Abstract
The removal of introns from mRNA precursors and its regulation by alternative splicing are key for eukaryotic gene expression and cellular function, as evidenced by the numerous pathologies induced or modified by splicing alterations. Major recent advances have been made in understanding the structures and functions of the splicing machinery, in the description and classification of physiological and pathological isoforms and in the development of the first therapies for genetic diseases based on modulation of splicing. Here, we review this progress and discuss important remaining challenges, including predicting splice sites from genomic sequences, understanding the variety of molecular mechanisms and logic of splicing regulation, and harnessing this knowledge for probing gene function and disease aetiology and for the design of novel therapeutic approaches.
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Acknowledgements
The authors thank M. Irimia, B. Lehner, members of our group and four reviewers for suggestions on the manuscript. M.E.R. was supported by a MSCA Postdoctoral Fellowship and C.V. by a FPI-Severo Ochoa PhD Fellowship from the Spanish Ministry of Economy and Competitiveness. Work in the authors' laboratory has been supported by the European Research Council, European Innovation Council, LaCaixa Health, Worldwide Cancer Research, AGAUR, Spanish Ministry of Economy and Competitiveness and the Centre of Excellence Severo Ochoa. The authors acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership and the CERCA Programme/Generalitat de Catalunya.
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Glossary
- Alternative splicing
-
The process by which intron and/or exon sequences are differentially recognized in different cell types or biological conditions to generate distinct mRNAs and long non-coding RNAs from the same primary transcript.
- Back splicing
-
The process by which a 5′ splice site is spliced to a 3′ splice site located upstream in the same pre-mRNA molecule, leading to the generation of a circular RNA, typically spanning one or a few exons.
- Branch point
-
(BP). An intronic adenosine nucleotide, typically located 15–45 nucleotides 5′ of the 3′ end of introns, which engages in formation of a 2′–5′ phosphodiester bond with the 5′ end of the intron after the first catalytic step of the splicing reaction.
- Exon definition
-
A model for the mutual stabilization of splicing factors recognizing splice sites flanking internal exons in multicellular organisms.
- Intron definition
-
A model for the mutual stabilization of splicing factors recognizing the splice sites across an intron, which likely has a major role in the efficient co-transcriptional splicing of many introns.
- Introns
-
Internal sequences within primary transcripts produced by eukaryotic RNA polymerase II (RNA Pol II) that are removed through the process of pre-mRNA splicing, allowing their flanking sequences (exons) to be spliced together and thus generate functional mRNAs and long non-coding RNAs.
- MicroRNAs
-
A class of small regulatory RNAs whose function is to induce the degradation or repress the translation of mRNAs with which they have full or partial complementarity, respectively. They are often transcribed as part of intronic sequences, from which they are released to be assembled with specific proteins on microRNA-induced silencing complexes.
- Premature termination codons
-
Translation termination codons in mRNA arising from single-nucleotide mutations or from alternative splicing events that disrupt an open reading frame, often leading to mRNA degradation by the process of nonsense-mediated decay.
- Recursive splicing
-
The sequential excision of shorter pieces of a long intron, each piece being separated from the next by a zero-length exon.
- Small nucleolar RNAs
-
(snoRNAs). A class of small regulatory RNAs whose function is to guide the addition of chemical modifications at specific residues in other RNAs, including ribosomal, transfer or small nuclear RNAs (snRNAs). They are often transcribed as part of intronic sequences, from which they are released to be assembled with specific proteins on small nucleolar RNP complexes.
- Spliceosome
-
The molecular machinery involved in intron removal, composed of 5 small nuclear ribonucleoprotein (snRNP) complexes (U1, U2, U4, U5 and U6) and more than 150 accessory proteins.
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Rogalska, M.E., Vivori, C. & Valcárcel, J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat Rev Genet 24, 251–269 (2023). https://doi.org/10.1038/s41576-022-00556-8
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DOI: https://doi.org/10.1038/s41576-022-00556-8
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