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Cell Mar 2015mRNA degradation represents a critical regulated step in gene expression. Although the major pathways in turnover have been identified, accounting for disparate...
mRNA degradation represents a critical regulated step in gene expression. Although the major pathways in turnover have been identified, accounting for disparate half-lives has been elusive. We show that codon optimality is one feature that contributes greatly to mRNA stability. Genome-wide RNA decay analysis revealed that stable mRNAs are enriched in codons designated optimal, whereas unstable mRNAs contain predominately non-optimal codons. Substitution of optimal codons with synonymous, non-optimal codons results in dramatic mRNA destabilization, whereas the converse substitution significantly increases stability. Further, we demonstrate that codon optimality impacts ribosome translocation, connecting the processes of translation elongation and decay through codon optimality. Finally, we show that optimal codon content accounts for the similar stabilities observed in mRNAs encoding proteins with coordinated physiological function. This work demonstrates that codon optimization exists as a mechanism to finely tune levels of mRNAs and, ultimately, proteins.
Topics: Codon; Protein Biosynthesis; RNA Stability; RNA, Fungal; RNA, Messenger; Saccharomyces cerevisiae
PubMed: 25768907
DOI: 10.1016/j.cell.2015.02.029 -
BMC Biology Dec 2015Zebrafish are able to regenerate various organs and tissues after damage or amputation. To understand better the genetic controls of this process, the authors of this...
Zebrafish are able to regenerate various organs and tissues after damage or amputation. To understand better the genetic controls of this process, the authors of this study investigated the expression of two genes previously implicated in fin regeneration using semi-quantitative RT-PCR, at three time points after fin amputation (T1, T2, and T3 in Fig. 1, corresponding to the initiation, middle, and end of fin regeneration, respectively). Briefly, the RT-PCR procedure involved isolating messenger RNA (mRNA) from a matched amount of zebrafish cells from the site of fin regeneration at the three time points, and using primers specific to each gene to selectively detect mRNA as an indicator of gene expression levels. The authors used total genomic DNA isolated from zebrafish cells as a positive control, and no RNA or DNA template as a negative control. They found that Gene 1 was only expressed early on in the process, while Gene 2 expression gradually increased during fin regeneration, reaching a peak of expression toward the end of the process. This provides some detailed information that could be useful in elucidating the function of these genes in fin regeneration.
Topics: Amputation, Surgical; Animal Fins; Animals; Gene Expression Regulation; RNA, Messenger; Regeneration; Reverse Transcriptase Polymerase Chain Reaction; Zebrafish
PubMed: 26694721
DOI: 10.1186/s12915-015-0217-2 -
Trends in Biochemical Sciences Nov 2022The term 'nonsense-mediated mRNA decay' (NMD) was initially coined to describe the translation-dependent degradation of mRNAs harboring premature termination codons... (Review)
Review
The term 'nonsense-mediated mRNA decay' (NMD) was initially coined to describe the translation-dependent degradation of mRNAs harboring premature termination codons (PTCs), but it is meanwhile known that NMD also targets many canonical mRNAs with numerous biological implications. The molecular mechanisms determining on which RNAs NMD ensues are only partially understood. Considering the broad range of NMD-sensitive RNAs and the variable degrees of their degradation, we highlight here the hallmarks of mammalian NMD and point out open questions. We review the links between NMD and disease by summarizing the role of NMD in cancer, neurodegeneration, and viral infections. Finally, we describe strategies to modulate NMD activity and specificity as potential therapeutic approaches for various diseases.
Topics: Animals; Codon, Nonsense; Mammals; Nonsense Mediated mRNA Decay; RNA, Messenger
PubMed: 35780009
DOI: 10.1016/j.tibs.2022.06.003 -
Viral Immunology Nov 2022
Topics: RNA, Messenger
PubMed: 36368000
DOI: 10.1089/vim.2022.0179.editorial -
Nucleic Acids Research Sep 2019Thousands of eukaryotic protein-coding genes generate circular RNAs that have covalently linked ends and are resistant to degradation by exonucleases. To prove their...
Thousands of eukaryotic protein-coding genes generate circular RNAs that have covalently linked ends and are resistant to degradation by exonucleases. To prove their circularity as well as biochemically enrich these transcripts, it has become standard in the field to use the 3'-5' exonuclease RNase R. Here, we demonstrate that standard protocols involving RNase R can fail to digest >20% of all highly expressed linear RNAs, but these shortcomings can largely be overcome. RNAs with highly structured 3' ends, including snRNAs and histone mRNAs, are naturally resistant to RNase R, but can be efficiently degraded once a poly(A) tail has been added to their ends. In addition, RNase R stalls in the body of many polyadenylated mRNAs, especially at G-rich sequences that have been previously annotated as G-quadruplex (G4) structures. Upon replacing K+ (which stabilizes G4s) with Li+ in the reaction buffer, we find that RNase R is now able to proceed through these sequences and fully degrade the mRNAs in their entirety. In total, our results provide important improvements to the current methods used to isolate circular RNAs as well as a way to reveal RNA structures that may naturally inhibit degradation by cellular exonucleases.
Topics: 3' Flanking Region; Exoribonucleases; G-Quadruplexes; HeLa Cells; Humans; Lithium; Polyadenylation; Potassium; RNA; RNA Cleavage; RNA, Circular; RNA, Messenger; RNA, Small Nuclear; Sequence Analysis, RNA
PubMed: 31269210
DOI: 10.1093/nar/gkz576 -
Wiley Interdisciplinary Reviews. RNA Jul 2020Alternative pre-mRNA splicing generates multiple mRNA isoforms of different structures and functions from a single gene. While the prevalence of alternative splicing... (Review)
Review
Alternative pre-mRNA splicing generates multiple mRNA isoforms of different structures and functions from a single gene. While the prevalence of alternative splicing control is widely recognized, and the underlying regulatory mechanisms have long been studied, the physiological relevance and biological necessity for alternative splicing are only slowly being revealed. Significant inroads have been made in the brain, where alternative splicing regulation is particularly pervasive and conserved. Various aspects of brain development and function (from neurogenesis, neuronal migration, synaptogenesis, to the homeostasis of neuronal activity) involve alternative splicing regulation. Recent studies have begun to interrogate the possible role of alternative splicing in axon formation, a neuron-exclusive morphological and functional characteristic. We discuss how alternative splicing plays an instructive role in each step of axon formation. Converging genetic, molecular, and cellular evidence from studies of multiple alternative splicing regulators in different systems shows that a biological process as complicated and unique as axon formation requires highly coordinated and specific alternative splicing events. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Development.
Topics: Alternative Splicing; Animals; Axons; Humans; RNA, Messenger
PubMed: 31922356
DOI: 10.1002/wrna.1585 -
Wiley Interdisciplinary Reviews.... Mar 2019Messenger RNA (mRNA) has become a promising class of drugs for diverse therapeutic applications in the past few years. A series of clinical trials are ongoing or will be... (Review)
Review
Messenger RNA (mRNA) has become a promising class of drugs for diverse therapeutic applications in the past few years. A series of clinical trials are ongoing or will be initiated in the near future for the treatment of a variety of diseases. Currently, mRNA-based therapeutics mainly focuses on ex vivo transfection and local administration in clinical studies. Efficient and safe delivery of therapeutically relevant mRNAs remains one of the major challenges for their broad applications in humans. Thus, effective delivery systems are urgently needed to overcome this limitation. In recent years, numerous nanoscale biomaterials have been constructed for mRNA delivery in order to protect mRNA from extracellular degradation and facilitate endosomal escape after cellular uptake. Nanoscale platforms have expanded the feasibility of mRNA-based therapeutics, and enabled its potential applications to protein replacement therapy, cancer immunotherapy, therapeutic vaccines, regenerative medicine, and genome editing. This review focuses on recent advances, challenges, and future directions in nanoscale platforms designed for mRNA delivery, including lipid and lipid-derived nanoparticles, polymer-based nanoparticles, protein derivatives mRNA complexes, and other types of nanomaterials. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
Topics: Animals; Gene Transfer Techniques; Humans; Lipids; Nanoparticles; Nanotechnology; Proteins; RNA, Messenger
PubMed: 29726120
DOI: 10.1002/wnan.1530 -
Advanced Healthcare Materials Jun 2023Messenger RNA (mRNA)-based therapies offer great promise for the treatment of a variety of diseases. In 2020, two FDA approvals of mRNA-based vaccines have elevated mRNA... (Review)
Review
Messenger RNA (mRNA)-based therapies offer great promise for the treatment of a variety of diseases. In 2020, two FDA approvals of mRNA-based vaccines have elevated mRNA vaccines to global recognition. However, the therapeutic capabilities of mRNA extend far beyond vaccines against infectious diseases. They hold potential for cancer vaccines, protein replacement therapies, gene editing therapies, and immunotherapies. For realizing such advanced therapies, it is crucial to develop effective carrier systems. Recent advances in materials science have led to the development of promising nonviral mRNA delivery systems. In comparison to other carriers like lipid nanoparticles, polymer-based delivery systems often receive less attention, despite their unique ability to carefully tune their chemical features to promote mRNA protection, their favorable pharmacokinetics, and their potential for targeting delivery. In this review, the central features of polymer-based systems for mRNA delivery highlighting the molecular design criteria, stability, and biodistribution are discussed. Finally, the role of targeting ligands for the future of RNA therapies is analyzed.
Topics: Polymers; RNA, Messenger; Tissue Distribution; Nanoparticles; Genetic Therapy; Cancer Vaccines
PubMed: 36785927
DOI: 10.1002/adhm.202202688 -
Biochimica Et Biophysica Acta. Gene... Mar 2019
Review
Topics: Adenine; Animals; Humans; Protein Biosynthesis; RNA Processing, Post-Transcriptional; RNA, Messenger
PubMed: 30342175
DOI: 10.1016/j.bbagrm.2018.10.006 -
International Journal of Molecular... May 2020Acute leukemias are genetic diseases caused by translocations or mutations, which dysregulate hematopoiesis towards malignant transformation. However, the molecular mode... (Review)
Review
Acute leukemias are genetic diseases caused by translocations or mutations, which dysregulate hematopoiesis towards malignant transformation. However, the molecular mode of action is highly versatile and ranges from direct transcriptional to post-transcriptional control, which includes RNA-binding proteins (RBPs) as crucial regulators of cell fate. RBPs coordinate RNA dynamics, including subcellular localization, translational efficiency and metabolism, by binding to their target messenger RNAs (mRNAs), thereby controlling the expression of the encoded proteins. In view of the growing interest in these regulators, this review summarizes recent research regarding the most influential RBPs relevant in acute leukemias in particular. The reported RBPs, either dysregulated or as components of fusion proteins, are described with respect to their functional domains, the pathways they affect, and clinical aspects associated with their dysregulation or altered functions.
Topics: Acute Disease; Animals; Gene Expression Regulation, Leukemic; Humans; Leukemia; Nucleic Acid Conformation; Protein Binding; Protein Domains; RNA, Messenger; RNA-Binding Proteins
PubMed: 32408494
DOI: 10.3390/ijms21103409