer disruption, and three tertiary amines to improve RNA binding. Additionally, hydroxyl and amide motifs are incorporated to further enhance RNA binding and improve LNP stability. Optimization of messenger RNA (mRNA) and small interfering RNA (siRNA) formulation conditions and lipid ratios produce LNPs with favorable diameter (<150 nm), polydispersity index (<0.15), and RNA encapsulation efficiency (>90%), all of which are preserved after 2 months at 4 or 37 °C storage in ready-to-use liquid form. The lipid and formulated LNPs are well-tolerated in animals and show no deleterious material-induced effects. Furthermore, 1 week after intravenous LNP administration, fluorescent signal from tagged RNA payloads are not detected. To demonstrate the long-term treatment potential for chronic diseases, repeated dosing of C3-K2-E14 LNPs containing siRNA that silences the colony stimulating factor-1 (CSF-1) gene can modulate leukocyte populations in vivo, further highlighting utility.
Topics: Animals; RNA, Small Interfering; RNA, Messenger; Nanoparticles; Lipids
PubMed: 37312676
DOI: 10.1002/smll.202302917 -
Nature Chemistry Sep 2023The presence of a hydroxyl group at the 2'-position in its ribose makes RNA susceptible to hydrolysis. Stabilization of RNAs for storage, transport and biological...
The presence of a hydroxyl group at the 2'-position in its ribose makes RNA susceptible to hydrolysis. Stabilization of RNAs for storage, transport and biological application thus remains a serious challenge, particularly for larger RNAs that are not accessible by chemical synthesis. Here we present reversible 2'-OH acylation as a general strategy to preserve RNA of any length or origin. High-yield polyacylation of 2'-hydroxyls ('cloaking') by readily accessible acylimidazole reagents effectively shields RNAs from both thermal and enzymatic degradation. Subsequent treatment with water-soluble nucleophilic reagents removes acylation adducts quantitatively ('uncloaking') and recovers a remarkably broad range of RNA functions, including reverse transcription, translation and gene editing. Furthermore, we show that certain α-dimethylamino- and α-alkoxy- acyl adducts are spontaneously removed in human cells, restoring messenger RNA translation with extended functional half-lives. These findings support the potential of reversible 2'-acylation as a simple and general molecular solution for enhancing RNA stability and provide mechanistic insights for stabilizing RNA regardless of length or origin.
Topics: Humans; RNA; Proteins; Water; Acylation; RNA, Messenger; Indicators and Reagents
PubMed: 37365334
DOI: 10.1038/s41557-023-01246-6 -
Journal of Genetics and Genomics = Yi... Apr 2024Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including... (Review)
Review
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
Topics: Ribosomes; Proteins; RNA, Messenger; Peptides; Gene Expression Regulation; Protein Biosynthesis
PubMed: 37536497
DOI: 10.1016/j.jgg.2023.07.009 -
Nucleic Acids Research Nov 2023N 6-methyladenosine (m6A) is an abundant RNA modification which plays critical roles in RNA function and cellular physiology. However, our understanding of how m6A is...
N 6-methyladenosine (m6A) is an abundant RNA modification which plays critical roles in RNA function and cellular physiology. However, our understanding of how m6A is spatially regulated remains limited due to a lack of methods for visualizing methylated transcripts of interest in cells. Here, we develop DART-FISH, a method for in situ visualization of specific m6A sites in target RNAs which enables simultaneous detection of both m6A-modified and unmodified transcript copies. We demonstrate the ability of DART-FISH to visualize m6A in a variety of mRNAs across diverse cell types and to provide information on the location and stoichiometry of m6A sites at single-cell resolution. Finally, we use DART-FISH to reveal that m6A is not sufficient for mRNA localization to stress granules during oxidative stress. This technique provides a powerful tool for examining m6A-modified transcript dynamics and investigating methylated RNA localization in individual cells.
Topics: RNA; RNA, Messenger; RNA Processing, Post-Transcriptional; In Situ Hybridization, Fluorescence
PubMed: 37811887
DOI: 10.1093/nar/gkad787 -
Annual Review of Virology Sep 2023Protein synthesis by the ribosome is the final stage of biological information transfer and represents an irreversible commitment to gene expression. Accurate... (Review)
Review
Protein synthesis by the ribosome is the final stage of biological information transfer and represents an irreversible commitment to gene expression. Accurate translation of messenger RNA is therefore essential to all life, and spontaneous errors by the translational machinery are highly infrequent (∼1/100,000 codons). Programmed -1 ribosomal frameshifting (-1PRF) is a mechanism in which the elongating ribosome is induced at high frequency to slip backward by one nucleotide at a defined position and to continue translation in the new reading frame. This is exploited as a translational regulation strategy by hundreds of RNA viruses, which rely on -1PRF during genome translation to control the stoichiometry of viral proteins. While early investigations of -1PRF focused on virological and biochemical aspects, the application of X-ray crystallography and cryo-electron microscopy (cryo-EM), and the advent of deep sequencing and single-molecule approaches have revealed unexpected structural diversity and mechanistic complexity. Molecular players from several model systems have now been characterized in detail, both in isolation and, more recently, in the context of the elongating ribosome. Here we provide a summary of recent advances and discuss to what extent a general model for -1PRF remains a useful way of thinking.
Topics: Frameshifting, Ribosomal; Cryoelectron Microscopy; Ribosomes; RNA, Messenger; RNA Viruses; RNA, Viral
PubMed: 37339768
DOI: 10.1146/annurev-virology-111821-120646 -
Chaos (Woodbury, N.Y.) Apr 2024Two well-known facets in protein synthesis in eukaryotic cells are transcription of DNA to pre-RNA in the nucleus and the translation of messenger-RNA (mRNA) to proteins...
Two well-known facets in protein synthesis in eukaryotic cells are transcription of DNA to pre-RNA in the nucleus and the translation of messenger-RNA (mRNA) to proteins in the cytoplasm. A critical intermediate step is the removal of segments (introns) containing ∼97% of the nucleic-acid sites in pre-RNA and sequential alignment of the retained segments (exons) to form mRNA through a process referred to as splicing. Alternative forms of splicing enrich the proteome while abnormal splicing can enhance the likelihood of a cell developing cancer or other diseases. Mechanisms for splicing and origins of splicing errors are only partially deciphered. Our goal is to determine if rules on splicing can be inferred from data analytics on nucleic-acid sequences. Toward that end, we represent a nucleic-acid site as a point in a plane defined in terms of the anterior and posterior sub-sequences of the site. The "point-set" representation expands analytical approaches, including the use of statistical tools, to characterize genome sequences. It is found that point-sets for exons and introns are visually different, and that the differences can be quantified using a family of generalized moments. We design a machine-learning algorithm that can recognize individual exons or introns with 91% accuracy. Point-set distributions and generalized moments are found to differ between organisms.
Topics: RNA Splicing; Introns; RNA; RNA, Messenger; Exons
PubMed: 38579148
DOI: 10.1063/5.0199364 -
ELife Feb 2024A new in vitro system called Rec-Seq sheds light on how mRNA molecules compete for the machinery that translates their genetic sequence into proteins.
A new in vitro system called Rec-Seq sheds light on how mRNA molecules compete for the machinery that translates their genetic sequence into proteins.
Topics: Protein Biosynthesis; Ribosomes; RNA, Messenger
PubMed: 38393777
DOI: 10.7554/eLife.96304 -
Science China. Life Sciences Dec 2023Primary open-angle glaucoma (POAG) is a prevalent cause of blindness worldwide, resulting in degeneration of retinal ganglion cells and permanent damage to the optic...
Primary open-angle glaucoma (POAG) is a prevalent cause of blindness worldwide, resulting in degeneration of retinal ganglion cells and permanent damage to the optic nerve. However, the underlying pathogenetic mechanisms of POAG are currently indistinct, and there has been no effective nonsurgical treatment regimen. The objective of this study is to identify novel biomarkers and potential therapeutic targets for POAG. The mRNA expression microarray datasets GSE27276 and GSE138125, as well as the single-cell high-throughput RNA sequencing (scRNA-seq) dataset GSE148371 were utilized to screen POAG-related differentially expressed genes (DEGs). Functional enrichment analyses, protein-protein interaction (PPI) analysis, and weighted gene co-expression network analysis (WGCNA) of the DEGs were performed. Subsequently, the hub genes were validated at a single-cell level, where trabecular cells were annotated, and the mRNA expression levels of target genes in different cell clusters were analyzed. Immunofluorescence and quantitative real-time PCR (qPCR) were performed for further validation. DEGs analysis identified 43 downregulated and 32 upregulated genes in POAG, which were mainly enriched in immune-related pathways, oxidative stress, and endoplasmic reticulum (ER) stress. PPI networks showed that FN1 and DUSP1 were the central hub nodes, while GPX3 and VAV3 were screened out as hub genes through WGCNA and subsequently validated by qPCR. Finally, FN1, GPX3, and VAV3 were determined to be pivotal core genes via single-cell validation. The relevant biomarkers involved in the pathogenesis of POAG, may serve as potential therapeutic targets. Further studies are necessary to unveil the mechanisms underlying the expression variations of these genes in POAG.
Topics: Humans; Glaucoma, Open-Angle; Biomarkers; Gene Expression Profiling; RNA, Messenger
PubMed: 37610681
DOI: 10.1007/s11427-022-2344-5