-
Nature Reviews. Genetics Nov 2019Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for transcriptome-wide analysis of differential gene expression and differential splicing... (Review)
Review
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for transcriptome-wide analysis of differential gene expression and differential splicing of mRNAs. However, as next-generation sequencing technologies have developed, so too has RNA-seq. Now, RNA-seq methods are available for studying many different aspects of RNA biology, including single-cell gene expression, translation (the translatome) and RNA structure (the structurome). Exciting new applications are being explored, such as spatial transcriptomics (spatialomics). Together with new long-read and direct RNA-seq technologies and better computational tools for data analysis, innovations in RNA-seq are contributing to a fuller understanding of RNA biology, from questions such as when and where transcription occurs to the folding and intermolecular interactions that govern RNA function.
Topics: Alternative Splicing; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; History, 21st Century; Humans; RNA, Messenger; Sequence Analysis, RNA
PubMed: 31341269
DOI: 10.1038/s41576-019-0150-2 -
Nature Nanotechnology Apr 2020CRISPR-Cas gene editing and messenger RNA-based protein replacement therapy hold tremendous potential to effectively treat disease-causing mutations with diverse...
CRISPR-Cas gene editing and messenger RNA-based protein replacement therapy hold tremendous potential to effectively treat disease-causing mutations with diverse cellular origin. However, it is currently impossible to rationally design nanoparticles that selectively target specific tissues. Here, we report a strategy termed selective organ targeting (SORT) wherein multiple classes of lipid nanoparticles are systematically engineered to exclusively edit extrahepatic tissues via addition of a supplemental SORT molecule. Lung-, spleen- and liver-targeted SORT lipid nanoparticles were designed to selectively edit therapeutically relevant cell types including epithelial cells, endothelial cells, B cells, T cells and hepatocytes. SORT is compatible with multiple gene editing techniques, including mRNA, Cas9 mRNA/single guide RNA and Cas9 ribonucleoprotein complexes, and is envisioned to aid the development of protein replacement and gene correction therapeutics in targeted tissues.
Topics: Animals; CRISPR-Cas Systems; Drug Delivery Systems; Gene Editing; Mice; Nanoparticles; Organ Specificity; RNA, Messenger
PubMed: 32251383
DOI: 10.1038/s41565-020-0669-6 -
Cold Spring Harbor Perspectives in... Oct 20193' untranslated regions (3' UTRs) of messenger RNAs (mRNAs) are best known to regulate mRNA-based processes, such as mRNA localization, mRNA stability, and translation.... (Review)
Review
3' untranslated regions (3' UTRs) of messenger RNAs (mRNAs) are best known to regulate mRNA-based processes, such as mRNA localization, mRNA stability, and translation. In addition, 3' UTRs can establish 3' UTR-mediated protein-protein interactions (PPIs), and thus can transmit genetic information encoded in 3' UTRs to proteins. This function has been shown to regulate diverse protein features, including protein complex formation or posttranslational modifications, but is also expected to alter protein conformations. Therefore, 3' UTR-mediated information transfer can regulate protein features that are not encoded in the amino acid sequence. This review summarizes both 3' UTR functions-the regulation of mRNA and protein-based processes-and highlights how each 3' UTR function was discovered with a focus on experimental approaches used and the concepts that were learned. This review also discusses novel approaches to study 3' UTR functions in the future by taking advantage of recent advances in technology.
Topics: 3' Untranslated Regions; Protein Binding; Protein Biosynthesis; RNA Stability; RNA, Messenger; RNA-Binding Proteins
PubMed: 30181377
DOI: 10.1101/cshperspect.a034728 -
Cold Spring Harbor Perspectives in... Feb 2019Nonsense-mediated mRNA decay (NMD) is arguably the best-studied eukaryotic messenger RNA (mRNA) surveillance pathway, yet fundamental questions concerning the molecular... (Review)
Review
Nonsense-mediated mRNA decay (NMD) is arguably the best-studied eukaryotic messenger RNA (mRNA) surveillance pathway, yet fundamental questions concerning the molecular mechanism of target RNA selection remain unsolved. Besides degrading defective mRNAs harboring premature termination codons (PTCs), NMD also targets many mRNAs encoding functional full-length proteins. Thus, NMD impacts on a cell's transcriptome and is implicated in a range of biological processes that affect a broad spectrum of cellular homeostasis. Here, we focus on the steps involved in the recognition of NMD targets and the activation of NMD. We summarize the accumulating evidence that tightly links NMD to translation termination and we further discuss the recruitment and activation of the mRNA degradation machinery and the regulation of this complex series of events. Finally, we review emerging ideas concerning the mechanistic details of NMD activation and the potential role of NMD as a general surveyor of translation efficacy.
Topics: Codon, Nonsense; Eukaryota; Nonsense Mediated mRNA Decay; Peptide Chain Termination, Translational; Protein Biosynthesis; RNA, Messenger
PubMed: 29891560
DOI: 10.1101/cshperspect.a032862 -
Nature Reviews. Genetics Oct 2020Gene expression involves transcription, translation and the turnover of mRNAs and proteins. The degree to which protein abundances scale with mRNA levels and the... (Review)
Review
Gene expression involves transcription, translation and the turnover of mRNAs and proteins. The degree to which protein abundances scale with mRNA levels and the implications in cases where this dependency breaks down remain an intensely debated topic. Here we review recent mRNA-protein correlation studies in the light of the quantitative parameters of the gene expression pathway, contextual confounders and buffering mechanisms. Although protein and mRNA levels typically show reasonable correlation, we describe how transcriptomics and proteomics provide useful non-redundant readouts. Integrating both types of data can reveal exciting biology and is an essential step in refining our understanding of the principles of gene expression control.
Topics: Computational Biology; Gene Expression Regulation; Humans; Protein Biosynthesis; Proteins; Proteome; RNA, Messenger; Transcriptome
PubMed: 32709985
DOI: 10.1038/s41576-020-0258-4 -
Human Vaccines & Immunotherapeutics Dec 2024The research and development of messenger RNA (mRNA) cancer vaccines have gradually overcome numerous challenges through the application of personalized cancer antigens,... (Review)
Review
The research and development of messenger RNA (mRNA) cancer vaccines have gradually overcome numerous challenges through the application of personalized cancer antigens, structural optimization of mRNA, and the development of alternative RNA-based vectors and efficient targeted delivery vectors. Clinical trials are currently underway for various cancer vaccines that encode tumor-associated antigens (TAAs), tumor-specific antigens (TSAs), or immunomodulators. In this paper, we summarize the optimization of mRNA and the emergence of RNA-based expression vectors in cancer vaccines. We begin by reviewing the advancement and utilization of state-of-the-art targeted lipid nanoparticles (LNPs), followed by presenting the primary classifications and clinical applications of mRNA cancer vaccines. Collectively, mRNA vaccines are emerging as a central focus in cancer immunotherapy, offering the potential to address multiple challenges in cancer treatment, either as standalone therapies or in combination with current cancer treatments.
Topics: Humans; Cancer Vaccines; mRNA Vaccines; Neoplasms; Antigens, Neoplasm; RNA, Messenger; RNA; Nanoparticles
PubMed: 38282471
DOI: 10.1080/21645515.2024.2307187 -
Cold Spring Harbor Protocols Jun 2019The polymerase chain reaction (PCR) underlies almost all of modern molecular cloning. Using PCR, a defined target sequence that occurs once within a DNA of high... (Review)
Review
The polymerase chain reaction (PCR) underlies almost all of modern molecular cloning. Using PCR, a defined target sequence that occurs once within a DNA of high complexity and large size-an entire mammalian genome, for example-can be rapidly and selectively amplified in a quasi-exponential chain reaction that generates millions of copies. The reaction is simple to set up, cheap, and undemanding, the only requirement being some knowledge of the nucleotide sequences of the target. In addition to its simplicity, PCR is robust, speedy, flexible, and sensitive.
Topics: DNA Contamination; DNA Primers; Oligonucleotides; Polymerase Chain Reaction; RNA, Messenger
PubMed: 31160389
DOI: 10.1101/pdb.top095109 -
Chemical Society Reviews May 2022The great success achieved by the two highly-effective messenger RNA (mRNA) vaccines during the COVID-19 pandemic highlights the great potential of mRNA technology.... (Review)
Review
The great success achieved by the two highly-effective messenger RNA (mRNA) vaccines during the COVID-19 pandemic highlights the great potential of mRNA technology. Through the evolution of mRNA technology, chemistry has played an important role from mRNA modification to the synthesis of mRNA delivery platforms, which allows various applications of mRNA to be achieved both and . In this tutorial review, we provide a summary and discussion on the significant progress of emerging mRNA technologies, as well as the underlying chemical designs and principles. Various nanoparticle (NP)-based delivery strategies including protein-mRNA complex, lipid-based carriers, polymer-based carriers, and hybrid carriers for the efficient delivery of mRNA molecules are presented. Furthermore, typical mRNA delivery platforms for various biomedical applications (, functional protein expression, vaccines, cancer immunotherapy, and genome editing) are highlighted. Finally, our insights into the challenges and future development towards clinical translation of these mRNA technologies are provided.
Topics: COVID-19; Humans; Immunotherapy; Nanoparticles; Pandemics; Proteins; RNA, Messenger
PubMed: 35437544
DOI: 10.1039/d1cs00617g -
Molecular Cancer May 2019N-methyladenosine (mA) is identified as the most common, abundant and conserved internal transcriptional modification, especially within eukaryotic messenger RNAs... (Review)
Review
N-methyladenosine (mA) is identified as the most common, abundant and conserved internal transcriptional modification, especially within eukaryotic messenger RNAs (mRNAs). MA modification is installed by the mA methyltransferases (METTL3/14, WTAP, RBM15/15B and KIAA1429, termed as "writers"), reverted by the demethylases (FTO and ALKBH5, termed as "erasers") and recognized by mA binding proteins (YTHDF1/2/3, IGF2BP1 and HNRNPA2B1, termed as "readers"). Acumulating evidence shows that, mA RNA methylation has an outsize effect on RNA production/metabolism and participates in the pathogenesis of multiple diseases including cancers. Until now, the molecular mechanisms underlying mA RNA methylation in various tumors have not been comprehensively clarified. In this review, we mainly summarize the recent advances in biological function of mA modifications in human cancer and discuss the potential therapeutic strategies.
Topics: Adenosine; Gene Expression Regulation, Neoplastic; Humans; Neoplasm Metastasis; Neoplasms; Prognosis; RNA Splicing; RNA Stability; RNA, Messenger
PubMed: 31142332
DOI: 10.1186/s12943-019-1033-z -
Nature Apr 2023Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for...
Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood. Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes. Exon junction complexes can multimerize through ALYREF, which suggests a mechanism for mRNP organization. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes. These results reveal how TREX may simultaneously recognize, compact and protect mRNAs to promote their packaging for nuclear export. The organization of mRNP globules provides a framework to understand how mRNP architecture facilitates mRNA biogenesis and export.
Topics: Humans; Active Transport, Cell Nucleus; Cell Nucleus; Cryoelectron Microscopy; RNA, Messenger; Transcription, Genetic; Exons
PubMed: 37020021
DOI: 10.1038/s41586-023-05904-0