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Xie J, Wang L, Lin RJ. Variations of intronic branchpoint motif: identification and functional implications in splicing and disease. Commun Biol 2023; 6:1142. [PMID: 37949953 PMCID: PMC10638238 DOI: 10.1038/s42003-023-05513-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
The branchpoint (BP) motif is an essential intronic element for spliceosomal pre-mRNA splicing. In mammals, its sequence composition, distance to the downstream exon, and number of BPs per 3´ splice site are highly variable, unlike the GT/AG dinucleotides at the intron ends. These variations appear to provide evolutionary advantages for fostering alternative splicing, satisfying more diverse cellular contexts, and promoting resilience to genetic changes, thus contributing to an extra layer of complexity for gene regulation. Importantly, variants in the BP motif itself or in genes encoding BP-interacting factors cause human genetic diseases or cancers, highlighting the critical function of BP motif and the need to precisely identify functional BPs for faithful interpretation of their roles in splicing. In this perspective, we will succinctly summarize the major findings related to BP motif variations, discuss the relevant issues/challenges, and provide our insights.
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Affiliation(s)
- Jiuyong Xie
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
| | - Ren-Jang Lin
- Center for RNA Biology & Therapeutics, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
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2
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Yıldırım B, Vogl C. Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract. J Evol Biol 2023; 36:1295-1312. [PMID: 37564008 PMCID: PMC10946897 DOI: 10.1111/jeb.14205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 08/12/2023]
Abstract
Among eukaryotes, the major spliceosomal pathway is highly conserved. While long introns may contain additional regulatory sequences, the ones in short introns seem to be nearly exclusively related to splicing. Although these regulatory sequences involved in splicing are well-characterized, little is known about their evolution. At the 3' end of introns, the splice signal nearly universally contains the dimer AG, which consists of purines, and the polypyrimidine tract upstream of this 3' splice signal is characterized by over-representation of pyrimidines. If the over-representation of pyrimidines in the polypyrimidine tract is also due to avoidance of a premature splicing signal, we hypothesize that AG should be the most under-represented dimer. Through the use of DNA-strand asymmetry patterns, we confirm this prediction in fruit flies of the genus Drosophila and by comparing the asymmetry patterns to a presumably neutrally evolving region, we quantify the selection strength acting on each motif. Moreover, our inference and simulation method revealed that the best explanation for the base composition evolution of the polypyrimidine tract is the joint action of purifying selection against a spurious 3' splice signal and the selection for pyrimidines. Patterns of asymmetry in other eukaryotes indicate that avoidance of premature splicing similarly affects the nucleotide composition in their polypyrimidine tracts.
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Affiliation(s)
- Burçin Yıldırım
- Department of Biomedical SciencesVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Claus Vogl
- Department of Biomedical SciencesVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
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3
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Glasser E, Maji D, Biancon G, Puthenpeedikakkal A, Cavender C, Tebaldi T, Jenkins J, Mathews D, Halene S, Kielkopf C. Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal. Nucleic Acids Res 2022; 50:5299-5312. [PMID: 35524551 PMCID: PMC9128377 DOI: 10.1093/nar/gkac287] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/03/2022] [Accepted: 04/12/2022] [Indexed: 11/24/2022] Open
Abstract
The essential pre-mRNA splicing factor U2AF2 (also called U2AF65) identifies polypyrimidine (Py) tract signals of nascent transcripts, despite length and sequence variations. Previous studies have shown that the U2AF2 RNA recognition motifs (RRM1 and RRM2) preferentially bind uridine-rich RNAs. Nonetheless, the specificity of the RRM1/RRM2 interface for the central Py tract nucleotide has yet to be investigated. We addressed this question by determining crystal structures of U2AF2 bound to a cytidine, guanosine, or adenosine at the central position of the Py tract, and compared U2AF2-bound uridine structures. Local movements of the RNA site accommodated the different nucleotides, whereas the polypeptide backbone remained similar among the structures. Accordingly, molecular dynamics simulations revealed flexible conformations of the central, U2AF2-bound nucleotide. The RNA binding affinities and splicing efficiencies of structure-guided mutants demonstrated that U2AF2 tolerates nucleotide substitutions at the central position of the Py tract. Moreover, enhanced UV-crosslinking and immunoprecipitation of endogenous U2AF2 in human erythroleukemia cells showed uridine-sensitive binding sites, with lower sequence conservation at the central nucleotide positions of otherwise uridine-rich, U2AF2-bound splice sites. Altogether, these results highlight the importance of RNA flexibility for protein recognition and take a step towards relating splice site motifs to pre-mRNA splicing efficiencies.
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Affiliation(s)
- Eliezra Glasser
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Debanjana Maji
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine and
Yale Cancer Center, Yale University School of Medicine,
New Haven,
CT 06520, USA
| | | | - Chapin E Cavender
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine and
Yale Cancer Center, Yale University School of Medicine,
New Haven,
CT 06520, USA
- Department of Cellular, Computational and Integrative Biology
(CIBIO), University of
Trento, Trento, Italy
| | - Jermaine L Jenkins
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - David H Mathews
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and
Yale Cancer Center, Yale University School of Medicine,
New Haven,
CT 06520, USA
- Yale Center for RNA Science and Medicine, Yale University
School of Medicine, New Haven,
CT 06520, USA
- Department of Pathology, Yale University School of
Medicine, New Haven,
CT 06520, USA
| | - Clara L Kielkopf
- Department of Biochemistry and Biophysics, and the Center for
RNA Biology, University of Rochester School of Medicine and
Dentistry, Rochester,
NY 14642, USA
- Wilmot Cancer Institute, University of Rochester School of
Medicine and Dentistry, Rochester,
NY 14642, USA
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Emery A, Swanstrom R. HIV-1: To Splice or Not to Splice, That Is the Question. Viruses 2021; 13:181. [PMID: 33530363 PMCID: PMC7912102 DOI: 10.3390/v13020181] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/05/2023] Open
Abstract
The transcription of the HIV-1 provirus results in only one type of transcript-full length genomic RNA. To make the mRNA transcripts for the accessory proteins Tat and Rev, the genomic RNA must completely splice. The mRNA transcripts for Vif, Vpr, and Env must undergo splicing but not completely. Genomic RNA (which also functions as mRNA for the Gag and Gag/Pro/Pol precursor polyproteins) must not splice at all. HIV-1 can tolerate a surprising range in the relative abundance of individual transcript types, and a surprising amount of aberrant and even odd splicing; however, it must not over-splice, which results in the loss of full-length genomic RNA and has a dramatic fitness cost. Cells typically do not tolerate unspliced/incompletely spliced transcripts, so HIV-1 must circumvent this cell policing mechanism to allow some splicing while suppressing most. Splicing is controlled by RNA secondary structure, cis-acting regulatory sequences which bind splicing factors, and the viral protein Rev. There is still much work to be done to clarify the combinatorial effects of these splicing regulators. These control mechanisms represent attractive targets to induce over-splicing as an antiviral strategy. Finally, splicing has been implicated in latency, but to date there is little supporting evidence for such a mechanism. In this review we apply what is known of cellular splicing to understand splicing in HIV-1, and present data from our newer and more sensitive deep sequencing assays quantifying the different HIV-1 transcript types.
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MESH Headings
- Alternative Splicing
- Exons
- Gene Expression Regulation, Viral
- HIV-1/genetics
- Nucleic Acid Conformation
- RNA Splicing
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Regulatory Sequences, Nucleic Acid
- Virus Latency/genetics
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Ann Emery
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA;
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
- Center for AIDS Research, University of North Carolina, Chapel Hill, NC 27599, USA
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Nguyen H, Das U, Xie J. Genome-wide evolution of wobble base-pairing nucleotides of branchpoint motifs with increasing organismal complexity. RNA Biol 2019; 17:311-324. [PMID: 31814500 DOI: 10.1080/15476286.2019.1697548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
How have the branchpoint motifs evolved in organisms of different complexity? Here we identified and examined the consensus motifs (R1C2T3R4A5Y6, R: A or G, Y: C or T) of 898 fungal genomes. In Ascomycota unicellular yeasts, the G4/A4 ratio is mostly (98%) below 0.125 but increases sharply in multicellular species by about 40 times on average, and in the more complex Basidiomycota, it increases further by about 7 times. The global G4 increase is consistent with A4 to G4 transitions in evolution. Of the G4/A4-interacting amino acids of the branchpoint binding protein MSL5 (SF1) and the HSH155 (SF3B1), as well as the 5' splice sites (SS) and U2 snRNA genes, the 5' SS G3/A3 co-vary with the G4 to some extent. However, corresponding increase of the G4-complementary GCAGTA-U2 gene is rare, suggesting wobble-base pairing between the G4-containing branchpoint motif and GTAGTA-U2 in most of these species. Interestingly, the G4/A4 ratio correlates well with the abundance of alternative splicing in the two phyla, and G4 enriched significantly at the alternative 3' SS of genes in RNA metabolism, kinases and membrane proteins. Similar wobble nucleotides also enriched at the 3' SS of multicellular fungi with only thousands of protein-coding genes. Thus, branchpoint motifs have evolved U2-complementarity in unicellular Ascomycota yeasts, but have gradually gained more wobble base-pairing nucleotides in fungi of higher complexity, likely to destabilize branchpoint motif-U2 interaction and/or branchpoint A protrusion for alternative splicing. This implies an important role of relaxing the branchpoint signals in the multicellularity and further complexity of fungi.
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Affiliation(s)
- Hai Nguyen
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.,Department of Applied Computer Sciences, University of Winnipeg, Winnipeg, Canada
| | - Urmi Das
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Jiuyong Xie
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
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Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes. Int J Mol Sci 2019; 20:ijms20153834. [PMID: 31390737 PMCID: PMC6695735 DOI: 10.3390/ijms20153834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions. The occurrences of alternative splicing mean that all exons could be classified to be either constitutively or alternatively spliced depending on whether they are virtually included into all mature mRNAs. From an evolutionary point of view, therefore, the alternatively spliced exons would have been associated with distinctive biological characteristics in comparison with constitutively spliced exons. In this paper, we first outline the representative types of alternative splicing events and exon classification, and then review sequence and evolutionary features for the alternatively spliced exons. The main purpose is to facilitate understanding of the biological implications of alternative splicing in eukaryotes. This knowledge is also helpful to establish computational approaches for predicting the splicing pattern of exons.
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