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Bursakov SA, Kovaleva AV, Brigida AV, Zaripov OG. Functional analysis of the GPAT4 gene mutation predicted to affect splicing. Anim Biotechnol 2024; 35:2269210. [PMID: 37906284 DOI: 10.1080/10495398.2023.2269210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The GPAT4 gene is considered as a potential functional candidate for single nucleotide polymorphism (SNP) studies in dairy cattle breeding due to its association with dairy performance in cattle by encoding an enzyme responsible for the presence of diacylglycerols and triacylglycerols in milk. Using the example of the GPAT4 gene, we applied the minigene splicing assay to analyze the functional consequences of its variant that was predicted to affect normal splicing. The results of functional analysis revealed the sequence variations (rs442541537), transfection experiments in a wild type and mutant cell line model system demonstrated that the investigated mutation in the second intron of the GPAT4 gene was responsible for the presence of a second exon in mature messenger RNA (mRNA). The cases of its absence in the spliced mature mRNA transcript resulted in a truncated dysfunctional protein due to the appearance of a stop codon. Thus, the discovered SNP led to alternative splicing in pre-mRNA by the 'cassette exon' ('exon skipping') mechanism. The studied mutation can potentially be a molecular genetic marker for alternative splicing for the GPAT4 gene and, therefore contributes to economic benefits in cattle breeding programs.
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Affiliation(s)
- Sergey A Bursakov
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
- Federal State Budgetary Scientific Institution "All-Russia Research Institute of Agricultural Biotechnology", Moscow, Russia
| | - Anastasia V Kovaleva
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
| | - Artyom V Brigida
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
| | - Oleg G Zaripov
- Institution of Innovative Biotechnology in Animal Husbandry - A Branch of the Federal Research Center for Animal Husbandry Named After Academy Member L.K. Ernst, Moscow, Russia
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2
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Capitanchik C, Wilkins OG, Wagner N, Gagneur J, Ule J. From computational models of the splicing code to regulatory mechanisms and therapeutic implications. Nat Rev Genet 2024:10.1038/s41576-024-00774-2. [PMID: 39358547 DOI: 10.1038/s41576-024-00774-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2024] [Indexed: 10/04/2024]
Abstract
Since the discovery of RNA splicing and its role in gene expression, researchers have sought a set of rules, an algorithm or a computational model that could predict the splice isoforms, and their frequencies, produced from any transcribed gene in a specific cellular context. Over the past 30 years, these models have evolved from simple position weight matrices to deep-learning models capable of integrating sequence data across vast genomic distances. Most recently, new model architectures are moving the field closer to context-specific alternative splicing predictions, and advances in sequencing technologies are expanding the type of data that can be used to inform and interpret such models. Together, these developments are driving improved understanding of splicing regulatory mechanisms and emerging applications of the splicing code to the rational design of RNA- and splicing-based therapeutics.
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Affiliation(s)
- Charlotte Capitanchik
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, London, UK
| | - Oscar G Wilkins
- The Francis Crick Institute, London, UK
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Nils Wagner
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
| | - Jernej Ule
- The Francis Crick Institute, London, UK.
- UK Dementia Research Institute at King's College London, London, UK.
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry Psychology & Neuroscience, King's College London, London, UK.
- National Institute of Chemistry, Ljubljana, Slovenia.
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3
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Martínez-Lumbreras S, Morguet C, Sattler M. Dynamic interactions drive early spliceosome assembly. Curr Opin Struct Biol 2024; 88:102907. [PMID: 39168044 DOI: 10.1016/j.sbi.2024.102907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024]
Abstract
Splicing is a critical processing step during pre-mRNA maturation in eukaryotes. The correct selection of splice sites during the early steps of spliceosome assembly is highly important and crucial for the regulation of alternative splicing. Splice site recognition and alternative splicing depend on cis-regulatory sequence elements in the RNA and trans-acting splicing factors that recognize these elements and crosstalk with the canonical splicing machinery. Structural mechanisms involving early spliceosome complexes are governed by dynamic RNA structures, protein-RNA interactions and conformational flexibility of multidomain RNA binding proteins. Here, we highlight structural studies and integrative structural biology approaches, which provide complementary information from cryo-EM, NMR, small angle scattering, and X-ray crystallography to elucidate mechanisms in the regulation of early spliceosome assembly and quality control, highlighting the role of conformational dynamics.
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Affiliation(s)
- Santiago Martínez-Lumbreras
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Clara Morguet
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstrasse 4, 85747 Garching, Germany.
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4
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Ruan X, Hu K, Yang Y, Yang R, Tseng E, Kang B, Kauffman A, Zhong R, Zhang X. Cell-type-specific splicing of transcription regulators and Ptbp1 by Rbfox1/2/3 in the developing neocortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612108. [PMID: 39314274 PMCID: PMC11419088 DOI: 10.1101/2024.09.09.612108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
How master splicing regulators crosstalk with each other and to what extent transcription regulators are differentially spliced remain unclear in the developing brain. Here, cell-type-specific RNA-Seq of the developing neocortex uncover that transcription regulators are enriched for differential splicing, altering protein isoforms or inducing nonsense-mediated mRNA decay. Transient expression of Rbfox proteins in radial glia progenitors induces neuronal splicing events preferentially in transcription regulators such as Meis2 and Tead1. Surprisingly, Rbfox proteins promote the inclusion of a mammal-specific alternative exon and a previously undescribed poison exon in Ptbp1. Simultaneous ablation of Rbfox1/2/3 in the neocortex downregulates neuronal isoforms and disrupts radial neuronal migration. Furthermore, the progenitor isoform of Meis2 promotes Tgfb3 transcription, while the Meis2 neuron isoform promotes neuronal differentiation. These observations indicate that transcription regulators are differentially spliced between cell types in the developing neocortex.
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Affiliation(s)
- Xiangbin Ruan
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Equal contributions
| | - Kaining Hu
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Equal contributions
| | - Yalan Yang
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Equal contributions
| | - Runwei Yang
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | | | - Bowei Kang
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Aileen Kauffman
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Rong Zhong
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaochang Zhang
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- The Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
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5
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Lin TC, Tsai CH, Shiau CK, Huang JH, Tsai HK. Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning. BMC Genomics 2024; 25:830. [PMID: 39227799 PMCID: PMC11373144 DOI: 10.1186/s12864-024-10667-7] [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: 10/30/2022] [Accepted: 07/25/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Alternative splicing is a pivotal mechanism of post-transcriptional modification that contributes to the transcriptome plasticity and proteome diversity in metazoan cells. Although many splicing regulations around the exon/intron regions are known, the relationship between promoter-bound transcription factors and the downstream alternative splicing largely remains unexplored. RESULTS In this study, we present computational approaches to unravel the regulatory relationship between promoter-bound transcription factor binding sites (TFBSs) and the splicing patterns. We curated a fine dataset that includes DNase I hypersensitive site sequencing and transcriptomes across fifteen human tissues from ENCODE. Specifically, we proposed different representations of TF binding context and splicing patterns to examine the associations between the promoter and downstream splicing events. While machine learning models demonstrated potential in predicting splicing patterns based on TFBS occupancies, the limitations in the generalization of predicting the splicing forms of singleton genes across diverse tissues was observed with carefully examination using different cross-validation methods. We further investigated the association between alterations in individual TFBS at promoters and shifts in exon splicing efficiency. Our results demonstrate that the convolutional neural network (CNN) models, trained on TF binding changes in the promoters, can predict the changes in splicing patterns. Furthermore, a systemic in silico substitutions analysis on the CNN models highlighted several potential splicing regulators. Notably, using empirical validation using K562 CTCFL shRNA knock-down data, we showed the significant role of CTCFL in splicing regulation. CONCLUSION In conclusion, our finding highlights the potential role of promoter-bound TFBSs in influencing the regulation of downstream splicing patterns and provides insights for discovering alternative splicing regulations.
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Affiliation(s)
- Tzu-Chieh Lin
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Hung Tsai
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Kai Shiau
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan
| | - Jia-Hsin Huang
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan.
- Taiwan AI Labs & Foundation, Taipei, 10351, Taiwan.
| | - Huai-Kuang Tsai
- Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan.
- Taiwan AI Labs & Foundation, Taipei, 10351, Taiwan.
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6
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Wang D, Gazzara MR, Jewell S, Wales-McGrath B, Brown CD, Choi PS, Barash Y. A Deep Dive into Statistical Modeling of RNA Splicing QTLs Reveals New Variants that Explain Neurodegenerative Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.01.610696. [PMID: 39282456 PMCID: PMC11398334 DOI: 10.1101/2024.09.01.610696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Genome-wide association studies (GWAS) have identified thousands of putative disease causing variants with unknown regulatory effects. Efforts to connect these variants with splicing quantitative trait loci (sQTLs) have provided functional insights, yet sQTLs reported by existing methods cannot explain many GWAS signals. We show current sQTL modeling approaches can be improved by considering alternative splicing representation, model calibration, and covariate integration. We then introduce MAJIQTL, a new pipeline for sQTL discovery. MAJIQTL includes two new statistical methods: a weighted multiple testing approach for sGene discovery and a model for sQTL effect size inference to improve variant prioritization. By applying MAJIQTL to GTEx, we find significantly more sGenes harboring sQTLs with functional significance. Notably, our analysis implicates the novel variant rs582283 in Alzheimer's disease. Using antisense oligonucleotides, we validate this variant's effect by blocking the implicated YBX3 binding site, leading to exon skipping in the gene MS4A3.
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7
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Schmok JC, Jain M, Street LA, Tankka AT, Schafer D, Her HL, Elmsaouri S, Gosztyla ML, Boyle EA, Jagannatha P, Luo EC, Kwon EJ, Jovanovic M, Yeo GW. Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. Nat Biotechnol 2024; 42:1429-1441. [PMID: 38168984 PMCID: PMC11389820 DOI: 10.1038/s41587-023-02014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 01/05/2024]
Abstract
RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion changes and used these to evaluate 718 human RBPs. We performed enhanced cross-linking immunoprecipitation, RNA sequencing and affinity purification-mass spectrometry to investigate a subset of candidates with no prior association with splicing. Integrative analysis of these assays indicates surprising roles for TRNAU1AP, SCAF8 and RTCA in the modulation of hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using these identified domains, we engineered programmable fusion proteins that outperform current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. This tethering approach characterizes the ability of RBPs to induce exon inclusion and yields new molecular parts for programmable splicing control.
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Affiliation(s)
- Jonathan C Schmok
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Manya Jain
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lena A Street
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alex T Tankka
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Danielle Schafer
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sara Elmsaouri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Evan A Boyle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Pratibha Jagannatha
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ester J Kwon
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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8
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Choquet K, Chaumont LP, Bache S, Baxter-Koenigs AR, Churchman LS. Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.610338. [PMID: 39257732 PMCID: PMC11383983 DOI: 10.1101/2024.08.29.610338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Quantitative trait loci analyses have revealed an important role for genetic variants in regulating alternative splicing (AS) and alternative cleavage and polyadenylation (APA) in humans. Yet, these studies are generally performed with mature mRNA, so they report on the outcome rather than the processes of RNA maturation and thus may overlook how variants directly modulate pre-mRNA processing. The order in which the many introns of a human gene are removed can substantially influence AS, while nascent RNA polyadenylation can affect RNA stability and decay. However, how splicing order and poly(A) tail length are regulated by genetic variation has never been explored. Here, we used direct RNA nanopore sequencing to investigate allele-specific pre-mRNA maturation in 12 human lymphoblastoid cell lines. We found frequent splicing order differences between alleles and uncovered significant single nucleotide polymorphism (SNP)-splicing order associations in 17 genes. This included SNPs located in or near splice sites as well as more distal intronic and exonic SNPs. Moreover, several genes showed allele-specific poly(A) tail lengths, many of which also had a skewed allelic abundance ratio. HLA class I transcripts, which encode proteins that play an essential role in antigen presentation, showed the most allele-specific splicing orders, which frequently co-occurred with allele-specific AS, APA or poly(A) tail length differences. Together, our results expose new layers of genetic regulation of pre-mRNA maturation and highlight the power of long-read RNA sequencing for allele-specific analyses.
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Affiliation(s)
- Karine Choquet
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Canada
- Research Centre on Aging, CIUSSS de l'Estrie-CHUS, Sherbrooke, Canada
| | - Louis-Philippe Chaumont
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Canada
- Research Centre on Aging, CIUSSS de l'Estrie-CHUS, Sherbrooke, Canada
| | - Simon Bache
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Canada
- Research Centre on Aging, CIUSSS de l'Estrie-CHUS, Sherbrooke, Canada
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9
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Xu C, Bao S, Wang Y, Li W, Chen H, Shen Y, Jiang T, Zhang C. Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome Res 2024; 34:1052-1065. [PMID: 39060028 PMCID: PMC11368187 DOI: 10.1101/gr.279044.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024]
Abstract
Alternative splicing plays a crucial role in protein diversity and gene expression regulation in higher eukaryotes, and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets. However, the current methods for the quantitative prediction of splice site usage still have limited accuracy. Here, we present DeltaSplice, a deep neural network model optimized to learn the impact of mutations on quantitative changes in alternative splicing from the comparative analysis of homologous genes. The model architecture enables DeltaSplice to perform "reference-informed prediction" by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods on various prediction tasks, including evolutionary sequence divergence on lineage-specific splicing and splicing-altering mutations in human populations and neurodevelopmental disorders, and demonstrated that DeltaSplice outperformed consistently. DeltaSplice predicted ∼15% of splicing quantitative trait loci (sQTLs) in the human brain as causal splicing-altering variants. It also predicted splicing-altering de novo mutations outside the splice sites in a subset of patients affected by autism and other neurodevelopmental disorders (NDDs), including 19 genes with recurrent splicing-altering mutations. Integration of splicing-altering mutations with other types of de novo mutation burdens allowed the prediction of eight novel NDD-risk genes. Our work expanded the capacity of in silico splicing models with potential applications in genetic diagnosis and the development of splicing-based precision medicine.
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Affiliation(s)
- Chencheng Xu
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
| | - Suying Bao
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Ye Wang
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
| | - Wenxing Li
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA
| | - Hao Chen
- Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
- Department of Biomedical Informatics, Columbia University, New York, New York 10032, USA
| | - Tao Jiang
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China;
- Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, New York 10032, USA;
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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10
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Zhang X. Splice-switching antisense oligonucleotides for pediatric neurological disorders. Front Mol Neurosci 2024; 17:1412964. [PMID: 39119251 PMCID: PMC11306167 DOI: 10.3389/fnmol.2024.1412964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Pediatric neurological disorders are frequently devastating and present unmet needs for effective medicine. The successful treatment of spinal muscular atrophy with splice-switching antisense oligonucleotides (SSO) indicates a feasible path to targeting neurological disorders by redirecting pre-mRNA splicing. One direct outcome is the development of SSOs to treat haploinsufficient disorders by targeting naturally occurring non-productive splice isoforms. The development of personalized SSO treatment further inspired the therapeutic exploration of rare diseases. This review will discuss the recent advances that utilize SSOs to treat pediatric neurological disorders.
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Affiliation(s)
- Xiaochang Zhang
- Department of Human Genetics, The Neuroscience Institute, University of Chicago, Chicago, IL, United States
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11
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Apostolides M, Choi B, Navickas A, Saberi A, Soto LM, Goodarzi H, Najafabadi HS. Accurate isoform quantification by joint short- and long-read RNA-sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603067. [PMID: 39026819 PMCID: PMC11257535 DOI: 10.1101/2024.07.11.603067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Accurate quantification of transcript isoforms is crucial for understanding gene regulation, functional diversity, and cellular behavior. Existing RNA sequencing methods have significant limitations: short-read (SR) sequencing provides high depth but struggles with isoform deconvolution, whereas long-read (LR) sequencing offers isoform resolution at the cost of lower depth, higher noise, and technical biases. Addressing this gap, we introduce Multi-Platform Aggregation and Quantification of Transcripts (MPAQT), a generative model that combines the complementary strengths of different sequencing platforms to achieve state-of-the-art isoform-resolved transcript quantification, as demonstrated by extensive simulations and experimental benchmarks. By applying MPAQT to an in vitro model of human embryonic stem cell differentiation into cortical neurons, followed by machine learning-based modeling of transcript abundances, we show that untranslated regions (UTRs) are major determinants of isoform proportion and exon usage; this effect is mediated through isoform-specific sequence features embedded in UTRs, which likely interact with RNA-binding proteins that modulate mRNA stability. These findings highlight MPAQT's potential to enhance our understanding of transcriptomic complexity and underline the role of splicing-independent post-transcriptional mechanisms in shaping the isoform and exon usage landscape of the cell.
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Affiliation(s)
- Michael Apostolides
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, Canada
| | - Benedict Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Present address: Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France
| | - Ali Saberi
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, Canada
- Department of Electrical and Computer Engineering, McGill University, Montreal, Canada
| | - Larisa M. Soto
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, Canada
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, 3181 Porter Drive, Palo Alto, CA, USA
| | - Hamed S. Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, Canada
- McGill Centre for RNA Sciences, McGill University, Montreal, Canada
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12
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Roesmann F, Müller L, Klaassen K, Heß S, Widera M. Interferon-Regulated Expression of Cellular Splicing Factors Modulates Multiple Levels of HIV-1 Gene Expression and Replication. Viruses 2024; 16:938. [PMID: 38932230 PMCID: PMC11209495 DOI: 10.3390/v16060938] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Type I interferons (IFN-Is) are pivotal in innate immunity against human immunodeficiency virus I (HIV-1) by eliciting the expression of IFN-stimulated genes (ISGs), which encompass potent host restriction factors. While ISGs restrict the viral replication within the host cell by targeting various stages of the viral life cycle, the lesser-known IFN-repressed genes (IRepGs), including RNA-binding proteins (RBPs), affect the viral replication by altering the expression of the host dependency factors that are essential for efficient HIV-1 gene expression. Both the host restriction and dependency factors determine the viral replication efficiency; however, the understanding of the IRepGs implicated in HIV-1 infection remains greatly limited at present. This review provides a comprehensive overview of the current understanding regarding the impact of the RNA-binding protein families, specifically the two families of splicing-associated proteins SRSF and hnRNP, on HIV-1 gene expression and viral replication. Since the recent findings show specifically that SRSF1 and hnRNP A0 are regulated by IFN-I in various cell lines and primary cells, including intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs), we particularly discuss their role in the context of the innate immunity affecting HIV-1 replication.
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Affiliation(s)
- Fabian Roesmann
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Katleen Klaassen
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Stefanie Heß
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
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13
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Abulfaraj AA, Alshareef SA. Concordant Gene Expression and Alternative Splicing Regulation under Abiotic Stresses in Arabidopsis. Genes (Basel) 2024; 15:675. [PMID: 38927612 PMCID: PMC11202685 DOI: 10.3390/genes15060675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
The current investigation endeavors to identify differentially expressed alternatively spliced (DAS) genes that exhibit concordant expression with splicing factors (SFs) under diverse multifactorial abiotic stress combinations in Arabidopsis seedlings. SFs serve as the post-transcriptional mechanism governing the spatiotemporal dynamics of gene expression. The different stresses encompass variations in salt concentration, heat, intensive light, and their combinations. Clusters demonstrating consistent expression profiles were surveyed to pinpoint DAS/SF gene pairs exhibiting concordant expression. Through rigorous selection criteria, which incorporate alignment with documented gene functionalities and expression patterns observed in this study, four members of the serine/arginine-rich (SR) gene family were delineated as SFs concordantly expressed with six DAS genes. These regulated SF genes encompass cactin, SR1-like, SR30, and SC35-like. The identified concordantly expressed DAS genes encode diverse proteins such as the 26.5 kDa heat shock protein, chaperone protein DnaJ, potassium channel GORK, calcium-binding EF hand family protein, DEAD-box RNA helicase, and 1-aminocyclopropane-1-carboxylate synthase 6. Among the concordantly expressed DAS/SF gene pairs, SR30/DEAD-box RNA helicase, and SC35-like/1-aminocyclopropane-1-carboxylate synthase 6 emerge as promising candidates, necessitating further examinations to ascertain whether these SFs orchestrate splicing of the respective DAS genes. This study contributes to a deeper comprehension of the varied responses of the splicing machinery to abiotic stresses. Leveraging these DAS/SF associations shows promise for elucidating avenues for augmenting breeding programs aimed at fortifying cultivated plants against heat and intensive light stresses.
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Affiliation(s)
- Aala A. Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah 21921, Saudi Arabia;
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14
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Graham SV. HPV and RNA Binding Proteins: What We Know and What Remains to Be Discovered. Viruses 2024; 16:783. [PMID: 38793664 PMCID: PMC11126060 DOI: 10.3390/v16050783] [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: 04/04/2024] [Revised: 05/08/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Papillomavirus gene regulation is largely post-transcriptional due to overlapping open reading frames and the use of alternative polyadenylation and alternative splicing to produce the full suite of viral mRNAs. These processes are controlled by a wide range of cellular RNA binding proteins (RPBs), including constitutive splicing factors and cleavage and polyadenylation machinery, but also factors that regulate these processes, for example, SR and hnRNP proteins. Like cellular RNAs, papillomavirus RNAs have been shown to bind many such proteins. The life cycle of papillomaviruses is intimately linked to differentiation of the epithelial tissues the virus infects. For example, viral late mRNAs and proteins are expressed only in the most differentiated epithelial layers to avoid recognition by the host immune response. Papillomavirus genome replication is linked to the DNA damage response and viral chromatin conformation, processes which also link to RNA processing. Challenges with respect to elucidating how RBPs regulate the viral life cycle include consideration of the orchestrated spatial aspect of viral gene expression in an infected epithelium and the epigenetic nature of the viral episomal genome. This review discusses RBPs that control viral gene expression, and how the connectivity of various nuclear processes might contribute to viral mRNA production.
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Affiliation(s)
- Sheila V Graham
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
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15
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McCue K, Burge CB. An interpretable model of pre-mRNA splicing for animal and plant genes. SCIENCE ADVANCES 2024; 10:eadn1547. [PMID: 38718117 PMCID: PMC11078188 DOI: 10.1126/sciadv.adn1547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/04/2024] [Indexed: 05/12/2024]
Abstract
Pre-mRNA splicing is a fundamental step in gene expression, conserved across eukaryotes, in which the spliceosome recognizes motifs at the 3' and 5' splice sites (SSs), excises introns, and ligates exons. SS recognition and pairing is often influenced by protein splicing factors (SFs) that bind to splicing regulatory elements (SREs). Here, we describe SMsplice, a fully interpretable model of pre-mRNA splicing that combines models of core SS motifs, SREs, and exonic and intronic length preferences. We learn models that predict SS locations with 83 to 86% accuracy in fish, insects, and plants and about 70% in mammals. Learned SRE motifs include both known SF binding motifs and unfamiliar motifs, and both motif classes are supported by genetic analyses. Our comparisons across species highlight similarities between non-mammals, increased reliance on intronic SREs in plant splicing, and a greater reliance on SREs in mammalian splicing.
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Affiliation(s)
- Kayla McCue
- Computational and Systems Biology PhD Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Christopher B. Burge
- Computational and Systems Biology PhD Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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16
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Recinos Y, Ustianenko D, Yeh YT, Wang X, Jacko M, Yesantharao LV, Wu Q, Zhang C. CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements. Nat Commun 2024; 15:3839. [PMID: 38714659 PMCID: PMC11076525 DOI: 10.1038/s41467-024-47140-8] [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: 06/21/2023] [Accepted: 03/16/2024] [Indexed: 05/10/2024] Open
Abstract
Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is hampered by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically inactive CRISPR-RfxCas13d RNA-targeting system (dCas13d/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to SMN2, a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identifies not only known SREs but also a previously unknown distal intronic SRE, which can be targeted to alter exon 7 splicing using either dCas13d/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.
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Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Flagship Pioneering, Cambridge, MA, 02142, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Martin Jacko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Aperture Therapeutics, Inc., San Carlos, CA, 94070, USA
| | - Lekha V Yesantharao
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Qiyang Wu
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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17
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Xu C, Bao S, Chen H, Jiang T, Zhang C. Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586363. [PMID: 38586002 PMCID: PMC10996483 DOI: 10.1101/2024.03.22.586363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Alternative splicing plays a crucial role in protein diversity and gene expression regulation in higher eukaryotes and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets. However, the current methods for the quantitative prediction of splice site usage still have limited accuracy. Here, we present DeltaSplice, a deep neural network model optimized to learn the impact of mutations on quantitative changes in alternative splicing from the comparative analysis of homologous genes. The model architecture enables DeltaSplice to perform "reference-informed prediction" by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods on various prediction tasks, including evolutionary sequence divergence on lineage-specific splicing and splicing-altering mutations in human populations and neurodevelopmental disorders, and demonstrated that DeltaSplice outperformed consistently. DeltaSplice predicted ~15% of splicing quantitative trait loci (sQTLs) in the human brain as causal splicing-altering variants. It also predicted splicing-altering de novo mutations outside the splice sites in a subset of patients affected by autism and other neurodevelopmental disorders, including 19 genes with recurrent splicing-altering mutations. Among the new candidate disease risk genes, MFN1 is involved in mitochondria fusion, which is frequently disrupted in autism patients. Our work expanded the capacity of in silico splicing models with potential applications in genetic diagnosis and the development of splicing-based precision medicine.
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Affiliation(s)
- Chencheng Xu
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
- Present address: Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Suying Bao
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Present address: Regeneron Pharmaceuticals, Terrytown, NY 10591, USA
| | - Hao Chen
- Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
- Present address: Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tao Jiang
- Bioinformatics Division, BNRIST, Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
- Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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18
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Zhou Z, Zhang J, Zheng X, Pan Z, Zhao F, Gao Y. CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308115. [PMID: 38308181 PMCID: PMC11005702 DOI: 10.1002/advs.202308115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Circular RNAs (circRNAs) are a crucial yet relatively unexplored class of transcripts known for their tissue- and cell-type-specific expression patterns. Despite the advances in single-cell and spatial transcriptomics, these technologies face difficulties in effectively profiling circRNAs due to inherent limitations in circRNA sequencing efficiency. To address this gap, a deep learning model, CIRI-deep, is presented for comprehensive prediction of circRNA regulation on diverse types of RNA-seq data. CIRI-deep is trained on an extensive dataset of 25 million high-confidence circRNA regulation events and achieved high performances on both test and leave-out data, ensuring its accuracy in inferring differential events from RNA-seq data. It is demonstrated that CIRI-deep and its adapted version enable various circRNA analyses, including cluster- or region-specific circRNA detection, BSJ ratio map visualization, and trans and cis feature importance evaluation. Collectively, CIRI-deep's adaptability extends to all major types of RNA-seq datasets including single-cell and spatial transcriptomic data, which will undoubtedly broaden the horizons of circRNA research.
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Affiliation(s)
- Zihan Zhou
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Jinyang Zhang
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Xin Zheng
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Zhicheng Pan
- Center for Computational Biology Flatiron InstituteNew York10010USA
| | - Fangqing Zhao
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Yuan Gao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
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19
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Su P, Yan S, Chen K, Huang L, Wang L, Lee FHF, Zhou H, Lai TKY, Jiang A, Samsom J, Wong AHC, Yang G, Liu F. EF1α-associated protein complexes affect dendritic spine plasticity by regulating microglial phagocytosis in Fmr1 knock-out mice. Mol Psychiatry 2024; 29:1099-1113. [PMID: 38212373 DOI: 10.1038/s41380-023-02396-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024]
Abstract
Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability. There is no specific treatment for FXS due to the lack of therapeutic targets. We report here that Elongation Factor 1α (EF1α) forms a complex with two other proteins: Tripartite motif-containing protein 3 (TRIM3) and Murine double minute (Mdm2). Both EF1α-Mdm2 and EF1α-TRIM3 protein complexes are increased in the brain of Fmr1 knockout mice as a result of FMRP deficiency, which releases the normal translational suppression of EF1α mRNA and increases EF1α protein levels. Increased EF1α-Mdm2 complex decreases PSD-95 ubiquitination (Ub-PSD-95) and Ub-PSD-95-C1q interaction. The elevated level of TRIM3-EF1α complex is associated with decreased TRIM3-Complement Component 3 (C3) complex that inhibits the activation of C3. Both protein complexes thereby contribute to a reduction in microglia-mediated phagocytosis and dendritic spine pruning. Finally, we created a peptide that disrupts both protein complexes and restores dendritic spine plasticity and behavioural deficits in Fmr1 knockout mice. The EF1α-Mdm2 and EF1α-TRIM3 complexes could thus be new therapeutic targets for FXS.
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Affiliation(s)
- Ping Su
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T1R8, Canada
| | - Shuxin Yan
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T1R8, Canada
| | - Kai Chen
- Department of Anesthesiology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Lianyan Huang
- Department of Anesthesiology, New York University School of Medicine, New York, NY, 10016, USA
| | - Le Wang
- Institute of Mental Health and Drug Discovery, Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Frankie Hang Fung Lee
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T1R8, Canada
| | - Hang Zhou
- Department of Anesthesiology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Terence Kai Ying Lai
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T1R8, Canada
- Department of Physiology, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Anlong Jiang
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T1R8, Canada
| | - James Samsom
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T1R8, Canada
| | - Albert H C Wong
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T1R8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5T 1R8, Canada
- Institutes of Medical Science, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Guang Yang
- Department of Anesthesiology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Fang Liu
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T1R8, Canada.
- Institute of Mental Health and Drug Discovery, Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Mental Health, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China.
- Department of Physiology, University of Toronto, Toronto, ON, M5T 1R8, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada.
- Institutes of Medical Science, University of Toronto, Toronto, ON, M5T 1R8, Canada.
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20
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Liu X, Zhang J, Wang Z, Yan M, Xu M, Li G, Shender V, Wei J, Li J, Shao C, Zhang S, Kong B, Song K, Liu Z. Splicing Factor PQBP1 Curtails BAX Expression to Promote Ovarian Cancer Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306229. [PMID: 38342602 PMCID: PMC11022708 DOI: 10.1002/advs.202306229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/27/2023] [Indexed: 02/13/2024]
Abstract
Splicing factor polyglutamine binding protein-1 (PQBP1) is abundantly expressed in the central nervous system during development, and mutations in the gene cause intellectual disability. However, the roles of PQBP1 in cancer progression remain largely unknown. Here, it is shown that PQBP1 overexpression promotes tumor progression and indicates worse prognosis in ovarian cancer. Integrative analysis of spyCLIP-seq and RNA-seq data reveals that PQBP1 preferentially binds to exon regions and modulates exon skipping. Mechanistically, it is shown that PQBP1 regulates the splicing of genes related to the apoptotic signaling pathway, including BAX. PQBP1 promotes BAX exon 2 skipping to generate a truncated isoform that undergoes degradation by nonsense-mediated mRNA decay, thus making cancer cells resistant to apoptosis. In contrast, PQBP1 depletion or splice-switching antisense oligonucleotides promote exon 2 inclusion and thus increase BAX expression, leading to inhibition of tumor growth. Together, the results demonstrate an oncogenic role of PQBP1 in ovarian cancer and suggest that targeting the aberrant splicing mediated by PQBP1 has therapeutic potential in cancer treatment.
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Affiliation(s)
- Xihan Liu
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
- Advanced Medical Research InstituteShandong UniversityJinan250012China
| | - Jiaojiao Zhang
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Zixiang Wang
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
- Advanced Medical Research InstituteShandong UniversityJinan250012China
| | - Mingyao Yan
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Meining Xu
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Gaoyuan Li
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Victoria Shender
- Center for Precision Genome Editing and Genetic Technologies for BiomedicineFederal Research and Clinical Center of Physical‐Chemical Medicine of Federal Medical Biological AgencyMoscow119435Russia
| | - Jian‐jun Wei
- Department of PathologyNorthwestern University School of MedicineChicagoIL60611USA
| | - Jianqiao Li
- Department of OphthalmologyQilu HospitalShandong UniversityJinan250012China
| | - Changshun Shao
- Key Laboratory of Radiation Medicine and ProtectionInstitutes for Translational MedicineSoochow UniversitySuzhou215127China
| | - Shiqian Zhang
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Beihua Kong
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Kun Song
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
| | - Zhaojian Liu
- Key Laboratory of Experimental TeratologyMinistry of EducationDepartment of Obstetrics and GynecologyQilu HospitalDepartment of Cell BiologySchool of Basic Medical ScienceShandong UniversityJinan250012China
- Advanced Medical Research InstituteShandong UniversityJinan250012China
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21
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Chen K, Zhou Y, Ding M, Wang Y, Ren Z, Yang Y. Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction. Brief Bioinform 2024; 25:bbae163. [PMID: 38605640 PMCID: PMC11009468 DOI: 10.1093/bib/bbae163] [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: 01/04/2024] [Revised: 02/22/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Language models pretrained by self-supervised learning (SSL) have been widely utilized to study protein sequences, while few models were developed for genomic sequences and were limited to single species. Due to the lack of genomes from different species, these models cannot effectively leverage evolutionary information. In this study, we have developed SpliceBERT, a language model pretrained on primary ribonucleic acids (RNA) sequences from 72 vertebrates by masked language modeling, and applied it to sequence-based modeling of RNA splicing. Pretraining SpliceBERT on diverse species enables effective identification of evolutionarily conserved elements. Meanwhile, the learned hidden states and attention weights can characterize the biological properties of splice sites. As a result, SpliceBERT was shown effective on several downstream tasks: zero-shot prediction of variant effects on splicing, prediction of branchpoints in humans, and cross-species prediction of splice sites. Our study highlighted the importance of pretraining genomic language models on a diverse range of species and suggested that SSL is a promising approach to enhance our understanding of the regulatory logic underlying genomic sequences.
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Affiliation(s)
- Ken Chen
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yue Zhou
- Peng Cheng Laboratory, Shenzhen, China
| | - Maolin Ding
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yu Wang
- Peng Cheng Laboratory, Shenzhen, China
| | | | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Machine Intelligence and Advanced Computing (Sun Yat-sen University), Ministry of Education, China
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22
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Wang F, Jin Z, Wang S, Yang L, Fan Z, Yao Y. ASAPA: a bioinformatic pipeline based on Iso-Seq that identifies the links among alternative splicing, alternative transcription initiation and alternative polyadenylation. Funct Integr Genomics 2024; 24:67. [PMID: 38528184 DOI: 10.1007/s10142-024-01332-z] [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: 09/07/2023] [Revised: 02/29/2024] [Accepted: 03/02/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Although the events associated with alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI) can be identified by many approaches based on isoform sequencing (Iso-Seq), these analyses are generally independent of each other and the links between these events are still rarely mentioned. However, an interdependency analysis can be achieved because the transcriptional start site, splice sites and polyA site could be simultaneously included in a long, full-length read from Iso-Seq. RESULTS We create ASAPA pipeline that enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data. We tested this pipeline using Arabidopsis data and found some interesting results: some adjacent introns tend to be simultaneously spliced or retained; coupling between AS and ATI or APA is limited to the initial or terminal intron; and ATI and APA are potentially linked in some special cases. CONCLUSION Our pipeline enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data, which is conducive to a better understanding of transcription landscape generation.
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Grants
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
- 32072537,31872068 This work is supported by the National Natural Science Foundation of China (32072537,31872068), fruit industry technology system of Shandong Province (SDAIT-06-03), and Agriculture Improved Variety Project of Shandong Province (2020LZGC008).
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Zhongxin Jin
- National Key Laboratory of Tropical Crop Breeding, Tropical Bioscience and Biotechnology Institute, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shengnan Wang
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Longcheng Yang
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Zongbao Fan
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Yuxin Yao
- State Key Laboratory of Crop Biology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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23
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Lynn N, Tuller T. Detecting and understanding meaningful cancerous mutations based on computational models of mRNA splicing. NPJ Syst Biol Appl 2024; 10:25. [PMID: 38453965 PMCID: PMC10920900 DOI: 10.1038/s41540-024-00351-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Cancer research has long relied on non-silent mutations. Yet, it has become overwhelmingly clear that silent mutations can affect gene expression and cancer cell fitness. One fundamental mechanism that apparently silent mutations can severely disrupt is alternative splicing. Here we introduce Oncosplice, a tool that scores mutations based on models of proteomes generated using aberrant splicing predictions. Oncosplice leverages a highly accurate neural network that predicts splice sites within arbitrary mRNA sequences, a greedy transcript constructor that considers alternate arrangements of splicing blueprints, and an algorithm that grades the functional divergence between proteins based on evolutionary conservation. By applying this tool to 12M somatic mutations we identify 8K deleterious variants that are significantly depleted within the healthy population; we demonstrate the tool's ability to identify clinically validated pathogenic variants with a positive predictive value of 94%; we show strong enrichment of predicted deleterious mutations across pan-cancer drivers. We also achieve improved patient survival estimation using a proposed set of novel cancer-involved genes. Ultimately, this pipeline enables accelerated insight-gathering of sequence-specific consequences for a class of understudied mutations and provides an efficient way of filtering through massive variant datasets - functionalities with immediate experimental and clinical applications.
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Affiliation(s)
- Nicolas Lynn
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, 69978, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, 69978, Israel.
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24
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Gupta K, Yang C, McCue K, Bastani O, Sharp PA, Burge CB, Solar-Lezama A. Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing. Genome Biol 2024; 25:23. [PMID: 38229106 PMCID: PMC10790492 DOI: 10.1186/s13059-023-03162-x] [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: 07/25/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024] Open
Abstract
Sequence-specific RNA-binding proteins (RBPs) play central roles in splicing decisions. Here, we describe a modular splicing architecture that leverages in vitro-derived RNA affinity models for 79 human RBPs and the annotated human genome to produce improved models of RBP binding and activity. Binding and activity are modeled by separate Motif and Aggregator components that can be mixed and matched, enforcing sparsity to improve interpretability. Training a new Adjusted Motif (AM) architecture on the splicing task not only yields better splicing predictions but also improves prediction of RBP-binding sites in vivo and of splicing activity, assessed using independent data.
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Affiliation(s)
- Kavi Gupta
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chenxi Yang
- Department of Computer Science, University of Texas at Austin, Austin, TX, 78712, USA
| | - Kayla McCue
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Osbert Bastani
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Phillip A Sharp
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Armando Solar-Lezama
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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25
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Tse V, Chacaltana G, Gutierrez M, Forino N, Jimenez A, Tao H, Do P, Oh C, Chary P, Quesada I, Hamrick A, Lee S, Stone M, Sanford J. An intronic RNA element modulates Factor VIII exon-16 splicing. Nucleic Acids Res 2024; 52:300-315. [PMID: 37962303 PMCID: PMC10783525 DOI: 10.1093/nar/gkad1034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Pathogenic variants in the human Factor VIII (F8) gene cause Hemophilia A (HA). Here, we investigated the impact of 97 HA-causing single-nucleotide variants on the splicing of 11 exons from F8. For the majority of F8 exons, splicing was insensitive to the presence of HA-causing variants. However, splicing of several exons, including exon-16, was impacted by variants predicted to alter exonic splicing regulatory sequences. Using exon-16 as a model, we investigated the structure-function relationship of HA-causing variants on splicing. Intriguingly, RNA chemical probing analyses revealed a three-way junction structure at the 3'-end of intron-15 (TWJ-3-15) capable of sequestering the polypyrimidine tract. We discovered antisense oligonucleotides (ASOs) targeting TWJ-3-15 partially rescue splicing-deficient exon-16 variants by increasing accessibility of the polypyrimidine tract. The apical stem loop region of TWJ-3-15 also contains two hnRNPA1-dependent intronic splicing silencers (ISSs). ASOs blocking these ISSs also partially rescued splicing. When used in combination, ASOs targeting both the ISSs and the region sequestering the polypyrimidine tract, fully rescue pre-mRNA splicing of multiple HA-linked variants of exon-16. Together, our data reveal a putative RNA structure that sensitizes F8 exon-16 to aberrant splicing.
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Affiliation(s)
- Victor Tse
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Guillermo Chacaltana
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Martin Gutierrez
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Nicholas M Forino
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Arcelia G Jimenez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Hanzhang Tao
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Phong H Do
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Catherine Oh
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Priyanka Chary
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Isabel Quesada
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Antonia Hamrick
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Sophie Lee
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jeremy R Sanford
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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26
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Polvèche H, Valat J, Fontrodona N, Lapendry A, Clerc V, Janczarski S, Mortreux F, Auboeuf D, Bourgeois CF. SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors. Database (Oxford) 2023; 2023:baad091. [PMID: 38128543 PMCID: PMC10735282 DOI: 10.1093/database/baad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/06/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
One challenge faced by scientists from the alternative RNA splicing field is to decode the cooperative or antagonistic effects of splicing factors (SFs) to understand and eventually predict splicing outcomes on a genome-wide scale. In this manuscript, we introduce SplicingLore, an open-access database and web resource that help to fill this gap in a straightforward manner. The database contains a collection of RNA-sequencing-derived lists of alternative exons regulated by a total of 75 different SFs. All datasets were processed in a standardized manner, ensuring valid comparisons and correlation analyses. The user can easily retrieve a factor-specific set of differentially included exons from the database or provide a list of exons and search which SF(s) control(s) their inclusion. Our simple workflow is fast and easy to run, and it ensures a reliable calculation of correlation scores between the tested datasets. As a proof of concept, we predicted and experimentally validated a novel functional cooperation between the RNA helicases DDX17 and DDX5 and the heterogeneous nuclear ribonucleoprotein C (HNRNPC) protein. SplicingLore is available at https://splicinglore.ens-lyon.fr/. Database URL: https://splicinglore.ens-lyon.fr/.
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Affiliation(s)
| | - Jessica Valat
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Nicolas Fontrodona
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Audrey Lapendry
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Valentine Clerc
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Stéphane Janczarski
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
| | - Franck Mortreux
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d’Italie, Lyon F-69364, France
- Equipe Labellisee Ligue Contre le Cancer, 4 allee d'Italie, Lyon 69007, France
- CECS/AFM, I-STEM, 28 rue Henri Desbrueres, Corbeil-Essonnes F-91100, France
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27
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Smith C, Kitzman JO. Benchmarking splice variant prediction algorithms using massively parallel splicing assays. Genome Biol 2023; 24:294. [PMID: 38129864 PMCID: PMC10734170 DOI: 10.1186/s13059-023-03144-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Variants that disrupt mRNA splicing account for a sizable fraction of the pathogenic burden in many genetic disorders, but identifying splice-disruptive variants (SDVs) beyond the essential splice site dinucleotides remains difficult. Computational predictors are often discordant, compounding the challenge of variant interpretation. Because they are primarily validated using clinical variant sets heavily biased to known canonical splice site mutations, it remains unclear how well their performance generalizes. RESULTS We benchmark eight widely used splicing effect prediction algorithms, leveraging massively parallel splicing assays (MPSAs) as a source of experimentally determined ground-truth. MPSAs simultaneously assay many variants to nominate candidate SDVs. We compare experimentally measured splicing outcomes with bioinformatic predictions for 3,616 variants in five genes. Algorithms' concordance with MPSA measurements, and with each other, is lower for exonic than intronic variants, underscoring the difficulty of identifying missense or synonymous SDVs. Deep learning-based predictors trained on gene model annotations achieve the best overall performance at distinguishing disruptive and neutral variants, and controlling for overall call rate genome-wide, SpliceAI and Pangolin have superior sensitivity. Finally, our results highlight two practical considerations when scoring variants genome-wide: finding an optimal score cutoff, and the substantial variability introduced by differences in gene model annotation, and we suggest strategies for optimal splice effect prediction in the face of these issues. CONCLUSION SpliceAI and Pangolin show the best overall performance among predictors tested, however, improvements in splice effect prediction are still needed especially within exons.
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Affiliation(s)
- Cathy Smith
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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28
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Sheng M, Zhang Y, Wang Y, Liu W, Wang X, Ke T, Liu P, Wang S, Shao W. Decoding the role of aberrant RNA alternative splicing in hepatocellular carcinoma: a comprehensive review. J Cancer Res Clin Oncol 2023; 149:17691-17708. [PMID: 37898981 DOI: 10.1007/s00432-023-05474-8] [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: 07/18/2023] [Accepted: 10/10/2023] [Indexed: 10/31/2023]
Abstract
During eukaryotic gene expression, alternative splicing of messenger RNA precursors is critical in increasing protein diversity and regulatory complexity. Multiple transcript isoforms could be produced by alternative splicing from a single gene; they could eventually be translated into protein isoforms with deleted, added, or altered domains or produce transcripts containing premature termination codons that could be targeted by nonsense-mediated mRNA decay. Alternative splicing can generate proteins with similar, different, or even opposite functions. Increasingly strong evidence indicates that abnormal RNA splicing is a prevalent and crucial occurrence in cellular differentiation, tissue advancement, and the development and progression of cancer. Aberrant alternative splicing could affect cancer cell activities such as growth, apoptosis, invasiveness, drug resistance, angiogenesis, and metabolism. This systematic review provides a comprehensive overview of the impact of abnormal RNA alternative splicing on the development and progression of hepatocellular carcinoma.
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Affiliation(s)
- Mengfei Sheng
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yuanyuan Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yaoyun Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Weiyi Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Xingyu Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Tiaoying Ke
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Pingyang Liu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Sihan Wang
- Department of Clinical Medicine, Bengbu Medical College, Bengbu, China
| | - Wei Shao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
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29
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Stepankiw N, Yang AWH, Hughes TR. The human genome contains over a million autonomous exons. Genome Res 2023; 33:1865-1878. [PMID: 37945377 PMCID: PMC10760453 DOI: 10.1101/gr.277792.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
Mammalian mRNA and lncRNA exons are often small compared to introns. The exon definition model predicts that exons splice autonomously, dependent on proximal exon sequence features, explaining their delineation within large introns. This model has not been examined on a genome-wide scale, however, leaving open the question of how often mRNA and lncRNA exons are autonomous. It is also unknown how frequently such exons can arise by chance. Here, we directly assayed large fragments (500-1000 bp) of the human genome by exon trapping, which detects exons spliced into a heterologous transgene, here designed with a large intron context. We define the trapped exons as "autonomous." We obtained ∼1.25 million trapped exons, including most known mRNA and well-annotated lncRNA internal exons, demonstrating that human exons are predominantly autonomous. mRNA exons are trapped with the highest efficiency. Nearly a million of the trapped exons are unannotated, most located in intergenic regions and antisense to mRNA, with depletion from the forward strand of introns. These exons are not conserved, suggesting they are nonfunctional and arose from random mutations. They are nonetheless highly enriched with known splicing promoting sequence features that delineate known exons. Novel autonomous exons are more numerous than annotated lncRNA exons, and computational models also indicate they will occur with similar frequency in any randomly generated sequence. These results show that most human coding exons splice autonomously, and provide an explanation for the existence of many unconserved lncRNAs, as well as a new annotation and inclusion levels of spliceable loci in the human genome.
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Affiliation(s)
- Nicholas Stepankiw
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Ally W H Yang
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada M5S 3E1;
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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30
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Zhang M, Wang H, Han J, Wang H, Jia Y, Hong W, Tang F, Li Z. Specific recognition and sensitive quantification of mRNA splice variants via one-pot ligation-dependent loop-mediated isothermal amplification. Analyst 2023; 148:5605-5611. [PMID: 37818948 DOI: 10.1039/d3an01382k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Specific recognition and sensitive quantification of mRNA alternative splice variants have been a necessity for exploring the regulatory mechanism of RNA splicing and revealing the association between pre-mRNA splicing and transcriptome function, as well as disease diagnosis. However, their wide abundance range and high sequence homology pose enormous challenges for high sensitivity and selectivity quantification of splice variants. Herein, taking advantage of the excellent specificity of ligation and the powerful nucleic acid replication feature of loop-mediated isothermal amplification (LAMP), we developed a one-pot method (termed one-pot ligation-LAMP) for specific recognition and sensitive quantification of mRNA splicing variants based on two splicing junction-specific stem-loop DNA probe ligation and the subsequently initiating LAMP. The one-pot ligation-LAMP can specifically detect as low as 100 aM mRNA splice variants without any nonspecific signals and quantify them with a wide dynamics range spanning at least six orders of magnitude. We have demonstrated that the one-pot ligation-LAMP is a versatile and practical strategy for accurately quantifying different splicing variants in complex biological samples with high sensitivity all in one tube within 90 min, thereby providing an attractive tool for mRNA splice variant-related studies.
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Affiliation(s)
- Mai Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Jun Han
- National Textile and Leather Product Quality Inspection and Testing Centre, 15 Xili-Balizhuang, Chaoyang District, Beijing 100025, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Yuting Jia
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Weixiang Hong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Fu Tang
- School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
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31
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Yue T, Wang Y, Zhang L, Gu C, Xue H, Wang W, Lyu Q, Dun Y. Deep Learning for Genomics: From Early Neural Nets to Modern Large Language Models. Int J Mol Sci 2023; 24:15858. [PMID: 37958843 PMCID: PMC10649223 DOI: 10.3390/ijms242115858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
The data explosion driven by advancements in genomic research, such as high-throughput sequencing techniques, is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in various fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning, since we expect a superhuman intelligence that explores beyond our knowledge to interpret the genome from deep learning. A powerful deep learning model should rely on the insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with proper deep learning-based architecture, and we remark on practical considerations of developing deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research and point out current challenges and potential research directions for future genomics applications. We believe the collaborative use of ever-growing diverse data and the fast iteration of deep learning models will continue to contribute to the future of genomics.
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Affiliation(s)
- Tianwei Yue
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Yuanxin Wang
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Longxiang Zhang
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Chunming Gu
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Haoru Xue
- The Robotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA;
| | - Wenping Wang
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Qi Lyu
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI 48824, USA;
| | - Yujie Dun
- School of Information and Communications Engineering, Xi’an Jiaotong University, Xi’an 710049, China;
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32
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Yang Y, Lee GC, Nakagaki-Silva E, Huang Y, Peacey M, Partridge R, Gooding C, Smith CJ. Cell-type specific regulator RBPMS switches alternative splicing via higher-order oligomerization and heterotypic interactions with other splicing regulators. Nucleic Acids Res 2023; 51:9961-9982. [PMID: 37548402 PMCID: PMC10570038 DOI: 10.1093/nar/gkad652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/28/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
Alternative pre-mRNA splicing decisions are regulated by RNA binding proteins (RBPs) that can activate or repress regulated splice sites. Repressive RBPs typically harness multivalent interactions to bind stably to target RNAs. Multivalency can be achieved by homomeric oligomerization and heteromeric interactions with other RBPs, often mediated by intrinsically disordered regions (IDRs), and by possessing multiple RNA binding domains. Cell-specific splicing decisions often involve the action of widely expressed RBPs, which are able to bind multivalently around target exons, but without effect in the absence of a cell-specific regulator. To address how cell-specific regulators can collaborate with constitutive RBPs in alternative splicing regulation, we used the smooth-muscle specific regulator RBPMS. Recombinant RBPMS is sufficient to confer smooth muscle cell specific alternative splicing of Tpm1 exon 3 in cell-free assays by preventing assembly of ATP-dependent splicing complexes. This activity depends upon a C-terminal IDR that facilitates dynamic higher-order self-assembly, cooperative binding to multivalent RNA and interactions with widely expressed splicing co-regulators, including MBNL1 and RBFOX2, allowing cooperative assembly of stable cell-specific regulatory complexes.
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Affiliation(s)
- Yi Yang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Giselle C Lee
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | | | - Yuling Huang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Matthew Peacey
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ruth Partridge
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Clare Gooding
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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Zheng J, Wu S, Tang M, Xi S, Wang Y, Ren J, Luo H, Hu P, Sun L, Du Y, Yang H, Wang F, Gao H, Dai Z, Ou X, Li Y. USP39 promotes hepatocellular carcinogenesis through regulating alternative splicing in cooperation with SRSF6/HNRNPC. Cell Death Dis 2023; 14:670. [PMID: 37821439 PMCID: PMC10567755 DOI: 10.1038/s41419-023-06210-3] [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: 03/27/2023] [Revised: 09/20/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023]
Abstract
Abnormal alternative splicing (AS) caused by alterations in spliceosomal factors is implicated in cancers. Standard models posit that splice site selection is mainly determined by early spliceosomal U1 and U2 snRNPs. Whether and how other mid/late-acting spliceosome components such as USP39 modulate tumorigenic splice site choice remains largely elusive. We observed that hepatocyte-specific overexpression of USP39 promoted hepatocarcinogenesis and potently regulated splice site selection in transgenic mice. In human liver cancer cells, USP39 promoted tumor proliferation in a spliceosome-dependent manner. USP39 depletion deregulated hundreds of AS events, including the oncogenic splice-switching of KANK2. Mechanistically, we developed a novel RBP-motif enrichment analysis and found that USP39 modulated exon inclusion/exclusion by interacting with SRSF6/HNRNPC in both humans and mice. Our data represented a paradigm for the control of splice site selection by mid/late-acting spliceosome proteins and their interacting RBPs. USP39 and possibly other mid/late-acting spliceosome proteins may represent potential prognostic biomarkers and targets for cancer therapy.
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Affiliation(s)
- Jingyi Zheng
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Shasha Wu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Mao Tang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Shaoyan Xi
- Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanchen Wang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jun Ren
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hao Luo
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Pengchao Hu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Liangzhan Sun
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuyang Du
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hui Yang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Fenfen Wang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Han Gao
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ziwei Dai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xijun Ou
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yan Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
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34
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Lee KC, Kim YC, Kim JK, Lee H, Lee JH. Regulation of Flowering Time and Other Developmental Plasticities by 3' Splicing Factor-Mediated Alternative Splicing in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:3508. [PMID: 37836248 PMCID: PMC10575287 DOI: 10.3390/plants12193508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Plants, as sessile organisms, show a high degree of plasticity in their growth and development and have various strategies to cope with these alterations under continuously changing environments and unfavorable stress conditions. In particular, the floral transition from the vegetative and reproductive phases in the shoot apical meristem (SAM) is one of the most important developmental changes in plants. In addition, meristem regions, such as the SAM and root apical meristem (RAM), which continually generate new lateral organs throughout the plant life cycle, are important sites for developmental plasticity. Recent findings have shown that the prevailing type of alternative splicing (AS) in plants is intron retention (IR) unlike in animals; thus, AS is an important regulatory mechanism conferring plasticity for plant growth and development under various environmental conditions. Although eukaryotes exhibit some similarities in the composition and dynamics of their splicing machinery, plants have differences in the 3' splicing characteristics governing AS. Here, we summarize recent findings on the roles of 3' splicing factors and their interacting partners in regulating the flowering time and other developmental plasticities in Arabidopsis thaliana.
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Affiliation(s)
- Keh Chien Lee
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden;
| | - Young-Cheon Kim
- Division of Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Jeollabuk-do, Republic of Korea;
| | - Jeong-Kook Kim
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea;
| | - Horim Lee
- Department of Biotechnology, Duksung Women’s University, Seoul 03169, Republic of Korea
| | - Jeong Hwan Lee
- Division of Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Jeollabuk-do, Republic of Korea;
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35
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Petri BJ, Piell KM, Wahlang B, Head KZ, Rouchka EC, Park JW, Hwang JY, Banerjee M, Cave MC, Klinge CM. Altered splicing factor and alternative splicing events in a mouse model of diet- and polychlorinated biphenyl-induced liver disease. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 103:104260. [PMID: 37683712 PMCID: PMC10591945 DOI: 10.1016/j.etap.2023.104260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is associated with human environmental exposure to polychlorinated biphenyls (PCBs). Alternative splicing (AS) is dysregulated in steatotic liver disease and is regulated by splicing factors (SFs) and N-6 methyladenosine (m6A) modification. Here integrated analysis of hepatic mRNA-sequencing data was used to identify differentially expressed SFs and differential AS events (ASEs) in the livers of high fat diet-fed C57BL/6 J male mice exposed to Aroclor1260, PCB126, Aroclor1260 + PCB126, or vehicle control. Aroclor1260 + PCB126 co-exposure altered 100 SFs and replicate multivariate analysis of transcript splicing (rMATS) identified 449 ASEs in 366 genes associated with NAFLD pathways. These ASEs were similar to those resulting from experimental perturbations in m6A writers, readers, and erasers. These results demonstrate specific hepatic SF and AS regulatory mechanisms are disrupted by HFD and PCB exposures, contributing to the expression of altered isoforms that may play a role in NAFLD progression to NASH.
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Affiliation(s)
- Belinda J Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Kellianne M Piell
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Banrida Wahlang
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Kimberly Z Head
- University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Eric C Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; KY INBRE Bioinformatics Core, University of Louisville, USA
| | - Juw Won Park
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; KY INBRE Bioinformatics Core, University of Louisville, USA; Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292 USA
| | - Jae Yeon Hwang
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Mayukh Banerjee
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292 USA
| | - Matthew C Cave
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA.
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36
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Zhang Q, Cao L, Song H, Lin K, Pang E. MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome. Brief Bioinform 2023; 24:bbad367. [PMID: 37833843 PMCID: PMC10576019 DOI: 10.1093/bib/bbad367] [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: 07/21/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Alternative splicing (AS) is an essential post-transcriptional mechanism that regulates many biological processes. However, identifying comprehensive types of AS events without guidance from a reference genome is still a challenge. Here, we proposed a novel method, MkcDBGAS, to identify all seven types of AS events using transcriptome alone, without a reference genome. MkcDBGAS, modeled by full-length transcripts of human and Arabidopsis thaliana, consists of three modules. In the first module, MkcDBGAS, for the first time, uses a colored de Bruijn graph with dynamic- and mixed- kmers to identify bubbles generated by AS with precision higher than 98.17% and detect AS types overlooked by other tools. In the second module, to further classify types of AS, MkcDBGAS added the motifs of exons to construct the feature matrix followed by the XGBoost-based classifier with the accuracy of classification greater than 93.40%, which outperformed other widely used machine learning models and the state-of-the-art methods. Highly scalable, MkcDBGAS performed well when applied to Iso-Seq data of Amborella and transcriptome of mouse. In the third module, MkcDBGAS provides the analysis of differential splicing across multiple biological conditions when RNA-sequencing data is available. MkcDBGAS is the first accurate and scalable method for detecting all seven types of AS events using the transcriptome alone, which will greatly empower the studies of AS in a wider field.
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Affiliation(s)
- Quanbao Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lei Cao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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37
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Sun Q, Han Y, He J, Wang J, Ma X, Ning Q, Zhao Q, Jin Q, Yang L, Li S, Li Y, Zhi Q, Zheng J, Dong D. Long-read sequencing reveals the landscape of aberrant alternative splicing and novel therapeutic target in colorectal cancer. Genome Med 2023; 15:76. [PMID: 37735421 PMCID: PMC10512518 DOI: 10.1186/s13073-023-01226-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Alternative splicing complexity plays a vital role in carcinogenesis and cancer progression. Improved understanding of novel splicing events and the underlying regulatory mechanisms may contribute new insights into developing new therapeutic strategies for colorectal cancer (CRC). METHODS Here, we combined long-read sequencing technology with short-read RNA-seq methods to investigate the transcriptome complexity in CRC. By using experiment assays, we explored the function of newly identified splicing isoform TIMP1 Δ4-5. Moreover, a CRISPR/dCasRx-based strategy to induce the TIMP1 exon 4-5 exclusion was introduced to inhibit neoplasm growth. RESULTS A total of 90,703 transcripts were identified, of which > 62% were novel compared with current transcriptome annotations. These novel transcripts were more likely to be sample specific, expressed at relatively lower levels with more exons, and oncogenes displayed a characteristic to generate more transcripts in CRC. Clinical outcome data analysis showed that 1472 differentially expressed alternative splicing events (DEAS) were tightly associated with CRC patients' prognosis, and many novel isoforms were likely to be important determinants for patient survival. Among these, newly identified splicing isoform TIMP1 Δ4-5 was significantly downregulated in CRC. Further in vitro and in vivo assays demonstrated that ectopic expression of TIMP1 Δ4-5 significantly suppresses tumor cell growth and metastasis. Serine/arginine-rich splicing factor 1 (SRSF1) acts as a onco-splicing regulator through sustaining the inclusion of TIMP1 exon 4-5. Furthermore, CRISPR/dCasRx-based strategies designed to induce TIMP1 exon 4-5 exclusion have the potential to restrain the CRC growth. CONCLUSIONS This data provides a rich resource for deeper studies of gastrointestinal malignancies. Newly identified splicing isoform TIMP1 Δ4-5 plays an important role in mediating CRC progression and may be a potential therapy target in CRC.
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Affiliation(s)
- Qiang Sun
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu, Xuzhou, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu, Xuzhou, 221004, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314100, China
| | - Ye Han
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianxing He
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China
| | - Jie Wang
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China
| | - Xuejie Ma
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China
| | - Qianqian Ning
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China
| | - Qing Zhao
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China
| | - Qian Jin
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China
| | - Lili Yang
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China
| | - Shuang Li
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314100, China
| | - Yang Li
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China
| | - Qiaoming Zhi
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Junnian Zheng
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu, Xuzhou, China.
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu, Xuzhou, 221004, China.
| | - Dong Dong
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu Province, China.
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu, Xuzhou, China.
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu, Xuzhou, 221004, China.
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38
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Wang R, Helbig I, Edmondson AC, Lin L, Xing Y. Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis. Brief Bioinform 2023; 24:bbad284. [PMID: 37580177 PMCID: PMC10516351 DOI: 10.1093/bib/bbad284] [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: 03/14/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 08/16/2023] Open
Abstract
Genomic variants affecting pre-messenger RNA splicing and its regulation are known to underlie many rare genetic diseases. However, common workflows for genetic diagnosis and clinical variant interpretation frequently overlook splice-altering variants. To better serve patient populations and advance biomedical knowledge, it has become increasingly important to develop and refine approaches for detecting and interpreting pathogenic splicing variants. In this review, we will summarize a few recent developments and challenges in using RNA sequencing technologies for rare disease investigation. Moreover, we will discuss how recent computational splicing prediction tools have emerged as complementary approaches for revealing disease-causing variants underlying splicing defects. We speculate that continuous improvements to sequencing technologies and predictive modeling will not only expand our understanding of splicing regulation but also bring us closer to filling the diagnostic gap for rare disease patients.
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Affiliation(s)
- Robert Wang
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- The Epilepsy NeuroGenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew C Edmondson
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lan Lin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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39
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Coronado-Zamora M, González J. Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains. Genome Res 2023; 33:1541-1553. [PMID: 37793782 PMCID: PMC10620055 DOI: 10.1101/gr.277565.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/08/2023] [Indexed: 10/06/2023]
Abstract
Transcriptomes are dynamic, with cells, tissues, and body parts expressing particular sets of transcripts. Transposable elements (TEs) are a known source of transcriptome diversity; however, studies often focus on a particular type of chimeric transcript, analyze single body parts or cell types, or are based on incomplete TE annotations from a single reference genome. In this work, we have implemented a method based on de novo transcriptome assembly that minimizes the potential sources of errors while identifying a comprehensive set of gene-TE chimeras. We applied this method to the head, gut, and ovary dissected from five Drosophila melanogaster natural strains, with individual reference genomes available. We found that ∼19% of body part-specific transcripts are gene-TE chimeras. Overall, chimeric transcripts contribute a mean of 43% to the total gene expression, and they provide protein domains for DNA binding, catalytic activity, and DNA polymerase activity. Our comprehensive data set is a rich resource for follow-up analysis. Moreover, because TEs are present in virtually all species sequenced to date, their role in spatially restricted transcript expression is likely not exclusive to the species analyzed in this work.
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Affiliation(s)
| | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona 08003, Spain
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40
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Recinos Y, Ustianenko D, Yeh YT, Wang X, Jacko M, Yesantharao LV, Wu Q, Zhang C. Deep screening of proximal and distal splicing-regulatory elements in a native sequence context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554109. [PMID: 37662340 PMCID: PMC10473672 DOI: 10.1101/2023.08.21.554109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is impeded by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically dead CRISPR-RfxCas13d RNA-targeting system (dCas13d/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to SMN2, a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identified not only known SREs, but also a novel distal intronic splicing enhancer, which can be targeted to alter exon 7 splicing using either dCas13d/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.
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Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Flagship Pioneering, Cambridge, MA 02142, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Martin Jacko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Aperture Therapeutics, Inc., San Carlos, CA 94070, USA
| | - Lekha V. Yesantharao
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
- Present address: Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qiyang Wu
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
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41
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Choquet K, Baxter-Koenigs AR, Dülk SL, Smalec BM, Rouskin S, Churchman LS. Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts. Nat Struct Mol Biol 2023; 30:1064-1076. [PMID: 37443198 PMCID: PMC10653200 DOI: 10.1038/s41594-023-01035-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Combinatorially, intron excision within a given nascent transcript could proceed down any of thousands of paths, each of which would expose different dynamic landscapes of cis-elements and contribute to alternative splicing. In this study, we found that post-transcriptional multi-intron splicing order in human cells is largely predetermined, with most genes spliced in one or a few predominant orders. Strikingly, these orders were conserved across cell types and stages of motor neuron differentiation. Introns flanking alternatively spliced exons were frequently excised last, after their neighboring introns. Perturbations to the spliceosomal U2 snRNA altered the preferred splicing order of many genes, and these alterations were associated with the retention of other introns in the same transcript. In one gene, early removal of specific introns was sufficient to induce delayed excision of three proximal introns, and this delay was caused by two distinct cis-regulatory mechanisms. Together, our results demonstrate that multi-intron splicing order in human cells is predetermined, is influenced by a component of the spliceosome and ensures splicing fidelity across long pre-mRNAs.
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Affiliation(s)
- Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | | | - Sarah-Luisa Dülk
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Silvi Rouskin
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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42
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Iwanami N, Richter AS, Sikora K, Boehm T. Tnpo3 controls splicing of the pre-mRNA encoding the canonical TCR α chain of iNKT cells. Nat Commun 2023; 14:3645. [PMID: 37339974 DOI: 10.1038/s41467-023-39422-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
Unconventional T cells, such as innate natural killer T cells (iNKT) cells, are an important part of vertebrate immune defences. iNKT recognise glycolipids through a T cell receptor (TCR) that is composed of a semi-invariant TCR α chain, paired with a restricted set of TCR β chains. Here, we show that splicing of the cognate Trav11-Traj18-Trac pre-mRNA encoding the characteristic Vα14Jα18 variable region of this semi-invariant TCR depends on the presence of Tnpo3. The Tnpo3 gene encodes a nuclear transporter of the β-karyopherin family whose cargo includes various splice regulators. The block of iNKT cell development in the absence of Tnpo3 can be overcome by transgenic provision of a rearranged Trav11-Traj18-Trac cDNA, indicating that Tnpo3 deficiency does not interfere with the development of iNKT cells per se. Our study thus identifies a role for Tnpo3 in regulating the splicing of the pre-mRNA encoding the cognate TCRα chain of iNKT cells.
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Affiliation(s)
- Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Andreas S Richter
- Bioinformatics Unit, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - Katarzyna Sikora
- Bioinformatics Unit, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Boehm
- Bioinformatics Unit, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Faculty of Medicine, Albert Ludwigs University, Freiburg, Germany.
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43
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Ruan X, Hu K, Zhang X. PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing. Nat Commun 2023; 14:3275. [PMID: 37280234 DOI: 10.1038/s41467-023-39054-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023] Open
Abstract
RNA-binding proteins (RBPs) are essential for gene regulation, but it remains a challenge to identify their RNA targets across cell types. Here we present PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing by conjugating C-to-U and A-to-I base editors to RBPs. We benchmark PIE-Seq and demonstrate its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs. Bulk PIE-Seq identifies canonical binding features for RBPs such as PUM2 and NOVA1, and nominates additional target genes for most tested RBPs such as SRSF1 and TDP-43/TARDBP. Homologous RBPs frequently edit similar sequences and gene sets in PIE-Seq while different RBP families show distinct targets. Single-cell PIE-PUM2 uncovers comparable targets to bulk samples and applying PIE-PUM2 to the developing mouse neocortex identifies neural-progenitor- and neuron-specific target genes such as App. In summary, PIE-Seq provides an orthogonal approach and resource to uncover RBP targets in mice and human cells.
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Affiliation(s)
- Xiangbin Ruan
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Kaining Hu
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Xiaochang Zhang
- Department of Human Genetics and The Neuroscience Institute, University of Chicago, Chicago, IL, USA.
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44
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Novosad VO. Identification of Significant RNA-Binding Proteins in the Process of CD44 Splicing Using the Boosted Beta Regression Algorithm. DOKL BIOCHEM BIOPHYS 2023; 510:99-103. [PMID: 37582871 DOI: 10.1134/s1607672923700199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 08/17/2023]
Abstract
The expression of RNA-binding proteins and their interaction with the spliced pre-mRNA are the key factors in determining the final isoform profile. Transmembrane protein CD44 is involved in differentiation, invasion, motility, growth and survival of tumor cells, and is also a commonly accepted marker of cancer stem cells and epithelial-mesenchymal transition. However, the functions of the isoforms of this protein differ significantly. In this paper, we developed a method based on the boosted beta regression algorithm for identification of the significant RNA-binding proteins in the splicing process by modeling the isoform ratio. The application of this method to the analysis of CD44 splicing in colorectal cancer cells revealed 20 significant RNA-binding proteins. Many of them were previously shown as EMT regulators, but for the first time presented as potential CD44 splicing factors.
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Affiliation(s)
- V O Novosad
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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45
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Wagner N, Çelik MH, Hölzlwimmer FR, Mertes C, Prokisch H, Yépez VA, Gagneur J. Aberrant splicing prediction across human tissues. Nat Genet 2023; 55:861-870. [PMID: 37142848 DOI: 10.1038/s41588-023-01373-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
Aberrant splicing is a major cause of genetic disorders but its direct detection in transcriptomes is limited to clinically accessible tissues such as skin or body fluids. While DNA-based machine learning models can prioritize rare variants for affecting splicing, their performance in predicting tissue-specific aberrant splicing remains unassessed. Here we generated an aberrant splicing benchmark dataset, spanning over 8.8 million rare variants in 49 human tissues from the Genotype-Tissue Expression (GTEx) dataset. At 20% recall, state-of-the-art DNA-based models achieve maximum 12% precision. By mapping and quantifying tissue-specific splice site usage transcriptome-wide and modeling isoform competition, we increased precision by threefold at the same recall. Integrating RNA-sequencing data of clinically accessible tissues into our model, AbSplice, brought precision to 60%. These results, replicated in two independent cohorts, substantially contribute to noncoding loss-of-function variant identification and to genetic diagnostics design and analytics.
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Affiliation(s)
- Nils Wagner
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany
| | - Muhammed H Çelik
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Florian R Hölzlwimmer
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Christian Mertes
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Data Science Institute, Technical University of Munich, Garching, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
| | - Vicente A Yépez
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany.
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany.
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46
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Liu H, Zhu Y, Ng KTP, Lo CM, Man K. The Landscape of Aberrant Alternative Splicing Events in Steatotic Liver Graft Post Transplantation via Transcriptome-Wide Analysis. Int J Mol Sci 2023; 24:ijms24098216. [PMID: 37175922 PMCID: PMC10179559 DOI: 10.3390/ijms24098216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/28/2023] [Accepted: 04/03/2023] [Indexed: 05/15/2023] Open
Abstract
The application of steatotic liver graft has been increased significantly due to the severe donor shortage and prevalence of non-alcoholic fatty liver disease. However, steatotic donor livers are vulnerable to acute phase inflammatory injury, which may result in cancer recurrence. Alternative splicing events (ASEs) are critical for diverse transcriptional variants in hepatocellular carcinoma (HCC). Here, we aimed to depict the landscape of ASEs, as well as to identify the differential ASEs in steatotic liver graft and their association with tumor recurrence after transplantation. The overall portrait of intragraft transcripts and ASEs were elucidated through RNA sequencing with the liver graft biopsies from patients and rat transplant models. Various differential ASEs were identified in steatotic liver grafts. CYP2E1, ADH1A, CYP2C8, ADH1C, and HGD, as corresponding genes to the common pathways involved differential ASEs in human and rats, were significantly associated with HCC patients' survival. The differential ASEs related RNA-binding proteins (RBPs) were enriched in metabolic pathways. The altered immune cell distribution, particularly macrophages and neutrophils, were perturbated by differential ASEs. The cancer hallmarks were enriched in steatotic liver grafts and closely associated with differential ASEs. Our work identified the differential ASE network with metabolic RBPs, immune cell distribution, and cancer hallmarks in steatotic liver grafts. We verified the link between steatotic liver graft injury and tumor recurrence at post-transcriptional level, offered new evidence to explore metabolism and immune responses, and provided the potential prognostic and therapeutic markers for tumor recurrence.
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Affiliation(s)
- Hui Liu
- Department of Surgery, School of Clinical Medicine, HKU-SZH & LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yueqin Zhu
- Department of Surgery, School of Clinical Medicine, HKU-SZH & LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kevin Tak-Pan Ng
- Department of Surgery, School of Clinical Medicine, HKU-SZH & LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chung-Mau Lo
- Department of Surgery, School of Clinical Medicine, HKU-SZH & LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kwan Man
- Department of Surgery, School of Clinical Medicine, HKU-SZH & LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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47
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LaForce GR, Philippidou P, Schaffer AE. mRNA isoform balance in neuronal development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1762. [PMID: 36123820 PMCID: PMC10024649 DOI: 10.1002/wrna.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Balanced mRNA isoform diversity and abundance are spatially and temporally regulated throughout cellular differentiation. The proportion of expressed isoforms contributes to cell type specification and determines key properties of the differentiated cells. Neurons are unique cell types with intricate developmental programs, characteristic cellular morphologies, and electrophysiological potential. Neuron-specific gene expression programs establish these distinctive cellular characteristics and drive diversity among neuronal subtypes. Genes with neuron-specific alternative processing are enriched in key neuronal functions, including synaptic proteins, adhesion molecules, and scaffold proteins. Despite the similarity of neuronal gene expression programs, each neuronal subclass can be distinguished by unique alternative mRNA processing events. Alternative processing of developmentally important transcripts alters coding and regulatory information, including interaction domains, transcript stability, subcellular localization, and targeting by RNA binding proteins. Fine-tuning of mRNA processing is essential for neuronal activity and maintenance. Thus, the focus of neuronal RNA biology research is to dissect the transcriptomic mechanisms that underlie neuronal homeostasis, and consequently, predispose neuronal subtypes to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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48
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Li L, Zhou B, Liu D, Wu H, Shi Q, Lin S, Yao W. Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo. Int J Mol Sci 2023; 24:ijms24087425. [PMID: 37108588 PMCID: PMC10138756 DOI: 10.3390/ijms24087425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Moso bamboo is capable of both sexual and asexual reproduction during natural growth, resulting in four distinct types of culms: the bamboo shoot-culm, the seedling stem, the leptomorph rhizome, and a long-ignored culm-the outward-rhizome. Sometimes, when the outward rhizomes break through the soil, they continue to grow longitudinally and develop into a new individual. However, the roles of alternative transcription start sites (aTSS) or termination sites (aTTS) as well as alternative splicing (AS) have not been comprehensively studied for their development. To re-annotate the moso bamboo genome and identify genome-wide aTSS, aTTS, and AS in growing culms, we utilized single-molecule long-read sequencing technology. In total, 169,433 non-redundant isoforms and 14,840 new gene loci were identified. Among 1311 lncRNAs, most of which showed a positive correlation with their target mRNAs, one-third of these IncRNAs were preferentially expressed in winter bamboo shoots. In addition, the predominant AS type observed in moso bamboo was intron retention, while aTSS and aTTS events occurred more frequently than AS. Notably, most genes with AS events were also accompanied by aTSS and aTTS events. Outward rhizome growth in moso bamboo was associated with a significant increase in intron retention, possibly due to changes in the growth environment. As different types of moso bamboo culms grow and develop, a significant number of isoforms undergo changes in their conserved domains due to the regulation of aTSS, aTTS, and AS. As a result, these isoforms may play different roles than their original functions. These isoforms then performed different functions from their original roles, contributing to the transcriptomic complexity of moso bamboo. Overall, this study provided a comprehensive overview of the transcriptomic changes underlying different types of moso bamboo culm growth and development.
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Affiliation(s)
- Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Binao Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Dong Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyu Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Qianqian Shi
- College of Landscape Architecture and Art, Northwest A&F University, Xianyang 712100, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Wenjing Yao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
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49
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Zhao F, Yan Y, Wang Y, Liu Y, Yang R. Splicing complexity as a pivotal feature of alternative exons in mammalian species. BMC Genomics 2023; 24:198. [PMID: 37046221 PMCID: PMC10099729 DOI: 10.1186/s12864-023-09247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND As a significant process of post-transcriptional gene expression regulation in eukaryotic cells, alternative splicing (AS) of exons greatly contributes to the complexity of the transcriptome and indirectly enriches the protein repertoires. A large number of studies have focused on the splicing inclusion of alternative exons and have revealed the roles of AS in organ development and maturation. Notably, AS takes place through a change in the relative abundance of the transcript isoforms produced by a single gene, meaning that exons can have complex splicing patterns. However, the commonly used percent spliced-in (Ψ) values only define the usage rate of exons, but lose information about the complexity of exons' linkage pattern. To date, the extent and functional consequence of splicing complexity of alternative exons in development and evolution is poorly understood. RESULTS By comparing splicing complexity of exons in six tissues (brain, cerebellum, heart, liver, kidney, and testis) from six mammalian species (human, chimpanzee, gorilla, macaque, mouse, opossum) and an outgroup species (chicken), we revealed that exons with high splicing complexity are prevalent in mammals and are closely related to features of genes. Using traditional machine learning and deep learning methods, we found that the splicing complexity of exons can be moderately predicted with features derived from exons, among which length of flanking exons and splicing strength of downstream/upstream splice sites are top predictors. Comparative analysis among human, chimpanzee, gorilla, macaque, and mouse revealed that, alternative exons tend to evolve to an increased level of splicing complexity and higher tissue specificity in splicing complexity. During organ development, not only developmentally regulated exons, but also 10-15% of non-developmentally regulated exons show dynamic splicing complexity. CONCLUSIONS Our analysis revealed that splicing complexity is an important metric to characterize the splicing dynamics of alternative exons during the development and evolution of mammals.
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Affiliation(s)
- Feiyang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yubin Yan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yaxi Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuan Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruolin Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
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50
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Tse V, Chacaltana G, Gutierrez M, Forino NM, Jimenez AG, Tao H, Do PH, Oh C, Chary P, Quesada I, Hamrick A, Lee S, Stone MD, Sanford JR. Rescue of blood coagulation Factor VIII exon-16 mis-splicing by antisense oligonucleotides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535160. [PMID: 37034721 PMCID: PMC10081312 DOI: 10.1101/2023.03.31.535160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The human Factor VIII ( F8 ) protein is essential for the blood coagulation cascade and specific F8 mutations cause the rare bleeding disorder Hemophilia A (HA). Here, we investigated the impact of HA-causing single-nucleotide mutations on F8 pre-mRNA splicing. We found that 14/97 (∼14.4%) coding sequence mutations tested in our study induced exon skipping. Splicing patterns of 4/11 (∼36.4%) F8 exons tested were especially sensitive to the presence of common disease-causing mutations. RNA-chemical probing analyses revealed a three-way junction structure at the 3' end of intron 15 (TWJ-3-15). TWJ-3-15 sequesters the polypyrimidine tract, a key determinant of 3' splice site strength. Using exon-16 of the F8 gene as a model, we designed specific antisense oligonucleotides (ASOs) that target TWJ-3-15 and identified three that promote the splicing of F8 exon-16. Interaction of TWJ-3-15 with ASOs increases accessibility of the polypyrimidine tract and inhibits the binding of hnRNPA1-dependent splicing silencing factors. Moreover, ASOs targeting TWJ-3-15 rescue diverse splicing-sensitive HA-causing mutations, most of which are distal to the 3' splice site being impacted. The TWJ-3-15 structure and its effect on mRNA splicing provide a model for HA etiology in patients harboring specific F8 mutations and provide a framework for precision RNA-based HA therapies.
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