Introduction to Molecular Biology
Martin G. Pomper, Juri G. Gelovani, Benjamin Tsui, Kathleen Gabrielson, Richard Wahl, S. Sam Gambhir, Jeff Bulte, Raymond Gibson, William C. Eckelman in Molecular Imaging in Oncology, 2008
RNA splicing is the process by which introns (the regions of RNA that do not code for proteins) are removed from the pre-mRNA and the remaining exons (regions that carry the code needed for protein synthesis) are connected to reform a single continuous RNA molecule. In 1989, Tom Cech won the Nobel Prize for his works on the mechanism of RNA splicing (9), prize that he shared with Sidney Altman for his work on RNA. Although the splicing occurs after the complete pre-mRNA synthesis and end-capping, some primary transcripts with many exons can be spliced during transcription. The splicing process needs to be very accurate, because an error in only one nucleotide (removal or addition) can cause a complete shift in the open reading frame of the code. This shift will, therefore, result in a new sequence of codons that will end in a completely different amino acid sequence or possibly insert a stop codon for the termination of the synthesis of the peptide. This kind of error in the splicing process accounts for about 15% of the genetic disease. The machine responsible for the RNA splicing is called spliceosome and is composed of a large enzymatic complex, which includes 145 different proteins (snRNPs or small nuclear ribonucleoproteins) and several snRNAs. This complex recognizes specific splice sites in the introns of pre-mRNA sequences. A pre-mRNA can be spliced in many different ways, thus producing different mature mRNAs that encode for different protein sequences. This process is called alternative splicing and it allows the production of a large amount of proteins from a limited amount of DNA.
Nucleic Acids as Therapeutic Targets and Agents
David E. Thurston, Ilona Pysz in Chemistry and Pharmacology of Anticancer Drugs, 2021
One example is the agent branaplam (Figure 5.100) which, as of July 2019, is in Phase I/II clinical trials for the treatment of children with Spinal Muscular Atrophy, branaplam is in a Phase II clinical trial SMA type 1. This molecule, based on a pyridazine building block, enhances the inclusion of exon 7, resulting in a full length and functional protein product. It represents the first example of splicing modulation using a sequence-selective small molecule and works by stabilizing the transient double-stranded RNA (dsRNA) structure formed between the SMN2 pre-mRNA and the U1 snRNP complex, a key component of the splicesome. It also increases the binding affinity of U1 snRNP to the 5’ splice site (5’ss) in a sequence-selective manner. Structure of branaplam (showing the keto-enol tautomers) which, as of July 2019, is in Phase I/II clinical trials for the treatment of children with spinal muscular atrophy (SMA).
Transcriptionally Regulatory Sequences of Phylogenetic Significance
S. K. Dutta in DNA Systematics, 2019
Many mRNAs show a conserved sequence of AAUAAA in the 3' end of poly A containing mRNA. Mutation in the sequence to AAGAAA or AAUAAG produces unusually long messages, which are unstable. Thus, at least for polymerase II, the termination of transcription obeys a sequence signal in the template. This signal is reflected in the terminus of its RNA in the form of a special hairpin structure which apparently facilitates post-transcriptional cleavage. The requirement of an endonucleolytic cleavage process on a small nuclear ribonucleoprotein “snRNP” has been clearly demonstrated with histone genes.238,239 Presumably, the sequence AAUAAA and perhaps another frequently occurring sequence CApyUG56 near the poly A addition site are being recognized by a small nuclear RNA, U4, in the “snRNP”. The situation is parallel to the splicing process for mRNA maturation, in which another class of “snRNP” is involved in aligning the intron-donor-acceptor sites with its U1 RNA,240 demonstrable by specific antibody inactivation.241 In yeast, the coding sequence for Ul-like RNA constitutes a portion of the 3' acceptor site of the intron of the same gene.119
Future avenues for therapy development for spinal muscular atrophy
Published in Expert Opinion on Drug Discovery, 2018
Because the genetic cause of SMA has long been known, significant research efforts have focused on understanding the cellular changes that occur when levels of SMN are reduced. Initial studies linked SMN to the biogenesis of small nuclear ribonucleoproteins (snRNPs), the protein–RNA complexes that are required for spliceosome formation [8]. This was later extended to general RNP biogenesis, as SMN was shown to be involved in the formation of a number of similar RNP complexes [9]. Because of this role, the function of SMN in RNA splicing has been extensively studied. Although SMN plays an important role in splicing, splicing defects in SMA appear to occur late in pathogenesis and might not be directly linked to cell-type-specific pathology, although this remains to be definitively determined [10,11].
Strategies for targeting RNA with small molecule drugs
Published in Expert Opinion on Drug Discovery, 2023
Christopher L. Haga, Donald G. Phinney
RNA splicing is a complicated key regulatory step in the generation of the diverse repertoire of human proteins from the limited protein-coding genome. The splicing process is carried out in the spliceosome, a large complex consisting of hundreds of proteins, snRNAs, and five small nuclear ribonucleoproteins (snRNP) which act in concert to bind and remove intronic sequences [63]. The vast majority of protein-coding transcripts undergo such carefully orchestrated splicing events. However, when pre-mRNA processing and splicing deviate from the norm, splicing disorders can occur. Because every intron-containing gene requires a certain level of processing and splicing, mutations falling within a canonical splice site can lead to aberrant gene translation and potentially to disease. Two such well-explored diseases concerning small molecule RNA targeting are familial dysautonomia (FD) and spinal muscular atrophy (SMA).
Inhibition of SF3b1 by pladienolide B evokes cycle arrest, apoptosis induction and p73 splicing in human cervical carcinoma cells
Published in Artificial Cells, Nanomedicine, and Biotechnology, 2019
Qianjing Zhang, Cuixia Di, Junfang Yan, Fang Wang, Tao Qu, Yupei Wang, Yuhong Chen, Xuetian Zhang, Yang Liu, Hongying Yang, Hong Zhang
Recently, considerable attention has been drawn to a new class of anticancer agents targeting the spliceosome [12,13]. For many eukaryotic introns, splicing is carried out in a series of reactions which are catalysed by the spliceosome, a complex of small nuclear ribonucleoproteins [14,15]. As such, the spliceosome has emerged as an attractive target for anticancer treatment [16]. SF3b1 is a principal player in the spliceosome and a target of inhibitor compounds [17,18]. Several spliceosome modulators have already been identified [19]. One of them is pladienolide B, which directly binds splicing factor 3b1 (SF3b1) in the spliceosome [20], inhibits the splicing process in tumor cells [21–23]. SF3B1 result in alternative splicing events and may constitute drivers and a novel therapeutic target in cancers [24]. Importantly, this compound has been demonstrated to be potent antitumor agents, and minimally toxic to normal cells [25].
Related Knowledge Centers
- Eukaryote
- Intron
- Primary Transcript
- Rna
- Rna Splicing
- Spliceosome
- Cell Nucleus
- Protein Complex
- Post-Transcriptional Modification
- U7 Small Nuclear Rna