-
Cell Reports Dec 2023Argonaute (AGO) proteins execute microRNA (miRNA)-mediated gene silencing. However, it is unclear whether all 4 mammalian AGO proteins (AGO1, AGO2, AGO3, and AGO4) are...
Argonaute (AGO) proteins execute microRNA (miRNA)-mediated gene silencing. However, it is unclear whether all 4 mammalian AGO proteins (AGO1, AGO2, AGO3, and AGO4) are required for miRNA activity. We generate Ago1, Ago3, and Ago4-deficient mice (Ago134) and find AGO1/3/4 to be redundant for miRNA biogenesis, homeostasis, or function, a role that is carried out by AGO2. Instead, AGO1/3/4 regulate the expansion of type 2 immunity via precursor mRNA splicing in CD4 T helper (Th) lymphocytes. Gain- and loss-of-function experiments demonstrate that nuclear AGO3 interacts directly with SF3B3, a component of the U2 spliceosome complex, to aid global mRNA splicing, and in particular the isoforms of the gene Nisch, resulting in a dysregulated Nisch isoform ratio. This work uncouples AGO1, AGO3, and AGO4 from miRNA-mediated RNA interference, identifies an AGO3:SF3B3 complex in the nucleus, and reveals a mechanism by which AGO proteins regulate inflammatory diseases.
Topics: Animals; Mice; Argonaute Proteins; Imidazoline Receptors; Mammals; MicroRNAs; RNA Interference; RNA Precursors; RNA Splicing; RNA, Messenger
PubMed: 38096048
DOI: 10.1016/j.celrep.2023.113515 -
Protein & Cell Aug 2022Precursor messenger RNA (pre-mRNA) splicing is catalyzed by an intricate ribonucleoprotein complex called the spliceosome. Although the spliceosome is considered to be... (Review)
Review
Precursor messenger RNA (pre-mRNA) splicing is catalyzed by an intricate ribonucleoprotein complex called the spliceosome. Although the spliceosome is considered to be general cell "housekeeping" machinery, mutations in core components of the spliceosome frequently correlate with cell- or tissue-specific phenotypes and diseases. In this review, we expound the links between spliceosome mutations, aberrant splicing, and human cancers. Remarkably, spliceosome-targeted therapies (STTs) have become efficient anti-cancer strategies for cancer patients with splicing defects. We also highlight the links between spliceosome and immune signaling. Recent studies have shown that some spliceosome gene mutations can result in immune dysregulation and notable phenotypes due to mis-splicing of immune-related genes. Furthermore, several core spliceosome components harbor splicing-independent immune functions within the cell, expanding the functional repertoire of these diverse proteins.
Topics: Humans; Neoplasms; RNA Precursors; RNA Splicing; RNA Splicing Factors; Spliceosomes
PubMed: 34196950
DOI: 10.1007/s13238-021-00856-5 -
International Journal of Molecular... Oct 2023Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates... (Review)
Review
Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.
Topics: Alternative Splicing; Plant Breeding; RNA Splicing; Arabidopsis; Crops, Agricultural; RNA Precursors
PubMed: 37894886
DOI: 10.3390/ijms242015205 -
Current Opinion in Structural Biology Dec 2022The spliceosome is a multi-megadalton RNA-protein complex responsible for the removal of non-coding introns from pre-mRNAs. Due to its complexity and dynamic nature, it... (Review)
Review
The spliceosome is a multi-megadalton RNA-protein complex responsible for the removal of non-coding introns from pre-mRNAs. Due to its complexity and dynamic nature, it has proven to be a very challenging target for structural studies. Developments in single particle cryo-EM have overcome these previous limitations and paved the way towards a structural characterisation of the splicing machinery. Despite tremendous progress, many aspects of spliceosome structure and function remain elusive. In particular, the events leading to the definition of exon-intron boundaries, alternative and non-canonical splicing events, and cross-talk with other cellular machineries. Efforts are being made to address these knowledge gaps and further our mechanistic understanding of the spliceosome. Here, we summarise recent progress in the structural and functional analysis of the spliceosome.
Topics: Spliceosomes; RNA Splicing; RNA Precursors; Introns; Exons
PubMed: 36116369
DOI: 10.1016/j.sbi.2022.102461 -
Genomics Sep 2020MicroRNAs (miRNAs) are small endogenous non-coding RNAs in eukaryotes which regulate the expression of numerous genes post-transcriptionally, thereby playing critical... (Review)
Review
MicroRNAs (miRNAs) are small endogenous non-coding RNAs in eukaryotes which regulate the expression of numerous genes post-transcriptionally, thereby playing critical roles in cells and organismal development. The high-throughput sequencing technologies enable the effective detection and annotation of miRNAs. Several miRNA variants with heterogeneous ends, lengths, and sequences can be generated from a single miRNA locus. Discovery of these miRNA variants, also known as miRNA isoforms or isomiRs, has made our understanding of the cells' miRNome deeper than previously pictured. Despite their wide presence in multiple datasets, the different possible origins and true biological significance of isomiRs are yet to be uncovered. Several recent emerging studies suggest that isomiRs are biologically active and non-randomly formed. This review aims to provide a comprehensive insight into the origins and biological importance of isomiRs, highlighting the enormous complexity of miRNA regulatory networks which broadens our knowledge about the post-transcriptional gene regulation in plants.
Topics: MicroRNAs; Plant Proteins; RNA Editing; RNA Precursors; RNA, Plant; Ribonuclease III
PubMed: 32561347
DOI: 10.1016/j.ygeno.2020.06.019 -
Experimental & Molecular Medicine Apr 2023Cells produce multiple mRNAs through alternative splicing, which ensures proteome diversity. Because most human genes undergo alternative splicing, key components of... (Review)
Review
Cells produce multiple mRNAs through alternative splicing, which ensures proteome diversity. Because most human genes undergo alternative splicing, key components of signal transduction pathways are no exception. Cells regulate various signal transduction pathways, including those associated with cell proliferation, development, differentiation, migration, and apoptosis. Since proteins produced through alternative splicing can exhibit diverse biological functions, splicing regulatory mechanisms affect all signal transduction pathways. Studies have demonstrated that proteins generated by the selective combination of exons encoding important domains can enhance or attenuate signal transduction and can stably and precisely regulate various signal transduction pathways. However, aberrant splicing regulation via genetic mutation or abnormal expression of splicing factors negatively affects signal transduction pathways and is associated with the onset and progression of various diseases, including cancer. In this review, we describe the effects of alternative splicing regulation on major signal transduction pathways and highlight the significance of alternative splicing.
Topics: Humans; Alternative Splicing; RNA Precursors; RNA Splicing; Cell Differentiation; Proteins; Signal Transduction
PubMed: 37009804
DOI: 10.1038/s12276-023-00981-7 -
Transcription Apr 2020The majority of eukaryotic messenger RNA precursors (pre-mRNAs) undergo cleavage and polyadenylation at their 3' end. This canonical 3'-end processing depends on... (Review)
Review
UNLABELLED
The majority of eukaryotic messenger RNA precursors (pre-mRNAs) undergo cleavage and polyadenylation at their 3' end. This canonical 3'-end processing depends on sequence elements in the pre-mRNA as well as a mega-dalton protein machinery. The cleavage site in mammalian pre-mRNAs is located between an upstream poly(A) signal, most frequently an AAUAAA hexamer, and a GU-rich downstream sequence element. This review will summarize recent advances from the studies on this canonical 3'-end processing machinery. They have revealed the molecular mechanism for the recognition of the poly(A) signal and provided the first glimpse into the overall architecture of the machinery. The studies also show that the machinery is highly dynamic conformationally, and extensive re-arrangements are necessary for its activation. Inhibitors targeting the active site of the CPSF73 nuclease of this machinery have anti-cancer, anti-inflammatory and anti-protozoal effects, indicating that CPSF73 and pre-mRNA 3'-end processing in general are attractive targets for drug discovery.
ABBREVIATIONS
APA: alternative polyadenylation; β-CASP: metallo-β-lactamase-associated CPSF Artemis SNM1/PSO2; CTD: C-terminal domain; CF: cleavage factor; CPF: cleavage and polyadenylation factor; CPSF: cleavage and polyadenylation specificity factor; CstF: cleavage stimulation factor; DSE: downstream element; HAT: half a TPR; HCC: histone pre-mRNA cleavage complex; mCF: mammalian cleavage factor; mPSF: mammalian polyadenylation specificity factor; mRNA: messenger RNA; nt: nucleotide; NTD: N-terminal domain; PAP: polyadenylate polymerase; PAS: polyadenylation signal; PIM: mPSF interaction motif; Poly(A): polyadenylation, polyadenylate; Pol II: RNA polymerase II; pre-mRNA: messenger RNA precursor; RRM: RNA recognition module, RNA recognition motif; snRNP: small nuclear ribonucleoprotein; TPR: tetratricopeptide repeat; UTR: untranslated region; ZF: zinc finger.
Topics: Cleavage And Polyadenylation Specificity Factor; Humans; RNA Precursors
PubMed: 32522085
DOI: 10.1080/21541264.2020.1777047 -
International Journal of Oncology Dec 2022Emerging evidence has suggested that N‑methyladenosine (m6A) modification, a typical RNA methylation modification, controls the fate of modified transcripts and is... (Review)
Review
Emerging evidence has suggested that N‑methyladenosine (m6A) modification, a typical RNA methylation modification, controls the fate of modified transcripts and is involved in the pathogenesis of various human diseases, such as metabolic disorders, nephropathology, osteoarthritis and malignant tumours. Long noncoding RNAs (lncRNAs), transcripts of >200 nt in length, have also been indicated to be involved in various diseases by participating in processes such as epigenetic modifications, transcriptional alternations and posttranslational regulation. Recent studies revealed that lncRNAs were widely modified by m6A, which has a critical role in various cellular processes that are associated with numerous disorders, particularly human cancers. The present review first examined functions of m6A modification of lncRNAs, including changing the lncRNA structure, mediating transcriptional regulation, affecting mRNA precursor splicing, and regulating lncRNA stability and translation. Furthermore, the regulatory mechanisms of m6A‑modified lncRNAs in cancers were summarized and the up‑to‑date detection methods and prediction tools for identifying m6A sites on lncRNAs were presented. In addition, viewpoints on potential future directions in the field were discussed, including more accurate detection methods, roles of lncRNAs‑encoded micropeptides in cancers, the relationship between m6A‑modified lncRNAs and the tumour microenvironment, and m6A‑modified lncRNAs as potential biomarkers and therapeutic targets in human cancer.
Topics: Humans; RNA, Long Noncoding; RNA Precursors; Neoplasms; Biomarkers; Tumor Microenvironment
PubMed: 36263625
DOI: 10.3892/ijo.2022.5442 -
RNA Biology Sep 2016Pre-mRNA splicing is a key post-transcriptional regulation process in which introns are excised and exons are ligated together. A novel class of structured intron was... (Review)
Review
Pre-mRNA splicing is a key post-transcriptional regulation process in which introns are excised and exons are ligated together. A novel class of structured intron was recently discovered in fish. Simple expansions of complementary AC and GT dimers at opposite boundaries of an intron were found to form a bridging structure, thereby enforcing correct splice site pairing across the intron. In some fish introns, the RNA structures are strong enough to bypass the need of regulatory protein factors for splicing. Here, we discuss the prevalence and potential functions of highly structured introns. In humans, structured introns usually arise through the co-occurrence of C and G-rich repeats at intron boundaries. We explore the potentially instructive example of the HLA receptor genes. In HLA pre-mRNA, structured introns flank the exons that encode the highly polymorphic β sheet cleft, making the processing of the transcript robust to variants that disrupt splicing factor binding. While selective forces that have shaped HLA receptor are fairly atypical, numerous other highly polymorphic genes that encode receptors contain structured introns. Finally, we discuss how the elevated mutation rate associated with the simple repeats that often compose structured intron can make structured introns themselves rapidly evolving elements.
Topics: Animals; Biological Evolution; Exons; Humans; Introns; Nucleic Acid Conformation; Polymorphism, Single Nucleotide; RNA; RNA Precursors; RNA Splicing; RNA, Messenger; Splicing Factor U2AF; Structure-Activity Relationship
PubMed: 27454491
DOI: 10.1080/15476286.2016.1208893 -
Metal Ions in Life Sciences 2011The spliceosome is a massive complex of 5 RNAs and many proteins that associate to catalyze precursor messenger RNA splicing. The process of splicing involves two... (Review)
Review
The spliceosome is a massive complex of 5 RNAs and many proteins that associate to catalyze precursor messenger RNA splicing. The process of splicing involves two phosphoryl transfer reactions that result in intron excision and ligation of the flanking exons. Since it is required for normal protein production in eukaryotic cells, pre-mRNA splicing is an essential step in gene expression. Although high resolution structural views of the spliceosome do not yet exist, a growing body of evidence indicates that the spliceosome is a magnesium-dependent enzyme that utilizes catalytic metal ions to stabilize both transition states during the two phosphoryl transfer steps of splicing. A wealth of data also indicate that the core of the spliceosome is comprised of RNA, and suggest that the spliceosome may be a ribozyme. This chapter presents the evidence for metal ion catalysis by the spliceosome, draws comparisons to similar RNA enzymes, and discusses the future directions for research into the mechanism of pre-mRNA splicing.
Topics: Base Sequence; Evolution, Molecular; Humans; Introns; Ions; Metals; Molecular Sequence Data; Nucleic Acid Conformation; RNA Precursors; RNA Splicing; RNA, Catalytic; Spliceosomes; Stereoisomerism
PubMed: 22010274
DOI: 10.1039/9781849732512-00235