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Moreno-Aguilera M, Neher AM, Mendoza MB, Dodel M, Mardakheh FK, Ortiz R, Gallego C. KIS counteracts PTBP2 and regulates alternative exon usage in neurons. eLife 2024; 13:e96048. [PMID: 38597390 PMCID: PMC11045219 DOI: 10.7554/elife.96048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/09/2024] [Indexed: 04/11/2024] Open
Abstract
Alternative RNA splicing is an essential and dynamic process in neuronal differentiation and synapse maturation, and dysregulation of this process has been associated with neurodegenerative diseases. Recent studies have revealed the importance of RNA-binding proteins in the regulation of neuronal splicing programs. However, the molecular mechanisms involved in the control of these splicing regulators are still unclear. Here, we show that KIS, a kinase upregulated in the developmental brain, imposes a genome-wide alteration in exon usage during neuronal differentiation in mice. KIS contains a protein-recognition domain common to spliceosomal components and phosphorylates PTBP2, counteracting the role of this splicing factor in exon exclusion. At the molecular level, phosphorylation of unstructured domains within PTBP2 causes its dissociation from two co-regulators, Matrin3 and hnRNPM, and hinders the RNA-binding capability of the complex. Furthermore, KIS and PTBP2 display strong and opposing functional interactions in synaptic spine emergence and maturation. Taken together, our data uncover a post-translational control of splicing regulators that link transcriptional and alternative exon usage programs in neuronal development.
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Affiliation(s)
| | - Alba M Neher
- Molecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Mónica B Mendoza
- Molecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Martin Dodel
- Barts Cancer Institute, Queen Mary University of LondonLondonUnited Kingdom
| | - Faraz K Mardakheh
- Barts Cancer Institute, Queen Mary University of LondonLondonUnited Kingdom
| | - Raúl Ortiz
- Molecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Carme Gallego
- Molecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
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Wong ACH, Wong JJL, Rasko JEJ, Schmitz U. SpliceWiz: interactive analysis and visualization of alternative splicing in R. Brief Bioinform 2023; 25:bbad468. [PMID: 38152981 PMCID: PMC10753292 DOI: 10.1093/bib/bbad468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/31/2023] [Accepted: 11/23/2023] [Indexed: 12/29/2023] Open
Abstract
Alternative splicing (AS) is a crucial mechanism for regulating gene expression and isoform diversity in eukaryotes. However, the analysis and visualization of AS events from RNA sequencing data remains challenging. Most tools require a certain level of computer literacy and the available means of visualizing AS events, such as coverage and sashimi plots, have limitations and can be misleading. To address these issues, we present SpliceWiz, an R package with an interactive Shiny interface that allows easy and efficient AS analysis and visualization at scale. A novel normalization algorithm is implemented to aggregate splicing levels within sample groups, thereby allowing group differences in splicing levels to be accurately visualized. The tool also offers downstream gene ontology enrichment analysis, highlighting ASEs belonging to functional pathways of interest. SpliceWiz is optimized for speed and efficiency and introduces a new file format for coverage data storage that is more efficient than BigWig. Alignment files are processed orders of magnitude faster than other R-based AS analysis tools and on par with command-line tools. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization. SpliceWiz is a Bioconductor package and is also available on GitHub (https://github.com/alexchwong/SpliceWiz).
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Affiliation(s)
- Alex C H Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, the University of Sydney, Camperdown, NSW 2050, Australia
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, the University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, the University of Sydney, Camperdown, NSW 2050, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Ulf Schmitz
- Biomedical Sciences and Molecular Biology, James Cook University, Townsville, QLD 4810, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD 4810, Australia
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Ali A, Thorgaard GH, Salem M. PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes. Front Genet 2021; 12:683408. [PMID: 34335690 PMCID: PMC8321248 DOI: 10.3389/fgene.2021.683408] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023] Open
Abstract
Rainbow trout is an important model organism that has received concerted international efforts to study the transcriptome. For this purpose, short-read sequencing has been primarily used over the past decade. However, these sequences are too short of resolving the transcriptome complexity. This study reported a first full-length transcriptome assembly of the rainbow trout using single-molecule long-read isoform sequencing (Iso-Seq). Extensive computational approaches were used to refine and validate the reconstructed transcriptome. The study identified 10,640 high-confidence transcripts not previously annotated, in addition to 1,479 isoforms not mapped to the current Swanson reference genome. Most of the identified lncRNAs were non-coding variants of coding transcripts. The majority of genes had multiple transcript isoforms (average ∼3 isoforms/locus). Intron retention (IR) and exon skipping (ES) accounted for 56% of alternative splicing (AS) events. Iso-Seq improved the reference genome annotation, which allowed identification of characteristic AS associated with fish growth, muscle accretion, disease resistance, stress response, and fish migration. For instance, an ES in GVIN1 gene existed in fish susceptible to bacterial cold-water disease (BCWD). Besides, under five stress conditions, there was a commonly regulated exon in prolyl 4-hydroxylase subunit alpha-2 (P4HA2) gene. The reconstructed gene models and their posttranscriptional processing in rainbow trout provide invaluable resources that could be further used for future genetics and genomics studies. Additionally, the study identified characteristic transcription events associated with economically important phenotypes, which could be applied in selective breeding.
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Affiliation(s)
- Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
| | - Gary H. Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
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Zhang Y, Cai Y, Roca X, Kwoh CK, Fullwood MJ. Chromatin loop anchors predict transcript and exon usage. Brief Bioinform 2021; 22:6319936. [PMID: 34263910 PMCID: PMC8575016 DOI: 10.1093/bib/bbab254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/16/2021] [Accepted: 05/25/2021] [Indexed: 11/24/2022] Open
Abstract
Epigenomics and transcriptomics data from high-throughput sequencing techniques such as RNA-seq and ChIP-seq have been successfully applied in predicting gene transcript expression. However, the locations of chromatin loops in the genome identified by techniques such as Chromatin Interaction Analysis with Paired End Tag sequencing (ChIA-PET) have never been used for prediction tasks. Here, we developed machine learning models to investigate if ChIA-PET could contribute to transcript and exon usage prediction. In doing so, we used a large set of transcription factors as well as ChIA-PET data. We developed different Gradient Boosting Trees models according to the different tasks with the integrated datasets from three cell lines, including GM12878, HeLaS3 and K562. We validated the models via 10-fold cross validation, chromosome-split validation and cross-cell validation. Our results show that both transcript and splicing-derived exon usage can be effectively predicted with at least 0.7512 and 0.7459 of accuracy, respectively, on all cell lines from all kinds of validations. Examining the predictive features, we found that RNA Polymerase II ChIA-PET was one of the most important features in both transcript and exon usage prediction, suggesting that chromatin loop anchors are predictive of both transcript and exon usage.
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Affiliation(s)
- Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yichao Cai
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore.,School of Biological Sciences, Nanyang Technological University, 637551, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Dr, Singapore 138673, Singapore
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Kwik M, Hainzl S, Oppelt J, Tichy B, Koller U, Bernardinelli E, Steiner M, Zara G, Nofziger C, Weis S, Paulmichl M, Dossena S, Patsch W, Soyal SM. Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases. Int J Mol Sci 2021; 22:3296. [PMID: 33804860 DOI: 10.3390/ijms22073296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 12/12/2022] Open
Abstract
The transcriptional regulator peroxisome proliferator activated receptor gamma coactivator 1A (PGC-1α), encoded by PPARGC1A, has been linked to neurodegenerative diseases. Recently discovered CNS-specific PPARGC1A transcripts are initiated far upstream of the reference promoter, spliced to exon 2 of the reference gene, and are more abundant than reference gene transcripts in post-mortem human brain samples. The proteins translated from the CNS and reference transcripts differ only at their N-terminal regions. To dissect functional differences between CNS-specific isoforms and reference proteins, we used clustered regularly interspaced short palindromic repeats transcriptional activation (CRISPRa) for selective endogenous activation of the CNS or the reference promoters in SH-SY5Y cells. Expression and/or exon usage of the targets was ascertained by RNA sequencing. Compared to controls, more differentially expressed genes were observed after activation of the CNS than the reference gene promoter, while the magnitude of alternative exon usage was comparable between activation of the two promoters. Promoter-selective associations were observed with canonical signaling pathways, mitochondrial and nervous system functions and neurological diseases. The distinct N-terminal as well as the shared downstream regions of PGC-1α isoforms affect the exon usage of numerous genes. Furthermore, associations of risk genes of amyotrophic lateral sclerosis and Parkinson's disease were noted with differentially expressed genes resulting from the activation of the CNS and reference gene promoter, respectively. Thus, CNS-specific isoforms markedly amplify the biological functions of PPARGC1A and CNS-specific isoforms and reference proteins have common, complementary and selective functions relevant for neurodegenerative diseases.
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