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Bioscience Reports Mar 2023RNA is a fundamental biomolecule that has many purposes within cells. Due to its single-stranded and flexible nature, RNA naturally folds into complex and dynamic... (Review)
Review
RNA is a fundamental biomolecule that has many purposes within cells. Due to its single-stranded and flexible nature, RNA naturally folds into complex and dynamic structures. Recent technological and computational advances have produced an explosion of RNA structural data. Many RNA structures have regulatory and functional properties. Studying the structure of nascent RNAs is particularly challenging due to their low abundance and long length, but their structures are important because they can influence RNA processing. Precursor RNA processing is a nexus of pathways that determines mature isoform composition and that controls gene expression. In this review, we examine what is known about human nascent RNA structure and the influence of RNA structure on processing of precursor RNAs. These known structures provide examples of how other nascent RNAs may be structured and show how novel RNA structures may influence RNA processing including splicing and polyadenylation. RNA structures can be targeted therapeutically to treat disease.
Topics: Humans; RNA Precursors; RNA Splicing; RNA; Polyadenylation; Gene Expression
PubMed: 36689327
DOI: 10.1042/BSR20220149 -
Nature Communications Aug 2023Cleavage and polyadenylation (CPA) is responsible for 3' end processing of eukaryotic poly(A)+ RNAs and preludes transcriptional termination. JTE-607, which targets...
Cleavage and polyadenylation (CPA) is responsible for 3' end processing of eukaryotic poly(A)+ RNAs and preludes transcriptional termination. JTE-607, which targets CPSF-73, is the first known CPA inhibitor (CPAi) in mammalian cells. Here we show that JTE-607 perturbs gene expression through both transcriptional readthrough and alternative polyadenylation (APA). Sensitive genes are associated with features similar to those previously identified for PCF11 knockdown, underscoring a unified transcriptomic signature of CPAi. The degree of inhibition of an APA site by JTE-607 correlates with its usage level and, consistently, cells with elevated CPA activities, such as those with induced overexpression of FIP1, display greater transcriptomic disturbances when treated with JTE-607. Moreover, JTE-607 causes S phase crisis and is hence synergistic with inhibitors of DNA damage repair pathways. Together, our data reveal CPA activity and proliferation rate as determinants of CPAi-mediated cell death, raising the possibility of using CPAi as an adjunct therapy to suppress certain cancers.
Topics: Animals; Polyadenylation; RNA Precursors; mRNA Cleavage and Polyadenylation Factors; RNA, Messenger; Mammals; Neoplasms
PubMed: 37528120
DOI: 10.1038/s41467-023-39793-8 -
Journal of Molecular Cell Biology Jan 2024During ribosome biogenesis, the small subunit (SSU) processome is responsible for 40S assembly. The BMS1/RCL1 complex is a core component of the SSU processome that...
During ribosome biogenesis, the small subunit (SSU) processome is responsible for 40S assembly. The BMS1/RCL1 complex is a core component of the SSU processome that plays an important role in 18S rRNA processing and maturation. Genetic studies using zebrafish mutants indicate that both Bms1-like (Bms1l) and Rcl1 are essential for digestive organ development. In spite of vital functions of this complex, the mutual dependence of these two nucleolar proteins for the stability and function remains elusive. In this study, we identified an RCL1-interacting domain in BMS1, which is conserved in zebrafish and humans. Moreover, both the protein stability and nucleolar entry of RCL1 depend on its interaction with BMS1, otherwise RCL1 degraded through the ubiquitination-proteasome pathway. Functional studies revealed that overexpression of RCL1 in BMS1-knockdown cells can partially rescue the defects in 18S rRNA processing and cell proliferation, and hepatocyte-specific overexpression of Rcl1 can resume zebrafish liver development in the bms1l substitution mutant bms1lsq163/sq163but not in the knockout mutant bms1lzju1/zju1, which is attributed to the nucleolar entry of Rcl1 in the former mutant. Our data demonstrate that BMS1 and RCL1 interaction is essential for not only pre-rRNA processing but also the communication between ribosome biogenesis and cell cycle regulation.
Topics: Animals; Humans; Nuclear Proteins; RNA Precursors; RNA Processing, Post-Transcriptional; RNA, Ribosomal, 18S; Zebrafish; N-Glycosyl Hydrolases; Proto-Oncogene Proteins
PubMed: 37451810
DOI: 10.1093/jmcb/mjad046 -
Genes & Development Feb 2022It is every biochemist's dream to reconstitute a biological process in vitro using defined components, because doing so not only reduces a biological phenomenon to one... (Review)
Review
It is every biochemist's dream to reconstitute a biological process in vitro using defined components, because doing so not only reduces a biological phenomenon to one or a series of biochemical reactions, but also defines the minimal list of essential components. In this issue of , Boreikaite and colleagues (pp. 210-224) and Schmidt and colleagues (pp. 195-209) report their independent reconstitution of human pre-mRNA 3' end processing.
Topics: Humans; RNA Precursors; RNA Processing, Post-Transcriptional; mRNA Cleavage and Polyadenylation Factors
PubMed: 35193945
DOI: 10.1101/gad.349453.122 -
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 -
Chemical Reviews Apr 2018Nuclear pre-mRNA splicing and group II intron self-splicing both proceed by two-step transesterification reactions via a lariat intron intermediate. Recently determined... (Review)
Review
Nuclear pre-mRNA splicing and group II intron self-splicing both proceed by two-step transesterification reactions via a lariat intron intermediate. Recently determined cryo-electron microscopy (cryo-EM) structures of catalytically active spliceosomes revealed the RNA-based catalytic core and showed how pre-mRNA substrates and reaction products are positioned in the active site. These findings highlight a strong structural similarity to the group II intron active site, strengthening the notion that group II introns and spliceosomes evolved from a common ancestor. Prp8, the largest and most conserved protein in the spliceosome, cradles the active site RNA. Prp8 and group II intron maturase have a similar domain architecture, suggesting that they also share a common evolutionary origin. The interactions between maturase and key group II intron RNA elements, such as the exon-binding loop and domains V and VI, are recapitulated in the interactions between Prp8 and key elements in the spliceosome's catalytic RNA core. Structural comparisons suggest that the extensive RNA scaffold of the group II intron was gradually replaced by proteins as the spliceosome evolved. A plausible model of spliceosome evolution is discussed.
Topics: Cell Nucleus; Cryoelectron Microscopy; Crystallography, X-Ray; Exons; Hydrolysis; Introns; Nucleic Acid Conformation; Phylogeny; RNA Precursors; RNA Splicing; RNA, Messenger; Spliceosomes
PubMed: 29377672
DOI: 10.1021/acs.chemrev.7b00499 -
Biochimica Et Biophysica Acta. Gene... 2019Although RNA circularization was first documented in the 1990s, the extent to which it occurs was not known until recent advances in high-throughput sequencing enabled... (Review)
Review
Although RNA circularization was first documented in the 1990s, the extent to which it occurs was not known until recent advances in high-throughput sequencing enabled the widespread identification of circular RNAs (circRNAs). Despite this, many aspects of circRNA biogenesis, structure, and function yet remain obscure. This review focuses on circular exonic RNAs, a subclass of circRNAs that are generated through backsplicing. Here, I hypothesize that RNA secondary structure can be the common factor that promotes both exon skipping and spliceosomal RNA circularization, and that backsplicing of double-stranded regions could generate topologically linked circRNA molecules. CircRNAs manifest themselves by the presence of tail-to-head exon junctions, which were previously attributed to post-transcriptional exon permutation and repetition. I revisit these observations and argue that backsplicing does not automatically imply RNA circularization because tail-to-head exon junctions give only local information about transcript architecture and, therefore, they are in principle insufficient to determine globally circular topology. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
Topics: Alternative Splicing; Animals; Exons; Humans; Models, Molecular; Nucleic Acid Conformation; RNA Precursors; RNA, Circular
PubMed: 31102674
DOI: 10.1016/j.bbagrm.2019.05.002 -
Cold Spring Harbor Perspectives in... Nov 2019The spliceosome is a highly complex, dynamic ribonucleoprotein molecular machine that undergoes numerous structural and compositional rearrangements that lead to the... (Review)
Review
The spliceosome is a highly complex, dynamic ribonucleoprotein molecular machine that undergoes numerous structural and compositional rearrangements that lead to the formation of its active site. Recent advances in cyroelectron microscopy (cryo-EM) have provided a plethora of near-atomic structural information about the inner workings of the spliceosome. Aided by previous biochemical, structural, and functional studies, cryo-EM has confirmed or provided a structural basis for most of the prevailing models of spliceosome function, but at the same time allowed novel insights into splicing catalysis and the intriguing dynamics of the spliceosome. The mechanism of pre-mRNA splicing is highly conserved between humans and yeast, but the compositional dynamics and ribonucleoprotein (RNP) remodeling of the human spliceosome are more complex. Here, we summarize recent advances in our understanding of the molecular architecture of the human spliceosome, highlighting differences between the human and yeast splicing machineries.
Topics: Catalysis; Cryoelectron Microscopy; Eukaryotic Cells; Mutation; Neoplasms; Nucleic Acid Conformation; Protein Conformation; RNA Precursors; RNA Splicing; RNA, Messenger; Ribonucleoproteins, Small Nuclear; Saccharomyces cerevisiae; Spliceosomes
PubMed: 30765414
DOI: 10.1101/cshperspect.a032417 -
Chembiochem : a European Journal of... Jul 2023The vast majority of RNA splicing in today's organisms is achieved by the highly regulated and precise removal of introns from pre-mRNAs via the spliceosome. Here we...
The vast majority of RNA splicing in today's organisms is achieved by the highly regulated and precise removal of introns from pre-mRNAs via the spliceosome. Here we present a model of how RNA splicing may have occurred in earlier life forms. We have designed a hairpin ribozyme derived spliceozyme that mediates two RNA cleavages and one ligation event at specific positions and thus cuts a segment (intron) out of a parent RNA and ligates the remaining fragments (exons). The cut-out intron then performs a downstream function, acting as a positive regulator of the activity of a bipartite DNAzyme. This simple scenario shows how small RNAs can perform complex RNA processing dynamics, involving the generation of new phenotypes by restructuring segments of given RNA species, as well as delivering small RNAs that may play a functional role in downstream processes.
Topics: RNA, Catalytic; RNA; RNA Splicing; RNA Precursors; Introns; Nucleic Acid Conformation
PubMed: 37184100
DOI: 10.1002/cbic.202300204 -
Trends in Plant Science Nov 2015The biogenesis of eukaryotic ribosomes is a fundamental process involving hundreds of ribosome biogenesis factors (RBFs) in three compartments of the cell, namely the... (Review)
Review
The biogenesis of eukaryotic ribosomes is a fundamental process involving hundreds of ribosome biogenesis factors (RBFs) in three compartments of the cell, namely the nucleolus, nucleus, and cytoplasm. Many RBFs are involved in the processing of the primary ribosomal (r)RNA transcript, in which three of the four rRNAs are imbedded. While pre-rRNA processing is well described for yeast and mammals, a detailed processing scheme for plants is lacking. Here, we discuss the emerging scheme of pre-rRNA processing in Arabidopsis thaliana in comparison to other eukaryotes, with a focus on plant characteristics. In addition, we highlight the impact of the ribosome and its biogenesis on developmental processes because common phenotypes can be observed for ribosomal protein and RBF mutants.
Topics: Arabidopsis; Organelle Biogenesis; RNA Precursors; RNA, Plant; Ribosomal Proteins; Ribosomes
PubMed: 26459664
DOI: 10.1016/j.tplants.2015.07.003