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Biochemical Society Transactions Feb 2022Members of the arginine-serine-rich protein family (SR proteins) are multifunctional RNA-binding proteins that have emerged as key determinants for mRNP formation,...
Members of the arginine-serine-rich protein family (SR proteins) are multifunctional RNA-binding proteins that have emerged as key determinants for mRNP formation, identity and fate. They bind to pre-mRNAs early during transcription in the nucleus and accompany bound transcripts until they are translated or degraded in the cytoplasm. SR proteins are mostly known for their essential roles in constitutive splicing and as regulators of alternative splicing. However, many additional activities of individual SR proteins, beyond splicing, have been reported in recent years. We will summarize the different functions of SR proteins and discuss how multifunctionality can be achieved. We will also highlight the difficulties of studying highly versatile SR proteins and propose approaches to disentangle their activities, which is transferrable to other multifunctional RBPs.
Topics: Alternative Splicing; RNA Precursors; RNA Splicing; RNA-Binding Proteins; Serine
PubMed: 34940860
DOI: 10.1042/BST20210325 -
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 -
Journal of Cellular Physiology Jan 2022Circular RNAs (circRNAs) are closed back-splicing products of precursor mRNA in eukaryotes. Compared with linear mRNAs, circRNAs have a special structure and stable... (Review)
Review
Circular RNAs (circRNAs) are closed back-splicing products of precursor mRNA in eukaryotes. Compared with linear mRNAs, circRNAs have a special structure and stable expression. A large number of studies have provided different regulatory mechanisms of circRNAs in tumors. Challenges exist in understanding the control of circRNAs because of their sequence overlap with linear mRNA. Here, we survey the most recent progress regarding the regulation of circRNA biogenesis by RNA-binding proteins, one of the vital functional proteins. Furthermore, substantial circRNAs exert compelling biological roles by acting as protein sponges, by being translated themselves or regulating posttranslational modifications of proteins. This review will help further explore more types of functional proteins that interact with circRNA in cancer and reveal other unknown mechanisms of circRNA regulation.
Topics: Humans; Neoplasms; RNA; RNA Precursors; RNA, Circular; RNA, Messenger; RNA-Binding Proteins
PubMed: 34676546
DOI: 10.1002/jcp.30608 -
Cell Reports Oct 2023Pre-mRNA splicing is surveilled at different stages by quality control (QC) mechanisms. The leukemia-associated DExH-box family helicase hDHX15/scPrp43 is known to...
Pre-mRNA splicing is surveilled at different stages by quality control (QC) mechanisms. The leukemia-associated DExH-box family helicase hDHX15/scPrp43 is known to disassemble spliceosomes after splicing. Here, using rapid protein depletion and analysis of nascent and mature RNA to enrich for direct effects, we identify a widespread splicing QC function for DHX15 in human cells, consistent with recent in vitro studies. We find that suboptimal introns with weak splice sites, multiple branch points, and cryptic introns are repressed by DHX15, suggesting a general role in promoting splicing fidelity. We identify SUGP1 as a G-patch factor that activates DHX15's splicing QC function. This interaction is dependent on both DHX15's ATPase activity and on SUGP1's U2AF ligand motif (ULM) domain. Together, our results support a model in which DHX15 plays a major role in splicing QC when recruited and activated by SUGP1.
Topics: Humans; RNA; RNA Helicases; RNA Precursors; RNA Splicing; RNA Splicing Factors; Spliceosomes; Splicing Factor U2AF
PubMed: 37805921
DOI: 10.1016/j.celrep.2023.113223 -
FEBS Letters Oct 2018Biological experiments have verified that EIciRNAs (a class of circRNA) produced from pre-mRNA can regulate gene expression, but the effect of regulation remains...
Biological experiments have verified that EIciRNAs (a class of circRNA) produced from pre-mRNA can regulate gene expression, but the effect of regulation remains unexplored. Here, we refine a mechanistic gene model from experimental facts, in which we assume pre-mRNA synthesizes EIciRNAs and mRNAs in a probabilistic manner, with the probability called the pathway strength, and the resulting EIciRNAs positively regulate the pre-mRNA synthesis. We show that there is a critical pathway strength such that the mRNA mean and the mRNA noise reach the highest and lowest levels, respectively. The EIciRNA can induce the unimodal and bimodal mRNA expressions, as well as the transition between them. Our investigation hints that EIciRNA is a non-negligible factor affecting cell-to-cell variability in gene expression.
Topics: Algorithms; Gene Expression Regulation; Models, Genetic; RNA; RNA Precursors; RNA, Circular; RNA, Messenger
PubMed: 30223292
DOI: 10.1002/1873-3468.13253 -
Annual Review of Biochemistry Jun 2020Splicing of the precursor messenger RNA, involving intron removal and exon ligation, is mediated by the spliceosome. Together with biochemical and genetic investigations... (Review)
Review
Splicing of the precursor messenger RNA, involving intron removal and exon ligation, is mediated by the spliceosome. Together with biochemical and genetic investigations of the past four decades, structural studies of the intact spliceosome at atomic resolution since 2015 have led to mechanistic delineation of RNA splicing with remarkable insights. The spliceosome is proven to be a protein-orchestrated metalloribozyme. Conserved elements of small nuclear RNA (snRNA) constitute the splicing active site with two catalytic metal ions and recognize three conserved intron elements through duplex formation, which are delivered into the splicing active site for branching and exon ligation. The protein components of the spliceosome stabilize the conformation of the snRNA, drive spliceosome remodeling, orchestrate the movement of the RNA elements, and facilitate the splicing reaction. The overall organization of the spliceosome and the configuration of the splicing active site are strictly conserved between human and yeast.
Topics: Catalytic Domain; Conserved Sequence; Exons; Humans; Introns; Models, Molecular; Nucleic Acid Conformation; Protein Structure, Secondary; RNA Helicases; RNA Precursors; RNA Splicing; RNA Splicing Factors; RNA, Small Nuclear; RNA-Binding Proteins; Ribonucleoprotein, U4-U6 Small Nuclear; Ribonucleoprotein, U5 Small Nuclear; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Spliceosomes
PubMed: 31815536
DOI: 10.1146/annurev-biochem-013118-111024 -
Radiation Research Apr 2023Altered cellular responses to DNA damage can contribute to cancer development, progression, and therapeutic resistance. Mutations in key DNA damage response factors...
Altered cellular responses to DNA damage can contribute to cancer development, progression, and therapeutic resistance. Mutations in key DNA damage response factors occur across many cancer types, and the DNA damage-responsive gene, TP53, is frequently mutated in a high percentage of cancers. We recently reported that an alternative splicing pathway induced by DNA damage regulates alternative splicing of TP53 RNA and further modulates cellular stress responses. Through damage-induced inhibition of the SMG1 kinase, TP53 pre-mRNA is alternatively spliced to generate TP53b mRNA and p53b protein is required for optimal induction of cellular senescence after ionizing radiation-induced DNA damage. Herein, we confirmed and extended these observations by demonstrating that the ATM protein kinase is required for repression of SMG1 kinase activity after ionizing radiation. We found that the RNA helicase and splicing factor, DDX5, interacts with SMG1, is required for alternative splicing of TP53 pre-mRNA to TP53b and TP53c mRNAs after DNA damage, and contributes to radiation-induced cellular senescence. Interestingly, the role of SMG1 in alternative splicing of p53 appears to be distinguishable from its role in regulating nonsense-mediated RNA decay. Thus, ATM, SMG1, and DDX5 participate in a DNA damage-induced alternative splicing pathway that regulates TP53 splicing and modulates radiation-induced cellular senescence.
Topics: Humans; Alternative Splicing; Protein Serine-Threonine Kinases; RNA Precursors; DNA Damage; Neoplasms; DEAD-box RNA Helicases; Ataxia Telangiectasia Mutated Proteins
PubMed: 36921295
DOI: 10.1667/RADE-22-00219.1 -
Wiley Interdisciplinary Reviews. RNA 2014The spliceosome and the microprocessor complex (MPC) are two important processing machineries that act on precursor (pre)-mRNA. Both cleave the pre-mRNA to generate... (Review)
Review
The spliceosome and the microprocessor complex (MPC) are two important processing machineries that act on precursor (pre)-mRNA. Both cleave the pre-mRNA to generate spliced mature transcripts and microRNAs (miRNAs), respectively. While spliceosomes identify in a complex manner correct splice sites, MPCs typically target RNA hairpins (pri-miRNA hairpins). In addition, pre-mRNA transcripts can contain pri-miRNA-like hairpins that are cleaved by the MPC without generating miRNAs. Recent evidence indicates that the position of hairpins on pre-mRNA, their distance from splice sites, and the relative efficiency of cropping and splicing contribute to determine the fate of a pre-mRNA. Depending on these factors, a pre-mRNA can be preferentially used to generate a miRNA, a constitutively or even an alternative spliced transcript. For example, competition between splicing and cropping on splice-site-overlapping miRNAs (SO miRNAs) results in alternative spliced isoforms and influences miRNA biogenesis. In several cases, the outcome of a pre-mRNA transcript and its final handling as miRNA or mRNA substrate can be frequently closely connected to the functional relationships between diverse pre-mRNA processing events. These events are influenced by both gene context and physiopathological conditions.
Topics: Alternative Splicing; Humans; Inverted Repeat Sequences; MicroRNAs; Protein Isoforms; RNA Precursors; RNA Processing, Post-Transcriptional; RNA Splicing; RNA, Messenger; Spliceosomes
PubMed: 24788135
DOI: 10.1002/wrna.1236 -
Wiley Interdisciplinary Reviews. RNA 2015Most, if not all RNAs, are transcribed as precursors that require processing to gain functionality. Ribosomal RNAs (rRNA) from all organisms undergo both exo- and... (Review)
Review
Most, if not all RNAs, are transcribed as precursors that require processing to gain functionality. Ribosomal RNAs (rRNA) from all organisms undergo both exo- and endonucleolytic processing. Also, in all organisms, rRNA processing occurs inside large preribosomal particles and is coupled to nucleotide modification, folding of the precursor rRNA (pre-rRNA), and assembly of the ribosomal proteins (r-proteins). In this review, we focus on the processing pathway of pre-rRNAs of cytoplasmic ribosomes in the yeast Saccharomyces cerevisiae, without doubt, the organism where this pathway is best characterized. We summarize the current understanding of the rRNA maturation process, particularly focusing on the pre-rRNA processing sites, the enzymes responsible for the cleavage or trimming reactions and the different mechanisms that monitor and regulate the pathway. Strikingly, the overall order of the various processing steps is reasonably well conserved in eukaryotes, perhaps reflecting common principles for orchestrating the concomitant events of pre-rRNA processing and ribosome assembly.
Topics: Models, Biological; Models, Molecular; RNA Precursors; RNA Processing, Post-Transcriptional; Saccharomyces cerevisiae
PubMed: 25327757
DOI: 10.1002/wrna.1267 -
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