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ACS Chemical Biology Apr 2020RNA splicing is a key component of gene expression and proteomic diversity in humans. The spliceosome assembles on and processes individual nascent pre-mRNA transcripts... (Review)
Review
RNA splicing is a key component of gene expression and proteomic diversity in humans. The spliceosome assembles on and processes individual nascent pre-mRNA transcripts into distinct mature mRNAs that can code for different proteins. Splicing programs can be affected by somatic mutations and changes in response to exogenous stimuli. Importantly, alterations in splicing can be direct drivers of diseases including cancers. This Review describes recent advances and the potential for targeting and controlling pre-mRNA splicing in humans with small molecules, ranging from targeting spliceosomal proteins to direct targeting of individual RNA transcripts.
Topics: G-Quadruplexes; Humans; Protein Kinase Inhibitors; RNA Precursors; RNA Splicing; Serine-Arginine Splicing Factors; Spliceosomes
PubMed: 32191432
DOI: 10.1021/acschembio.0c00001 -
Trends in Pharmacological Sciences Dec 2021RNA splicing, the process by which precursor mRNA (pre-mRNA) is processed to mature mRNA, is catalyzed by the spliceosome. Recently, Chatrikhi et al. identified...
RNA splicing, the process by which precursor mRNA (pre-mRNA) is processed to mature mRNA, is catalyzed by the spliceosome. Recently, Chatrikhi et al. identified pharmacologic means to perturb splicing by enhancing the spliceosome's binding to pre-mRNA. This represents a novel chemical target and mechanism for therapeutic modulation of splicing.
Topics: Humans; Mutation; RNA Precursors; RNA Splicing Factors; RNA, Messenger; Spliceosomes
PubMed: 34602305
DOI: 10.1016/j.tips.2021.09.006 -
Biophysical Journal Feb 2022Nascent pre-mRNA 3'-end cleavage and polyadenylation (C/P) involves numerous proteins that recognize multiple RNA elements. Human CSTF2 binds to a downstream U- or...
Nascent pre-mRNA 3'-end cleavage and polyadenylation (C/P) involves numerous proteins that recognize multiple RNA elements. Human CSTF2 binds to a downstream U- or G/U-rich sequence through its RNA recognition motif (RRM) regulating C/P. We previously reported the only known disease-related CSTF2 RRM mutant (CSTF2) and showed that it changed the on-rate of RNA binding, leading to alternative polyadenylation in brains of mice carrying the same mutation. In this study, we further investigated the role of electrostatic interactions in the thermodynamics and kinetics of RNA binding for the CSTF2 RRM and the downstream consequences for regulation of C/P. By combining mutagenesis with NMR spectroscopy and biophysical assays, we confirmed that electrostatic attraction is the dominant factor in RRM binding to a naturally occurring U-rich RNA sequence. Moreover, we demonstrate that RNA binding is accompanied by an enthalpy-entropy compensation mechanism that is supported by changes in pico-to-nanosecond timescale RRM protein dynamics. We suggest that the dynamic binding of the RRM to U-rich RNA supports the diversity of sequences it encounters in the nucleus. Lastly, in vivo C/P assays demonstrate a competition between fast, high affinity RNA binding and efficient, correct C/P. These results highlight the importance of the surface charge of the RRM in RNA binding and the balance between nascent mRNA binding and C/P in vivo.
Topics: Animals; Mice; Polyadenylation; Protein Binding; RNA; RNA Precursors; RNA Recognition Motif; Static Electricity
PubMed: 35090899
DOI: 10.1016/j.bpj.2022.01.005 -
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 -
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 -
Yi Chuan = Hereditas Jun 2018Circular RNAs (circRNAs) are covalently closed, conserved single-stranded transcripts that are produced from precursor mRNA (pre-mRNA) back-splicing. They could function... (Review)
Review
Circular RNAs (circRNAs) are covalently closed, conserved single-stranded transcripts that are produced from precursor mRNA (pre-mRNA) back-splicing. They could function as microRNA sponges, interfere with splicing and bind to protein to regulate the expression of parental genes and linear mRNAs. Next-generation RNA sequencing (RNA-seq) has recently shown that the expression of circRNAs is widespread in plants. circRNAs participate in multiple biological processes such as floral development, fruit ripening, and biotic and abiotic stress responses by cell type-specific and tissue-specific expression patterns, indicating that they may play an important role in plant development. In this review, we summarize the current knowledge of plant circRNAs in recent years, including the biogenesis, detection, databases, expression pattern, and potential functions in comparison with animal results to provide new insights for functional research interests of circRNAs in the future.
Topics: MicroRNAs; Plants; RNA; RNA Precursors; RNA Splicing; RNA, Circular; RNA, Plant
PubMed: 29959119
DOI: 10.16288/j.yczz.18-009 -
The Journal of Cell Biology Dec 2023Current models posit that nuclear speckles (NSs) serve as reservoirs of splicing factors and facilitate posttranscriptional mRNA processing. Here, we discovered that...
Current models posit that nuclear speckles (NSs) serve as reservoirs of splicing factors and facilitate posttranscriptional mRNA processing. Here, we discovered that ribotoxic stress induces a profound reorganization of NSs with enhanced recruitment of factors required for splice-site recognition, including the RNA-binding protein TIAR, U1 snRNP proteins and U2-associated factor 65, as well as serine 2 phosphorylated RNA polymerase II. NS reorganization relies on the stress-activated p38 mitogen-activated protein kinase (MAPK) pathway and coincides with splicing activation of both pre-existing and newly synthesized pre-mRNAs. In particular, ribotoxic stress causes targeted excision of retained introns from pre-mRNAs of immediate early genes (IEGs), whose transcription is induced during the stress response. Importantly, enhanced splicing of the IEGs ZFP36 and FOS is accompanied by relocalization of the corresponding nuclear mRNA foci to NSs. Our study reveals NSs as a dynamic compartment that is remodeled under stress conditions, whereby NSs appear to become sites of IEG transcription and efficient cotranscriptional splicing.
Topics: Genes, Immediate-Early; Introns; Nuclear Speckles; Ribonucleoprotein, U1 Small Nuclear; RNA Precursors; RNA Splicing; RNA, Messenger; Humans
PubMed: 37956386
DOI: 10.1083/jcb.202111151 -
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 -
Molecular Human Reproduction Jun 2023Human meiosis in oocytes entails an intricate regulation of the transcriptome to support late oocyte growth and early embryo development, both crucial to reproductive...
Human meiosis in oocytes entails an intricate regulation of the transcriptome to support late oocyte growth and early embryo development, both crucial to reproductive success. Currently, little is known about the co- and post-transcriptional mRNA processing mechanisms regulating the last meiotic phases, which contribute to transcriptome complexity and influence translation rates. We analyzed gene expression changes, splicing and pre-mRNA processing in an RNA sequencing set of 40 human oocytes at different meiotic maturation stages, matured both in vivo and in vitro. We found abundant untranslated region (UTR) processing, mostly at the 3' end, of meiosis-related genes between the germinal vesicle (GV) and metaphase II (MII) stages, supported by the differential expression of spliceosome and pre-mRNA processing related genes. Importantly, we found very few differences among GV oocytes across several durations of IVM, as long as they did not reach MII, suggesting an association of RNA processing and successful meiosis transit. Changes in protein isoforms are minor, although specific and consistent for genes involved in chromosome organization and spindle assembly. In conclusion, we reveal a dynamic transcript remodeling during human female meiosis, and show how pre-mRNA processing, specifically 3'UTR shortening, drives a selective translational regulation of transcripts necessary to reach final meiotic maturation.
Topics: Humans; Female; In Vitro Oocyte Maturation Techniques; RNA Precursors; Oocytes; Meiosis; Oogenesis
PubMed: 37261882
DOI: 10.1093/molehr/gaad021 -
Cold Spring Harbor Perspectives in... Aug 2019At each active protein-encoding gene, nascent RNA is tethered to the DNA axis by elongating RNA polymerase II (Pol II) and is continuously altered by splicing and other... (Review)
Review
At each active protein-encoding gene, nascent RNA is tethered to the DNA axis by elongating RNA polymerase II (Pol II) and is continuously altered by splicing and other processing events during its synthesis. This review discusses the development of three major methods that enable us to track the conversion of precursor messenger RNA (pre-mRNA) to messenger RNA (mRNA) products in vivo: live-cell imaging, metabolic labeling of RNA, and RNA-seq of purified nascent RNA. These approaches are complementary, addressing distinct issues of transcription rates and intron lifetimes alongside spatial information regarding the gene position of Pol II at which spliceosomes act. The findings will be placed in the context of active transcription units, each of which-because of the presence of nascent RNA, Pol II, and features of the chromatin environment-will recruit a potentially gene-specific constellation of RNA binding proteins and processing machineries.
Topics: Alternative Splicing; Animals; Chromatin; Gene Expression Profiling; Humans; Immunoprecipitation; Introns; Microscopy, Fluorescence; RNA; RNA Folding; RNA Polymerase II; RNA Precursors; Saccharomyces cerevisiae; Spliceosomes; Transcription, Genetic
PubMed: 31371351
DOI: 10.1101/cshperspect.a032227