1
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Villagra UMM, da Cunha BR, Polachini GM, Henrique T, Stefanini ACB, de Castro TB, da Silva CHTP, Feitosa OA, Fukuyama EE, López RVM, Dias-Neto E, Nunes FD, Severino P, Tajara EH. Expression of Truncated Products at the 5'-Terminal Region of RIPK2 and Evolutive Aspects that Support Their Biological Importance. Genome Biol Evol 2024; 16:evae106. [PMID: 38752399 PMCID: PMC11221433 DOI: 10.1093/gbe/evae106] [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] [Accepted: 05/10/2024] [Indexed: 07/04/2024] Open
Abstract
Alternative splicing is the process of generating different mRNAs from the same primary transcript, which contributes to increase the transcriptome and proteome diversity. Abnormal splicing has been associated with the development of several diseases including cancer. Given that mutations and abnormal levels of the RIPK2 transcript and RIP-2 protein are frequent in tumors, and that RIP-2 modulates immune and inflammatory responses, we investigated alternative splicing events that result in partial deletions of the kinase domain at the N-terminus of RIP-2. We also investigated the structure and expression of the RIPK2 truncated variants and isoforms in different environments. In addition, we searched data throughout Supraprimates evolution that could support the biological importance of RIPK2 alternatively spliced products. We observed that human variants and isoforms were differentially regulated following temperature stress, and that the truncated transcript was more expressed than the long transcript in tumor samples. The inverse was found for the longer protein isoform. The truncated variant was also detected in chimpanzee, gorilla, hare, pika, mouse, rat, and tree shrew. The fact that the same variant has been preserved in mammals with divergence times up to 70 million years raises the hypothesis that it may have a functional significance.
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Affiliation(s)
- Ulises M M Villagra
- Faculty of Exact Sciences, Biotechnology and Molecular Biology Institute (IBBM), National University of La Plata-CCT, CONICET, La Plata, Argentina
| | - Bianca R da Cunha
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Giovana M Polachini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Tiago Henrique
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Ana Carolina Buzzo Stefanini
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Tialfi Bergamin de Castro
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Microbial Pathogenesis Department, University of Maryland Baltimore, School of Dentistry, Baltimore, MD, USA
| | - Carlos H T P da Silva
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo/USP, Ribeirão Preto, SP, Brazil
| | - Olavo A Feitosa
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo/USP, Ribeirão Preto, SP, Brazil
| | - Erica E Fukuyama
- Head and Neck Surgery Department, Arnaldo Vieira de Carvalho Cancer Institute, São Paulo, SP, Brazil
| | - Rossana V M López
- Comprehensive Center for Precision Oncology, Center for Translational Research in Oncology, State of São Paulo Cancer Institute—ICESP, Clinics Hospital, Sao Paulo University Medical School, São Paulo, SP, Brazil
| | - Emmanuel Dias-Neto
- Laboratory of Medical Genomics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Fabio D Nunes
- Department of Stomatology, School of Dentistry, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Patricia Severino
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Eloiza H Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
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2
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Ulicevic J, Shao Z, Jasnovidova O, Bressin A, Gajos M, Ng AH, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A. Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol 2024; 20:767-798. [PMID: 38755290 PMCID: PMC11219738 DOI: 10.1038/s44320-024-00039-4] [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: 10/20/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform changes upon cell-state-transitions during cell differentiation, the determinants and functional consequences have largely remained unclear. Here, we established an improved model for human neurogenesis in vitro that is amenable for systems-wide analyses of gene expression. Our multi-omics analysis reveals that the pronounced alterations in cell morphology correlate strongly with widespread changes in RNA isoform expression. Our approach identifies thousands of new RNA isoforms that are expressed at distinct differentiation stages. RNA isoforms mainly arise from exon skipping and the alternative usage of transcription start and polyadenylation sites during human neurogenesis. The transcript isoform changes can remodel the identity and functions of protein isoforms. Finally, our study identifies a set of RNA binding proteins as a potential determinant of differentiation stage-specific global isoform changes. This work supports the view of regulated isoform changes that underlie state-transitions during neurogenesis.
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Affiliation(s)
- Jelena Ulicevic
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Zhihao Shao
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Olga Jasnovidova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martyna Gajos
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Alex Hm Ng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Siddharth Annaldasula
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, USA
| | - Volker Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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3
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McWhite CD, Sae-Lee W, Yuan Y, Mallam AL, Gort-Freitas NA, Ramundo S, Onishi M, Marcotte EM. Alternative proteoforms and proteoform-dependent assemblies in humans and plants. Mol Syst Biol 2024:10.1038/s44320-024-00048-3. [PMID: 38918600 DOI: 10.1038/s44320-024-00048-3] [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: 02/01/2023] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
The variability of proteins at the sequence level creates an enormous potential for proteome complexity. Exploring the depths and limits of this complexity is an ongoing goal in biology. Here, we systematically survey human and plant high-throughput bottom-up native proteomics data for protein truncation variants, where substantial regions of the full-length protein are missing from an observed protein product. In humans, Arabidopsis, and the green alga Chlamydomonas, approximately one percent of observed proteins show a short form, which we can assign by comparison to RNA isoforms as either likely deriving from transcript-directed processes or limited proteolysis. While some detected protein fragments align with known splice forms and protein cleavage events, multiple examples are previously undescribed, such as our observation of fibrocystin proteolysis and nuclear translocation in a green alga. We find that truncations occur almost entirely between structured protein domains, even when short forms are derived from transcript variants. Intriguingly, multiple endogenous protein truncations of phase-separating translational proteins resemble cleaved proteoforms produced by enteroviruses during infection. Some truncated proteins are also observed in both humans and plants, suggesting that they date to the last eukaryotic common ancestor. Finally, we describe novel proteoform-specific protein complexes, where the loss of a domain may accompany complex formation.
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Affiliation(s)
- Claire D McWhite
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
| | - Wisath Sae-Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yaning Yuan
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Anna L Mallam
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Silvia Ramundo
- Gregor Mendel Institute of Molecular Plant Biology, 1030, Wien, Austria
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
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4
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Xiao MS, Damodaran AP, Kumari B, Dickson E, Xing K, On TA, Parab N, King HE, Perez AR, Guiblet WM, Duncan G, Che A, Chari R, Andresson T, Vidigal JA, Weatheritt RJ, Aregger M, Gonatopoulos-Pournatzis T. Genome-scale exon perturbation screens uncover exons critical for cell fitness. Mol Cell 2024:S1097-2765(24)00447-7. [PMID: 38917794 DOI: 10.1016/j.molcel.2024.05.024] [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: 10/01/2023] [Revised: 04/04/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
CRISPR-Cas technology has transformed functional genomics, yet understanding of how individual exons differentially shape cellular phenotypes remains limited. Here, we optimized and conducted massively parallel exon deletion and splice-site mutation screens in human cell lines to identify exons that regulate cellular fitness. Fitness-promoting exons are prevalent in essential and highly expressed genes and commonly overlap with protein domains and interaction interfaces. Conversely, fitness-suppressing exons are enriched in nonessential genes, exhibiting lower inclusion levels, and overlap with intrinsically disordered regions and disease-associated mutations. In-depth mechanistic investigation of the screen-hit TAF5 alternative exon-8 revealed that its inclusion is required for assembly of the TFIID general transcription initiation complex, thereby regulating global gene expression output. Collectively, our orthogonal exon perturbation screens established a comprehensive repository of phenotypically important exons and uncovered regulatory mechanisms governing cellular fitness and gene expression.
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Affiliation(s)
- Mei-Sheng Xiao
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Arun Prasath Damodaran
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| | - Bandana Kumari
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Ethan Dickson
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Kun Xing
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Tyler A On
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Nikhil Parab
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Helen E King
- EMBL Australia and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Alexendar R Perez
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wilfried M Guiblet
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Gerard Duncan
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Anney Che
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Joana A Vidigal
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Robert J Weatheritt
- EMBL Australia and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2010, Australia
| | - Michael Aregger
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| | - Thomas Gonatopoulos-Pournatzis
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
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5
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Lu X, Ni P, Suarez-Meade P, Ma Y, Forrest EN, Wang G, Wang Y, Quiñones-Hinojosa A, Gerstein M, Jiang YH. Transcriptional determinism and stochasticity contribute to the complexity of autism-associated SHANK family genes. Cell Rep 2024; 43:114376. [PMID: 38900637 DOI: 10.1016/j.celrep.2024.114376] [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: 01/09/2024] [Revised: 05/08/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Precision of transcription is critical because transcriptional dysregulation is disease causing. Traditional methods of transcriptional profiling are inadequate to elucidate the full spectrum of the transcriptome, particularly for longer and less abundant mRNAs. SHANK3 is one of the most common autism causative genes. Twenty-four Shank3-mutant animal lines have been developed for autism modeling. However, their preclinical validity has been questioned due to incomplete Shank3 transcript structure. We apply an integrative approach combining cDNA-capture and long-read sequencing to profile the SHANK3 transcriptome in humans and mice. We unexpectedly discover an extremely complex SHANK3 transcriptome. Specific SHANK3 transcripts are altered in Shank3-mutant mice and postmortem brain tissues from individuals with autism spectrum disorder. The enhanced SHANK3 transcriptome significantly improves the detection rate for potential deleterious variants from genomics studies of neuropsychiatric disorders. Our findings suggest that both deterministic and stochastic transcription of the genome is associated with SHANK family genes.
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Affiliation(s)
- Xiaona Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Yu Ma
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Emily Niemitz Forrest
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Guilin Wang
- Keck Microarray Shared Resource, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yi Wang
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA; Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT 06520, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA; Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA.
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6
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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J. Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P. Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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7
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Han Y, Wennersten SA, Pandi BP, Ng DCM, Lau E, Lam MPY. A Ratiometric Catalog of Protein Isoform Shifts in the Cardiac Fetal Gene Program. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588716. [PMID: 38645170 PMCID: PMC11030362 DOI: 10.1101/2024.04.09.588716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The fetal genetic program orchestrates cardiac development and the re-expression of fetal genes is thought to underlie cardiac disease and adaptation. Here, a proteomics ratio test using mass spectrometry is applied to find protein isoforms with statistically significant usage differences in the fetal vs. postnatal mouse heart. Changes in isoform usage ratios are pervasive at the protein level, with 104 significant events observed, including 88 paralog-derived isoform switching events and 16 splicing-derived isoform switching events between fetal and postnatal hearts. The ratiometric proteomic comparisons rediscovered hallmark fetal gene signatures including a postnatal switch from fetal β (MYH7) toward ɑ (MYH6) myosin heavy chains and from slow skeletal muscle (TNNI1) toward cardiac (TNNI3) troponin I. Altered usages in metabolic proteins are prominent, including a platelet to muscle phosphofructokinase (PFKP - PFKM), enolase 1 to 3 (ENO1 - ENO3), and alternative splicing of pyruvate kinase M2 toward M1 (PKM2 - PKM1) isoforms in glycolysis. The data also revealed a parallel change in mitochondrial proteins in cardiac development, suggesting the shift toward aerobic respiration involves also a remodeling of the mitochondrial protein isoform proportion. Finally, a number of glycolytic protein isoforms revert toward their fetal forms in adult hearts under pathological cardiac hypertrophy, suggesting their functional roles in adaptive or maladaptive response, but this reversal is partial. In summary, this work presents a catalog of ratiometric protein markers of the fetal genetic program of the mouse heart, including previously unreported splice isoform markers.
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Affiliation(s)
- Yu Han
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Sara A Wennersten
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Boomathi P Pandi
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Dominic C M Ng
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Edward Lau
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Maggie P Y Lam
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, CO 80045, USA
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8
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Ciampi L, Serrano L, Irimia M. Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States. Mol Syst Biol 2024; 20:296-310. [PMID: 38438733 PMCID: PMC10987577 DOI: 10.1038/s44320-024-00020-1] [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: 10/31/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 03/06/2024] Open
Abstract
Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.
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Affiliation(s)
- Ludovica Ciampi
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Luis Serrano
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Manuel Irimia
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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9
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Lu X, Ni P, Suarez-Meade P, Ma Y, Forrest EN, Wang G, Wang Y, Quiñones-Hinojosa A, Gerstein M, Jiang YH. Transcriptional Determinism and Stochasticity Contribute to the Complexity of Autism Associated SHANK Family Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585480. [PMID: 38562714 PMCID: PMC10983920 DOI: 10.1101/2024.03.18.585480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Precision of transcription is critical because transcriptional dysregulation is disease causing. Traditional methods of transcriptional profiling are inadequate to elucidate the full spectrum of the transcriptome, particularly for longer and less abundant mRNAs. SHANK3 is one of the most common autism causative genes. Twenty-four Shank3 mutant animal lines have been developed for autism modeling. However, their preclinical validity has been questioned due to incomplete Shank3 transcript structure. We applied an integrative approach combining cDNA-capture and long-read sequencing to profile the SHANK3 transcriptome in human and mice. We unexpectedly discovered an extremely complex SHANK3 transcriptome. Specific SHANK3 transcripts were altered in Shank3 mutant mice and postmortem brains tissues from individuals with ASD. The enhanced SHANK3 transcriptome significantly improved the detection rate for potential deleterious variants from genomics studies of neuropsychiatric disorders. Our findings suggest the stochastic transcription of genome associated with SHANK family genes.
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Affiliation(s)
- Xiaona Lu
- Department of Genetics, Yale University School of Medicine New Haven, CT, 06520 USA
| | - Pengyu Ni
- Biomedical Informatics & Data Science, Yale University School of Medicine New Haven, CT, 06520 USA
| | | | - Yu Ma
- Department of Neurology, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | | | - Guilin Wang
- Yale Center for Genome Analysis, Yale University School of Medicine New Haven, CT, 06520 USA
| | - Yi Wang
- Department of Neurology, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | | | - Mark Gerstein
- Biomedical Informatics & Data Science, Yale University School of Medicine New Haven, CT, 06520 USA
- Yale Center for Genome Analysis, Yale University School of Medicine New Haven, CT, 06520 USA
| | - Yong-hui Jiang
- Department of Genetics, Yale University School of Medicine New Haven, CT, 06520 USA
- Neuroscienc, Yale University School of Medicine New Haven, CT, 06520 USA
- Pediatrics, Yale University School of Medicine New Haven, CT, 06520 USA
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10
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Bénitière F, Necsulea A, Duret L. Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans. eLife 2024; 13:RP93629. [PMID: 38470242 DOI: 10.7554/elife.93629] [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] [Indexed: 03/13/2024] Open
Abstract
Most eukaryotic genes undergo alternative splicing (AS), but the overall functional significance of this process remains a controversial issue. It has been noticed that the complexity of organisms (assayed by the number of distinct cell types) correlates positively with their genome-wide AS rate. This has been interpreted as evidence that AS plays an important role in adaptive evolution by increasing the functional repertoires of genomes. However, this observation also fits with a totally opposite interpretation: given that 'complex' organisms tend to have small effective population sizes (Ne), they are expected to be more affected by genetic drift, and hence more prone to accumulate deleterious mutations that decrease splicing accuracy. Thus, according to this 'drift barrier' theory, the elevated AS rate in complex organisms might simply result from a higher splicing error rate. To test this hypothesis, we analyzed 3496 transcriptome sequencing samples to quantify AS in 53 metazoan species spanning a wide range of Ne values. Our results show a negative correlation between Ne proxies and the genome-wide AS rates among species, consistent with the drift barrier hypothesis. This pattern is dominated by low abundance isoforms, which represent the vast majority of the splice variant repertoire. We show that these low abundance isoforms are depleted in functional AS events, and most likely correspond to errors. Conversely, the AS rate of abundant isoforms, which are relatively enriched in functional AS events, tends to be lower in more complex species. All these observations are consistent with the hypothesis that variation in AS rates across metazoans reflects the limits set by drift on the capacity of selection to prevent gene expression errors.
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Affiliation(s)
- Florian Bénitière
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Anamaria Necsulea
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Laurent Duret
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
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11
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Pandi B, Brenman S, Black A, Ng DCM, Lau E, Lam MPY. Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart. J Proteome Res 2024. [PMID: 38456420 DOI: 10.1021/acs.jproteome.3c00789] [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] [Indexed: 03/09/2024]
Abstract
A computational analysis of mass spectrometry data was performed to uncover alternative splicing derived protein variants across chambers of the human heart. Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventricle, including 52 isoforms not documented on SwissProt and recovered using an RNA sequencing derived database. Among non-canonical isoforms, 29 show signs of regulation based on statistically significant preferences in tissue usage, including a ventricular enriched protein isoform of tensin-1 (TNS1) and an atrium-enriched PDZ and LIM Domain 3 (PDLIM3) isoform 2 (PDLIM3-2/ALP-H). Examined variant regions that differ between alternative and canonical isoforms are highly enriched with intrinsically disordered regions. Moreover, over two-thirds of such regions are predicted to function in protein binding and RNA binding. The analysis here lends further credence to the notion that alternative splicing diversifies the proteome by rewiring intrinsically disordered regions, which are increasingly recognized to play important roles in the generation of biological function from protein sequences.
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12
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Petrova M, Margasyuk S, Vorobeva M, Skvortsov D, Dontsova O, Pervouchine DD. BRD2 and BRD3 genes independently evolved RNA structures to control unproductive splicing. NAR Genom Bioinform 2024; 6:lqad113. [PMID: 38226395 PMCID: PMC10789245 DOI: 10.1093/nargab/lqad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/13/2023] [Accepted: 12/28/2023] [Indexed: 01/17/2024] Open
Abstract
The mammalian BRD2 and BRD3 genes encode structurally related proteins from the bromodomain and extraterminal domain protein family. The expression of BRD2 is regulated by unproductive splicing upon inclusion of exon 3b, which is located in the region encoding a bromodomain. Bioinformatic analysis indicated that BRD2 exon 3b inclusion is controlled by a pair of conserved complementary regions (PCCR) located in the flanking introns. Furthermore, we identified a highly conserved element encoding a cryptic poison exon 5b and a previously unknown PCCR in the intron between exons 5 and 6 of BRD3, however, outside of the homologous bromodomain. Minigene mutagenesis and blockage of RNA structure by antisense oligonucleotides demonstrated that RNA structure controls the rate of inclusion of poison exons. The patterns of BRD2 and BRD3 expression and splicing show downregulation upon inclusion of poison exons, which become skipped in response to transcription elongation slowdown, further confirming a role of PCCRs in unproductive splicing regulation. We conclude that BRD2 and BRD3 independently acquired poison exons and RNA structures to dynamically control unproductive splicing. This study describes a convergent evolution of regulatory unproductive splicing mechanisms in these genes, providing implications for selective modulation of their expression in therapeutic applications.
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Affiliation(s)
- Marina Petrova
- Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, str. 1, Moscow 121205, Russia
| | - Sergey Margasyuk
- Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, str. 1, Moscow 121205, Russia
| | - Margarita Vorobeva
- Faculty of Chemistry, Moscow State University, GSP-1, 1-3 Leninskiye Gory, Moscow 119991, Russia
| | - Dmitry Skvortsov
- Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, str. 1, Moscow 121205, Russia
- Faculty of Chemistry, Moscow State University, GSP-1, 1-3 Leninskiye Gory, Moscow 119991, Russia
| | - Olga A Dontsova
- Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, str. 1, Moscow 121205, Russia
- Faculty of Chemistry, Moscow State University, GSP-1, 1-3 Leninskiye Gory, Moscow 119991, Russia
| | - Dmitri D Pervouchine
- Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, str. 1, Moscow 121205, Russia
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13
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Santos LGC, Parreira VDSC, da Silva EMG, Santos MDM, Fernandes ADF, Neves-Ferreira AGDC, Carvalho PC, Freitas FCDP, Passetti F. SpliceProt 2.0: A Sequence Repository of Human, Mouse, and Rat Proteoforms. Int J Mol Sci 2024; 25:1183. [PMID: 38256255 PMCID: PMC10816255 DOI: 10.3390/ijms25021183] [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: 10/31/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
SpliceProt 2.0 is a public proteogenomics database that aims to list the sequence of known proteins and potential new proteoforms in human, mouse, and rat proteomes. This updated repository provides an even broader range of computationally translated proteins and serves, for example, to aid with proteomic validation of splice variants absent from the reference UniProtKB/SwissProt database. We demonstrate the value of SpliceProt 2.0 to predict orthologous proteins between humans and murines based on transcript reconstruction, sequence annotation and detection at the transcriptome and proteome levels. In this release, the annotation data used in the reconstruction of transcripts based on the methodology of ternary matrices were acquired from new databases such as Ensembl, UniProt, and APPRIS. Another innovation implemented in the pipeline is the exclusion of transcripts predicted to be susceptible to degradation through the NMD pathway. Taken together, our repository and its applications represent a valuable resource for the proteogenomics community.
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Affiliation(s)
- Letícia Graziela Costa Santos
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Vinícius da Silva Coutinho Parreira
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Esdras Matheus Gomes da Silva
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Av. Brazil 4036, Campus Maré, Rio de Janeiro 21040-361, RJ, Brazil
| | - Marlon Dias Mariano Santos
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Alexander da Franca Fernandes
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Ana Gisele da Costa Neves-Ferreira
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Av. Brazil 4036, Campus Maré, Rio de Janeiro 21040-361, RJ, Brazil
| | - Paulo Costa Carvalho
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
| | - Flávia Cristina de Paula Freitas
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luis, Km 235, São Carlos 13565-905, SP, Brazil
| | - Fabio Passetti
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil
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14
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Solovyeva EM, Utzinger S, Vissières A, Mitchelmore J, Ahrné E, Hermes E, Poetsch T, Ronco M, Bidinosti M, Merkl C, Serluca FC, Fessenden J, Naumann U, Voshol H, Meyer AS, Hoersch S. Integrative Proteogenomics for Differential Expression and Splicing Variation in a DM1 Mouse Model. Mol Cell Proteomics 2024; 23:100683. [PMID: 37993104 PMCID: PMC10770608 DOI: 10.1016/j.mcpro.2023.100683] [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: 07/31/2022] [Revised: 09/02/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023] Open
Abstract
Dysregulated mRNA splicing is involved in the pathogenesis of many diseases including cancer, neurodegenerative diseases, and muscular dystrophies such as myotonic dystrophy type 1 (DM1). Comprehensive assessment of dysregulated splicing on the transcriptome and proteome level has been methodologically challenging, and thus investigations have often been targeting only few genes. Here, we performed a large-scale coordinated transcriptomic and proteomic analysis to characterize a DM1 mouse model (HSALR) in comparison to wild type. Our integrative proteogenomics approach comprised gene- and splicing-level assessments for mRNAs and proteins. It recapitulated many known instances of aberrant mRNA splicing in DM1 and identified new ones. It enabled the design and targeting of splicing-specific peptides and confirmed the translation of known instances of aberrantly spliced disease-related genes (e.g., Atp2a1, Bin1, Ryr1), complemented by novel findings (Flnc and Ywhae). Comparative analysis of large-scale mRNA and protein expression data showed quantitative agreement of differentially expressed genes and splicing patterns between disease and wild type. We hence propose this work as a suitable blueprint for a robust and scalable integrative proteogenomic strategy geared toward advancing our understanding of splicing-based disorders. With such a strategy, splicing-based biomarker candidates emerge as an attractive and accessible option, as they can be efficiently asserted on the mRNA and protein level in coordinated fashion.
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Affiliation(s)
- Elizaveta M Solovyeva
- Research Informatics, Biomedical Research at Novartis, Basel, Switzerland; V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.
| | - Stephan Utzinger
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | | | - Joanna Mitchelmore
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | - Erik Ahrné
- Discovery Sciences, Biomedical Research at Novartis, Basel, Switzerland
| | - Erwin Hermes
- Discovery Sciences, Biomedical Research at Novartis, Basel, Switzerland
| | - Tania Poetsch
- Discovery Sciences, Biomedical Research at Novartis, Basel, Switzerland
| | - Marie Ronco
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | - Michael Bidinosti
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | - Claudia Merkl
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | - Fabrizio C Serluca
- Research Informatics, Biomedical Research at Novartis, Cambridge, Massachusetts, USA
| | - James Fessenden
- Neurodegenerative Diseases, Biomedical Research at Novartis, Cambridge, Massachusetts, USA
| | - Ulrike Naumann
- Discovery Sciences, Biomedical Research at Novartis, Basel, Switzerland
| | - Hans Voshol
- Discovery Sciences, Biomedical Research at Novartis, Basel, Switzerland
| | - Angelika S Meyer
- Diseases of Aging and Regenerative Medicine, Biomedical Research at Novartis, Basel, Switzerland
| | - Sebastian Hoersch
- Research Informatics, Biomedical Research at Novartis, Basel, Switzerland.
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15
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Sinitcyn P, Richards AL, Weatheritt RJ, Brademan DR, Marx H, Shishkova E, Meyer JG, Hebert AS, Westphall MS, Blencowe BJ, Cox J, Coon JJ. Global detection of human variants and isoforms by deep proteome sequencing. Nat Biotechnol 2023; 41:1776-1786. [PMID: 36959352 PMCID: PMC10713452 DOI: 10.1038/s41587-023-01714-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/15/2023] [Indexed: 03/25/2023]
Abstract
An average shotgun proteomics experiment detects approximately 10,000 human proteins from a single sample. However, individual proteins are typically identified by peptide sequences representing a small fraction of their total amino acids. Hence, an average shotgun experiment fails to distinguish different protein variants and isoforms. Deeper proteome sequencing is therefore required for the global discovery of protein isoforms. Using six different human cell lines, six proteases, deep fractionation and three tandem mass spectrometry fragmentation methods, we identify a million unique peptides from 17,717 protein groups, with a median sequence coverage of approximately 80%. Direct comparison with RNA expression data provides evidence for the translation of most nonsynonymous variants. We have also hypothesized that undetected variants likely arise from mutation-induced protein instability. We further observe comparable detection rates for exon-exon junction peptides representing constitutive and alternative splicing events. Our dataset represents a resource for proteoform discovery and provides direct evidence that most frame-preserving alternatively spliced isoforms are translated.
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Affiliation(s)
- Pavel Sinitcyn
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
- Morgridge Institute for Research, Madison, WI, USA
| | - Alicia L Richards
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Robert J Weatheritt
- EMBL Australia and Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Dain R Brademan
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Harald Marx
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jesse G Meyer
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander S Hebert
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael S Westphall
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Benjamin J Blencowe
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI, USA.
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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16
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Varabyou A, Sommer MJ, Erdogdu B, Shinder I, Minkin I, Chao KH, Park S, Heinz J, Pockrandt C, Shumate A, Rincon N, Puiu D, Steinegger M, Salzberg SL, Pertea M. CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure. Genome Biol 2023; 24:249. [PMID: 37904256 PMCID: PMC10614308 DOI: 10.1186/s13059-023-03088-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
CHESS 3 represents an improved human gene catalog based on nearly 10,000 RNA-seq experiments across 54 body sites. It significantly improves current genome annotation by integrating the latest reference data and algorithms, machine learning techniques for noise filtering, and new protein structure prediction methods. CHESS 3 contains 41,356 genes, including 19,839 protein-coding genes and 158,377 transcripts, with 14,863 protein-coding transcripts not in other catalogs. It includes all MANE transcripts and at least one transcript for most RefSeq and GENCODE genes. On the CHM13 human genome, the CHESS 3 catalog contains an additional 129 protein-coding genes. CHESS 3 is available at http://ccb.jhu.edu/chess .
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Affiliation(s)
- Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.
| | - Markus J Sommer
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA
| | - Beril Erdogdu
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA
| | - Ida Shinder
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Cross Disciplinary Graduate Program in Biomedical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ilia Minkin
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA
| | - Kuan-Hao Chao
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Sukhwan Park
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
| | - Jakob Heinz
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA
| | - Christopher Pockrandt
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA
| | - Alaina Shumate
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA
| | - Natalia Rincon
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA
| | - Daniela Puiu
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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17
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Peng L, Zhang X, Du Y, Li F, Han J, Liu O, Dai S, Zhang X, Liu GE, Yang L, Zhou Y. New insights into transcriptome variation during cattle adipocyte adipogenesis by direct RNA sequencing. iScience 2023; 26:107753. [PMID: 37692285 PMCID: PMC10492216 DOI: 10.1016/j.isci.2023.107753] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/31/2023] [Accepted: 08/24/2023] [Indexed: 09/12/2023] Open
Abstract
We performed direct RNA sequencing (DRS) together with PCR-amplified cDNA long and short read sequencing for cattle adipocyte at different stages. We proved that the DRS was with advantages to avoid artificial transcripts and questionable exitrons. Totally, we obtained 68,124 transcripts with information of alternative splicing, poly (A) length and mRNA modification. The number of transcripts for adipogenesis was expanded by alternative splicing, which lead regulation mechanisms far more complex than ever known. We detected 891 differentially expressed genes (DEGs). However, 62.78% transcripts of DEGs were not significantly differentially expressed, and 248 transcripts showed opposite changing directions with their genes. The poly (A) tail became globally shorter in differentiated adipocyte than in primary adipocyte, and had a weak negative correlation with gene/transcript expression. Moreover, the study of different mRNA modifications implied their potential roles in gene expression and alternative splicing. Overall, our study promoted better understanding of adipogenesis mechanisms in cattle adipocytes.
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Affiliation(s)
- Lingwei Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqin Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiazheng Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Oujin Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Shoulu Dai
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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18
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Dam SH, Olsen LR, Vitting-Seerup K. Expression and splicing mediate distinct biological signals. BMC Biol 2023; 21:220. [PMID: 37858135 PMCID: PMC10588054 DOI: 10.1186/s12915-023-01724-w] [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: 12/01/2022] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Through alternative splicing, most human genes produce multiple isoforms in a cell-, tissue-, and disease-specific manner. Numerous studies show that alternative splicing is essential for development, diseases, and their treatments. Despite these important examples, the extent and biological relevance of splicing are currently unknown. RESULTS To solve this problem, we developed pairedGSEA and used it to profile transcriptional changes in 100 representative RNA-seq datasets. Our systematic analysis demonstrates that changes in splicing, on average, contribute to 48.1% of the biological signal in expression analyses. Gene-set enrichment analysis furthermore indicates that expression and splicing both convey shared and distinct biological signals. CONCLUSIONS These findings establish alternative splicing as a major regulator of the human condition and suggest that most contemporary RNA-seq studies likely miss out on critical biological insights. We anticipate our results will contribute to the transition from a gene-centric to an isoform-centric research paradigm.
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Affiliation(s)
- Søren Helweg Dam
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lars Rønn Olsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kristoffer Vitting-Seerup
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.
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19
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Fair B, Najar CBA, Zhao J, Lozano S, Reilly A, Mossian G, Staley JP, Wang J, Li YI. Global impact of aberrant splicing on human gene expression levels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557588. [PMID: 37745605 PMCID: PMC10515962 DOI: 10.1101/2023.09.13.557588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Alternative splicing (AS) is pervasive in human genes, yet the specific function of most AS events remains unknown. It is widely assumed that the primary function of AS is to diversify the proteome, however AS can also influence gene expression levels by producing transcripts rapidly degraded by nonsense-mediated decay (NMD). Currently, there are no precise estimates for how often the coupling of AS and NMD (AS-NMD) impacts gene expression levels because rapidly degraded NMD transcripts are challenging to capture. To better understand the impact of AS on gene expression levels, we analyzed population-scale genomic data in lymphoblastoid cell lines across eight molecular assays that capture gene regulation before, during, and after transcription and cytoplasmic decay. Sequencing nascent mRNA transcripts revealed frequent aberrant splicing of human introns, which results in remarkably high levels of mRNA transcripts subject to NMD. We estimate that ~15% of all protein-coding transcripts are degraded by NMD, and this estimate increases to nearly half of all transcripts for lowly-expressed genes with many introns. Leveraging genetic variation across cell lines, we find that GWAS trait-associated loci explained by AS are similarly likely to associate with NMD-induced expression level differences as with differences in protein isoform usage. Additionally, we used the splice-switching drug risdiplam to perturb AS at hundreds of genes, finding that ~3/4 of the splicing perturbations induce NMD. Thus, we conclude that AS-NMD substantially impacts the expression levels of most human genes. Our work further suggests that much of the molecular impact of AS is mediated by changes in protein expression levels rather than diversification of the proteome.
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Affiliation(s)
- Benjamin Fair
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Carlos Buen Abad Najar
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Junxing Zhao
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Stephanie Lozano
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Present address: Center for Neuroscience, University of California Davis, Davis, CA 95618, USA
| | - Austin Reilly
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Gabriela Mossian
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
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20
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Dwivedi SL, Quiroz LF, Reddy ASN, Spillane C, Ortiz R. Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs. Int J Mol Sci 2023; 24:15205. [PMID: 37894886 PMCID: PMC10607462 DOI: 10.3390/ijms242015205] [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: 09/02/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053 Alnarp, SE, Sweden
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21
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Pandi B, Brenman S, Black A, Ng DCM, Lau E, Lam MPY. Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561375. [PMID: 37873130 PMCID: PMC10592692 DOI: 10.1101/2023.10.08.561375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A computational analysis of mass spectrometry data was performed to uncover alternative splicing derived protein variants across chambers of the human heart. Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventricle, including 52 isoforms not documented on SwissProt and recovered using an RNA sequencing derived database. Among non-canonical isoforms, 29 show signs of regulation based on statistically significant preferences in tissue usage, including a ventricular enriched protein isoform of tensin-1 (TNS1) and an atrium-enriched PDZ and LIM Domain 3 (PDLIM3) isoform 2 (PDLIM3-2/ALP-H). Examined variant regions that differ between alternative and canonical isoforms are highly enriched in intrinsically disordered regions, and over two-thirds of such regions are predicted to function in protein binding and/or RNA binding. The analysis here lends further credence to the notion that alternative splicing diversifies the proteome by rewiring intrinsically disordered regions, which are increasingly recognized to play important roles in the generation of biological function from protein sequences.
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Affiliation(s)
- Boomathi Pandi
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Stella Brenman
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Alexander Black
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Dominic C. M. Ng
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Edward Lau
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Consortium for Fibrosis Research and Translation (CFReT), University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Maggie P. Y. Lam
- Department of Medicine/Division of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Consortium for Fibrosis Research and Translation (CFReT), University of Colorado School of Medicine, Aurora, CO 80045, USA
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22
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Dou Y, Liu Y, Yi X, Olsen LK, Zhu H, Gao Q, Zhou H, Zhang B. SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics. Nat Commun 2023; 14:5809. [PMID: 37726316 PMCID: PMC10509223 DOI: 10.1038/s41467-023-41558-2] [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: 10/13/2022] [Accepted: 09/06/2023] [Indexed: 09/21/2023] Open
Abstract
Shotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is challenging due to the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in normal and disease biology. We systematically assess the challenge and opportunities of shotgun proteomics-based protein isoform characterization using in silico and experimental data, and then present SEPepQuant, a graph theory-based approach to maximize isoform characterization. Using published data from one induced pluripotent stem cell study and two human hepatocellular carcinoma studies, we demonstrate the ability of SEPepQuant in addressing the key limitations of existing methods, providing more comprehensive isoform-level characterization, identifying hundreds of isoform-level regulation events, and facilitating streamlined cross-study comparisons. Our analysis provides solid evidence to support a widespread role of protein isoform regulation in normal and disease processes, and SEPepQuant has broad applications to biological and translational research.
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Affiliation(s)
- Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuejia Liu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, 210023, Nanjing, Jiangsu, China
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lindsey K Olsen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongwen Zhu
- Department of Analytical Chemistry, State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, 201203, Shanghai, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, 180 Fenglin Road, 200032, Shanghai, China
| | - Hu Zhou
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, 210023, Nanjing, Jiangsu, China
- Department of Analytical Chemistry, State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, 201203, Shanghai, China
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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23
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Prensner JR, Abelin JG, Kok LW, Clauser KR, Mudge JM, Ruiz-Orera J, Bassani-Sternberg M, Moritz RL, Deutsch EW, van Heesch S. What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome? Mol Cell Proteomics 2023; 22:100631. [PMID: 37572790 PMCID: PMC10506109 DOI: 10.1016/j.mcpro.2023.100631] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/21/2023] [Accepted: 08/08/2023] [Indexed: 08/14/2023] Open
Abstract
Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands of noncanonical sites of ribosome translation outside the currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7000 noncanonical ORFs are translated, which, at first glance, has the potential to expand the number of human protein CDSs by 30%, from ∼19,500 annotated CDSs to over 26,000 annotated CDSs. Yet, additional scrutiny of these ORFs has raised numerous questions about what fraction of them truly produce a protein product and what fraction of those can be understood as proteins according to conventional understanding of the term. Adding further complication is the fact that published estimates of noncanonical ORFs vary widely by around 30-fold, from several thousand to several hundred thousand. The summation of this research has left the genomics and proteomics communities both excited by the prospect of new coding regions in the human genome but searching for guidance on how to proceed. Here, we discuss the current state of noncanonical ORF research, databases, and interpretation, focusing on how to assess whether a given ORF can be said to be "protein coding."
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Affiliation(s)
- John R Prensner
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| | | | - Leron W Kok
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, Agora Center Bugnon 25A, University of Lausanne, Lausanne, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland; Agora Cancer Research Centre, Lausanne, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology (ISB), Seattle, Washington, USA
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington, USA
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24
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Goldtzvik Y, Sen N, Lam SD, Orengo C. Protein diversification through post-translational modifications, alternative splicing, and gene duplication. Curr Opin Struct Biol 2023; 81:102640. [PMID: 37354790 DOI: 10.1016/j.sbi.2023.102640] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/05/2023] [Accepted: 05/24/2023] [Indexed: 06/26/2023]
Abstract
Proteins provide the basis for cellular function. Having multiple versions of the same protein within a single organism provides a way of regulating its activity or developing novel functions. Post-translational modifications of proteins, by means of adding/removing chemical groups to amino acids, allow for a well-regulated and controlled way of generating functionally distinct protein species. Alternative splicing is another method with which organisms possibly generate new isoforms. Additionally, gene duplication events throughout evolution generate multiple paralogs of the same genes, resulting in multiple versions of the same protein within an organism. In this review, we discuss recent advancements in the study of these three methods of protein diversification and provide illustrative examples of how they affect protein structure and function.
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Affiliation(s)
- Yonathan Goldtzvik
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Neeladri Sen
- Department of Structural and Molecular Biology, University College London, London, United Kingdom. https://twitter.com/@NeeladriSen
| | - Su Datt Lam
- Department of Structural and Molecular Biology, University College London, London, United Kingdom; Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Christine Orengo
- Department of Structural and Molecular Biology, University College London, London, United Kingdom.
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25
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Beusch I, Rao B, Studer MK, Luhovska T, Šukytė V, Lei S, Oses-Prieto J, SeGraves E, Burlingame A, Jonas S, Madhani HD. Targeted high-throughput mutagenesis of the human spliceosome reveals its in vivo operating principles. Mol Cell 2023; 83:2578-2594.e9. [PMID: 37402368 PMCID: PMC10484158 DOI: 10.1016/j.molcel.2023.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/15/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
The spliceosome is a staggeringly complex machine, comprising, in humans, 5 snRNAs and >150 proteins. We scaled haploid CRISPR-Cas9 base editing to target the entire human spliceosome and investigated the mutants using the U2 snRNP/SF3b inhibitor, pladienolide B. Hypersensitive substitutions define functional sites in the U1/U2-containing A complex but also in components that act as late as the second chemical step after SF3b is dissociated. Viable resistance substitutions map not only to the pladienolide B-binding site but also to the G-patch domain of SUGP1, which lacks orthologs in yeast. We used these mutants and biochemical approaches to identify the spliceosomal disassemblase DHX15/hPrp43 as the ATPase ligand for SUGP1. These and other data support a model in which SUGP1 promotes splicing fidelity by triggering early spliceosome disassembly in response to kinetic blocks. Our approach provides a template for the analysis of essential cellular machines in humans.
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Affiliation(s)
- Irene Beusch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Beiduo Rao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Michael K Studer
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Tetiana Luhovska
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Viktorija Šukytė
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Susan Lei
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Juan Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, USA
| | - Em SeGraves
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, USA
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, USA.
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26
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Hoppe ER, Udy DB, Bradley RK. Recursive splicing discovery using lariats in total RNA sequencing. Life Sci Alliance 2023; 6:e202201889. [PMID: 37137707 PMCID: PMC10156609 DOI: 10.26508/lsa.202201889] [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: 12/23/2022] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
Recursive splicing is a non-canonical splicing mechanism in which an intron is removed in segments via multiple splicing reactions. Relatively few recursive splice sites have been identified with high confidence in human introns, and more comprehensive analyses are needed to better characterize where recursive splicing happens and whether or not it has a regulatory function. In this study, we use an unbiased approach using intron lariats to search for recursive splice sites in constitutive introns and alternative exons in the human transcriptome. We find evidence for recursive splicing in a broader range of intron sizes than previously reported and detail a new location for recursive splicing at the distal ends of cassette exons. In addition, we identify evidence for the conservation of these recursive splice sites among higher vertebrates and the use of these sites to influence alternative exon exclusion. Together, our data demonstrate the prevalence of recursive splicing and its potential influence on gene expression through alternatively spliced isoforms.
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Affiliation(s)
- Emma R Hoppe
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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27
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Prensner JR, Abelin JG, Kok LW, Clauser KR, Mudge JM, Ruiz-Orera J, Bassani-Sternberg M, Deutsch EW, van Heesch S. What can Ribo-seq and proteomics tell us about the non-canonical proteome? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541049. [PMID: 37292611 PMCID: PMC10245706 DOI: 10.1101/2023.05.16.541049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ribosome profiling (Ribo-seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands of non-canonical sites of ribosome translation outside of the currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7,000 non-canonical open reading frames (ORFs) are translated, which, at first glance, has the potential to expand the number of human protein-coding sequences by 30%, from ∼19,500 annotated CDSs to over 26,000. Yet, additional scrutiny of these ORFs has raised numerous questions about what fraction of them truly produce a protein product and what fraction of those can be understood as proteins according to conventional understanding of the term. Adding further complication is the fact that published estimates of non-canonical ORFs vary widely by around 30-fold, from several thousand to several hundred thousand. The summation of this research has left the genomics and proteomics communities both excited by the prospect of new coding regions in the human genome, but searching for guidance on how to proceed. Here, we discuss the current state of non-canonical ORF research, databases, and interpretation, focusing on how to assess whether a given ORF can be said to be "protein-coding". In brief The human genome encodes thousands of non-canonical open reading frames (ORFs) in addition to protein-coding genes. As a nascent field, many questions remain regarding non-canonical ORFs. How many exist? Do they encode proteins? What level of evidence is needed for their verification? Central to these debates has been the advent of ribosome profiling (Ribo-seq) as a method to discern genome-wide ribosome occupancy, and immunopeptidomics as a method to detect peptides that are processed and presented by MHC molecules and not observed in traditional proteomics experiments. This article provides a synthesis of the current state of non-canonical ORF research and proposes standards for their future investigation and reporting. Highlights Combined use of Ribo-seq and proteomics-based methods enables optimal confidence in detecting non-canonical ORFs and their protein products.Ribo-seq can provide more sensitive detection of non-canonical ORFs, but data quality and analytical pipelines will impact results.Non-canonical ORF catalogs are diverse and span both high-stringency and low-stringency ORF nominations.A framework for standardized non-canonical ORF evidence will advance the research field.
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Affiliation(s)
- John R. Prensner
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Leron W. Kok
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Karl R. Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jonathan M. Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, 1011 Lausanne, Switzerland
| | - Eric W. Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
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28
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Jia ZC, Das D, Zhang Y, Fernie AR, Liu YG, Chen M, Zhang J. Plant serine/arginine-rich proteins: versatile players in RNA processing. PLANTA 2023; 257:109. [PMID: 37145304 DOI: 10.1007/s00425-023-04132-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/05/2023] [Indexed: 05/06/2023]
Abstract
MAIN CONCLUSION Serine/arginine-rich (SR) proteins participate in RNA processing by interacting with precursor mRNAs or other splicing factors to maintain plant growth and stress responses. Alternative splicing is an important mechanism involved in mRNA processing and regulation of gene expression at the posttranscriptional level, which is the main reason for the diversity of genes and proteins. The process of alternative splicing requires the participation of many specific splicing factors. The SR protein family is a splicing factor in eukaryotes. The vast majority of SR proteins' existence is an essential survival factor. Through its RS domain and other unique domains, SR proteins can interact with specific sequences of precursor mRNA or other splicing factors and cooperate to complete the correct selection of splicing sites or promote the formation of spliceosomes. They play essential roles in the composition and alternative splicing of precursor mRNAs, providing pivotal functions to maintain growth and stress responses in animals and plants. Although SR proteins have been identified in plants for three decades, their evolutionary trajectory, molecular function, and regulatory network remain largely unknown compared to their animal counterparts. This article reviews the current understanding of this gene family in eukaryotes and proposes potential key research priorities for future functional studies.
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Affiliation(s)
- Zi-Chang Jia
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences and Technology, 52 Agricultural Building, University of Missouri, Columbia, MO, 65201, USA
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Youjun Zhang
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Moxian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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29
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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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30
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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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Cui H, Diedrich JK, Wu DC, Lim JJ, Nottingham RM, Moresco JJ, Yates JR, Blencowe BJ, Lambowitz AM, Schimmel P. Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2. Nat Cell Biol 2023; 25:592-603. [PMID: 37059883 DOI: 10.1038/s41556-023-01118-8] [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: 03/28/2022] [Accepted: 02/27/2023] [Indexed: 04/16/2023]
Abstract
Cells respond to perturbations such as inflammation by sensing changes in metabolite levels. Especially prominent is arginine, which has known connections to the inflammatory response. Aminoacyl-tRNA synthetases, enzymes that catalyse the first step of protein synthesis, can also mediate cell signalling. Here we show that depletion of arginine during inflammation decreased levels of nuclear-localized arginyl-tRNA synthetase (ArgRS). Surprisingly, we found that nuclear ArgRS interacts and co-localizes with serine/arginine repetitive matrix protein 2 (SRRM2), a spliceosomal and nuclear speckle protein, and that decreased levels of nuclear ArgRS correlated with changes in condensate-like nuclear trafficking of SRRM2 and splice-site usage in certain genes. These splice-site usage changes cumulated in the synthesis of different protein isoforms that altered cellular metabolism and peptide presentation to immune cells. Our findings uncover a mechanism whereby an aminoacyl-tRNA synthetase cognate to a key amino acid that is metabolically controlled during inflammation modulates the splicing machinery.
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Affiliation(s)
- Haissi Cui
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Douglas C Wu
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA
| | - Justin J Lim
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin J Blencowe
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA.
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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32
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Marasco LE, Kornblihtt AR. The physiology of alternative splicing. Nat Rev Mol Cell Biol 2023; 24:242-254. [PMID: 36229538 DOI: 10.1038/s41580-022-00545-z] [Citation(s) in RCA: 99] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/09/2022]
Abstract
Alternative splicing is a substantial contributor to the high complexity of transcriptomes of multicellular eukaryotes. In this Review, we discuss the accumulated evidence that most of this complexity is reflected at the protein level and fundamentally shapes the physiology and pathology of organisms. This notion is supported not only by genome-wide analyses but, mainly, by detailed studies showing that global and gene-specific modulations of alternative splicing regulate highly diverse processes such as tissue-specific and species-specific cell differentiation, thermal regulation, neuron self-avoidance, infrared sensing, the Warburg effect, maintenance of telomere length, cancer and autism spectrum disorders (ASD). We also discuss how mastering the control of alternative splicing paved the way to clinically approved therapies for hereditary diseases.
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Affiliation(s)
- Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina.
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33
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Lan J, Zhou Y, Liu Y, Xia Y, Wan Y, Cao J. Role of ADAM33 short isoform as a tumor suppressor in the pathogenesis of thyroid cancer via oncogenic function disruption of full-length ADAM33. Hum Cell 2023:10.1007/s13577-023-00898-3. [PMID: 36977901 DOI: 10.1007/s13577-023-00898-3] [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: 11/10/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023]
Abstract
Thyroid cancer is the most prevalent endocrine malignancy globally; however, its underlying pathogenesis remains unclarified. Reportedly, alternative splicing is involved in processes such as embryonic stem and precursor cell differentiation, cell lineage reprogramming, and epithelial-mesenchymal transitions. ADAM33-n, an alternative splicing isoform of ADAM33, encodes a small protein containing 138 amino acids of the N-terminal of full-length ADAM33, which constructs a chaperone-like domain that was previously reported to bind and block the proteolysis activity of ADAM33. In this study, we reported for the first time that ADAM33-n was downregulated in thyroid cancer. The results of cell counting kit-8 and colony formation assays showed that ectopic ADAM33-n in papillary thyroid cancer cell lines restricted cell proliferation and colony formation. Moreover, we demonstrated that ectopic ADAM33-n reversed the oncogenic function of full-length ADAM33 in cell growth and colony formation in the MDA-T32 and BCPAP cells. These findings indicate the tumor suppressor ability of ADAM33-n. Altogether, our study findings present a potential explanatory model of how the downregulation of the oncogenic gene ADAM33 promotes the pathogenesis of thyroid cancer.
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Affiliation(s)
- Jing Lan
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China
| | - Yehui Zhou
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China
| | - Yang Liu
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China
| | - Yu Xia
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China
| | - Yuqiu Wan
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China.
| | - Jianbo Cao
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China.
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Manuel JM, Guilloy N, Khatir I, Roucou X, Laurent B. Re-evaluating the impact of alternative RNA splicing on proteomic diversity. Front Genet 2023; 14:1089053. [PMID: 36845399 PMCID: PMC9947481 DOI: 10.3389/fgene.2023.1089053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Alternative splicing (AS) constitutes a mechanism by which protein-coding genes and long non-coding RNA (lncRNA) genes produce more than a single mature transcript. From plants to humans, AS is a powerful process that increases transcriptome complexity. Importantly, splice variants produced from AS can potentially encode for distinct protein isoforms which can lose or gain specific domains and, hence, differ in their functional properties. Advances in proteomics have shown that the proteome is indeed diverse due to the presence of numerous protein isoforms. For the past decades, with the help of advanced high-throughput technologies, numerous alternatively spliced transcripts have been identified. However, the low detection rate of protein isoforms in proteomic studies raised debatable questions on whether AS contributes to proteomic diversity and on how many AS events are really functional. We propose here to assess and discuss the impact of AS on proteomic complexity in the light of the technological progress, updated genome annotation, and current scientific knowledge.
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Affiliation(s)
- Jeru Manoj Manuel
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Inès Khatir
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada,Quebec Network for Research on Protein Function Structure and Engineering, PROTEO, Québec, QC, Canada
| | - Benoit Laurent
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,*Correspondence: Benoit Laurent,
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35
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Identification of Alternative Splicing in Proteomes of Human Melanoma Cell Lines without RNA Sequencing Data. Int J Mol Sci 2023; 24:ijms24032466. [PMID: 36768787 PMCID: PMC9916885 DOI: 10.3390/ijms24032466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/31/2023] Open
Abstract
Alternative splicing is one of the main regulation pathways in living cells beyond simple changes in the level of protein expression. Most of the approaches proposed in proteomics for the identification of specific splicing isoforms require a preliminary deep transcriptomic analysis of the sample under study, which is not always available, especially in the case of the re-analysis of previously acquired data. Herein, we developed new algorithms for the identification and validation of protein splice isoforms in proteomic data in the absence of RNA sequencing of the samples under study. The bioinformatic approaches were tested on the results of proteome analysis of human melanoma cell lines, obtained earlier by high-resolution liquid chromatography and mass spectrometry (LC-MS). A search for alternative splicing events for each of the cell lines studied was performed against the database generated from all known transcripts (RefSeq) and the one composed of peptide sequences, which included all biologically possible combinations of exons. The identifications were filtered using the prediction of both retention times and relative intensities of fragment ions in the corresponding mass spectra. The fragmentation mass spectra corresponding to the discovered alternative splicing events were additionally examined for artifacts. Selected splicing events were further validated at the mRNA level by quantitative PCR.
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36
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Han Y, Wennersten SA, Wright JM, Ludwig RW, Lau E, Lam MPY. Proteogenomics reveals sex-biased aging genes and coordinated splicing in cardiac aging. Am J Physiol Heart Circ Physiol 2022; 323:H538-H558. [PMID: 35930447 PMCID: PMC9448281 DOI: 10.1152/ajpheart.00244.2022] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/20/2022] [Accepted: 07/31/2022] [Indexed: 01/24/2023]
Abstract
The risks of heart diseases are significantly modulated by age and sex, but how these factors influence baseline cardiac gene expression remains incompletely understood. Here, we used RNA sequencing and mass spectrometry to compare gene expression in female and male young adult (4 mo) and early aging (20 mo) mouse hearts, identifying thousands of age- and sex-dependent gene expression signatures. Sexually dimorphic cardiac genes are broadly distributed, functioning in mitochondrial metabolism, translation, and other processes. In parallel, we found over 800 genes with differential aging response between male and female, including genes in cAMP and PKA signaling. Analysis of the sex-adjusted aging cardiac transcriptome revealed a widespread remodeling of exon usage patterns that is largely independent from differential gene expression, concomitant with upstream changes in RNA-binding protein and splice factor transcripts. To evaluate the impact of the splicing events on cardiac proteoform composition, we applied an RNA-guided proteomics computational pipeline to analyze the mass spectrometry data and detected hundreds of putative splice variant proteins that have the potential to rewire the cardiac proteome. Taken together, the results here suggest that cardiac aging is associated with 1) widespread sex-biased aging genes and 2) a rewiring of RNA splicing programs, including sex- and age-dependent changes in exon usages and splice patterns that have the potential to influence cardiac protein structure and function. These changes contribute to the emerging evidence for considerable sexual dimorphism in the cardiac aging process that should be considered in the search for disease mechanisms.NEW & NOTEWORTHY Han et al. used proteogenomics to compare male and female mouse hearts at 4 and 20 mo. Sex-biased cardiac genes function in mitochondrial metabolism, translation, autophagy, and other processes. Hundreds of cardiac genes show sex-by-age interactions, that is, sex-biased aging genes. Cardiac aging is accompanied with a remodeling of exon usage in functionally coordinated genes, concomitant with differential expression of RNA-binding proteins and splice factors. These features represent an underinvestigated aspect of cardiac aging that may be relevant to the search for disease mechanisms.
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Grants
- R21-HL150456 HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R00-HL144829 HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R00 HL127302 NHLBI NIH HHS
- R03-OD032666 HHS | NIH | NIH Office of the Director (OD)
- R01 HL141278 NHLBI NIH HHS
- F32 HL149191 NHLBI NIH HHS
- F32-HL149191 HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R00-HL127302 HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R21 HL150456 NHLBI NIH HHS
- R03 OD032666 NIH HHS
- R00 HL144829 NHLBI NIH HHS
- R01-HL141278 HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- University of Colorado
- University of Colorado School of Medicine, Anschutz Medical Campus
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Affiliation(s)
- Yu Han
- Department of Medicine, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
| | - Sara A Wennersten
- Department of Medicine, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
| | - Julianna M Wright
- Department of Medicine, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
| | - R W Ludwig
- Department of Medicine, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
| | | | - Maggie P Y Lam
- Department of Medicine, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, Colorado
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37
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Demin DE, Stasevich EM, Murashko MM, Tkachenko EA, Uvarova AN, Schwartz AM. Full and D-BOX-Deficient PTTG1 Isoforms: Effects on Cell Proliferation. Mol Biol 2022. [DOI: 10.1134/s0026893322060061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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38
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Wright CJ, Smith CWJ, Jiggins CD. Alternative splicing as a source of phenotypic diversity. Nat Rev Genet 2022; 23:697-710. [PMID: 35821097 DOI: 10.1038/s41576-022-00514-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/27/2022]
Abstract
A major goal of evolutionary genetics is to understand the genetic processes that give rise to phenotypic diversity in multicellular organisms. Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits. It is well established that alternative splicing contributes to key innovations over long evolutionary timescales, such as brain development in bilaterians. However, recent developments in long-read sequencing and the generation of high-quality genome assemblies for diverse organisms has facilitated comparisons of splicing profiles between closely related species, providing insights into how alternative splicing evolves over shorter timescales. Although most splicing variants are probably non-functional, alternative splicing is nonetheless emerging as a dynamic, evolutionarily labile process that can facilitate adaptation and contribute to species divergence.
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Affiliation(s)
- Charlotte J Wright
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK. .,Department of Zoology, University of Cambridge, Cambridge, UK.
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
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Bao G, Li T, Guan X, Yao Y, Liang J, Xiang Y, Zhong X. Development of a Prognostic Alternative Splicing Signature Associated With Tumor Microenvironment Immune Profiles in Lung Adenocarcinoma. Front Oncol 2022; 12:880478. [PMID: 35832557 PMCID: PMC9271776 DOI: 10.3389/fonc.2022.880478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/24/2022] [Indexed: 12/24/2022] Open
Abstract
Background Alternative splicing (AS), a pivotal post-transcriptional process across more than 95% of human transcripts, is involved in transcript structural variations and protein complexity. Clinical implications of AS events and their interaction with tumor immunity were systematically analyzed in lung adenocarcinoma (LUAD). Methods Transcriptome profiling as well as AS data of LUAD were retrospectively curated. Then, the network of the overall survival (OS)-relevant AS events with splicing factors was established. After screening OS-relevant AS events, a LASSO prognostic model was conducted and evaluated with ROC curves. A nomogram that integrated independent prognostic indicators was created. Immune response and immune cell infiltration were estimated with ESTIMATE, CIBERSORT, and ssGSEA algorithms. Drug sensitivity was inferred with pRRophetic package. Results In total, 2415 OS-relevant AS events were identified across LUAD patients. The interaction network of splicing factors with OS-relevant AS events uncovered the underlying regulatory mechanisms of AS events in LUAD. Thereafter, a prognostic model containing 12 AS events was developed, which acted as a reliable and independent prognostic indicator following verification. A nomogram that constituted stage and risk score displayed great effectiveness in evaluating the survival likelihood. Moreover, the AS-based prognostic model was in relation to immune response and immune cell infiltration. Patients with a high-risk score displayed therapeutic superiority to cisplatin, erlotinib, gefitinib, and gemcitabine. Finally, three AS-relevant genes (CDKN2A, TTC39C, and PKIB) were identified as prognostic markers. Conclusion Collectively, our findings developed an AS event signature with powerful prognostic predictive efficacy in LUAD.
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Affiliation(s)
- Guangyao Bao
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi’an, China
| | - Xiaojiao Guan
- Department of Pathology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Yao Yao
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Jie Liang
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Yifan Xiang
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Xinwen Zhong
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
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40
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Zhou D, Tran Y, Abou Elela S, Scott MS. SAPFIR: A webserver for the identification of alternative protein features. BMC Bioinformatics 2022; 23:250. [PMID: 35751026 PMCID: PMC9229502 DOI: 10.1186/s12859-022-04804-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022] Open
Abstract
Background Alternative splicing can increase the diversity of gene functions by generating multiple isoforms with different sequences and functions. However, the extent to which splicing events have functional consequences remains unclear and predicting the impact of splicing events on protein activity is limited to gene-specific analysis. Results To accelerate the identification of functionally relevant alternative splicing events we created SAPFIR, a predictor of protein features associated with alternative splicing events. This webserver tool uses InterProScan to predict protein features such as functional domains, motifs and sites in the human and mouse genomes and link them to alternative splicing events. Alternative protein features are displayed as functions of the transcripts and splice sites. SAPFIR could be used to analyze proteins generated from a single gene or a group of genes and can directly identify alternative protein features in large sequence data sets. The accuracy and utility of SAPFIR was validated by its ability to rediscover previously validated alternative protein domains. In addition, our de novo analysis of public datasets using SAPFIR indicated that only a small portion of alternative protein domains was conserved between human and mouse, and that in human, genes involved in nervous system process, regulation of DNA-templated transcription and aging are more likely to produce isoforms missing functional domains due to alternative splicing. Conclusion Overall SAPFIR represents a new tool for the rapid identification of functional alternative splicing events and enables the identification of cellular functions affected by a defined splicing program. SAPFIR is freely available at https://bioinfo-scottgroup.med.usherbrooke.ca/sapfir/, a website implemented in Python, with all major browsers supported. The source code is available at https://github.com/DelongZHOU/SAPFIR. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04804-w.
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Affiliation(s)
- Delong Zhou
- Département de Microbiologie et d'infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Yvan Tran
- Département de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de Microbiologie et d'infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada.
| | - Michelle S Scott
- Département de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada.
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Guillaudeux N, Belleannée C, Blanquart S. Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog. BMC Genomics 2022; 23:216. [PMID: 35303798 PMCID: PMC8933948 DOI: 10.1186/s12864-022-08429-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In eukaryote transcriptomes, a significant amount of transcript diversity comes from genes' capacity to generate different transcripts through alternative splicing. Identifying orthologous alternative transcripts across multiple species is of particular interest for genome annotators. However, there is no formal definition of transcript orthology based on the splicing structure conservation. Likewise there is no public dataset benchmark providing groups of orthologous transcripts sharing a conserved splicing structure. RESULTS We introduced a formal definition of splicing structure orthology and we predicted transcript orthologs in human, mouse and dog. Applying a selective strategy, we analyzed 2,167 genes and their 18,109 known transcripts and identified a set of 253 gene orthologs that shared a conserved splicing structure in all three species. We predicted 6,861 transcript CDSs (coding sequence), mainly for dog, an emergent model species. Each predicted transcript was an ortholog of a known transcript: both share the same CDS splicing structure. Evidence for the existence of the predicted CDSs was found in external data. CONCLUSIONS We generated a dataset of 253 gene triplets, structurally conserved and sharing all their CDSs in human, mouse and dog, which correspond to 879 triplets of spliced CDS orthologs. We have released the dataset both as an SQL database and as tabulated files. The data consists of the 879 CDS orthology groups with their detailed splicing structures, and the predicted CDSs, associated with their experimental evidence. The 6,861 predicted CDSs are provided in GTF files. Our data may contribute to compare highly conserved genes across three species, for comparative transcriptomics at the isoform level, or for benchmarking splice aligners and methods focusing on the identification of splicing orthologs. The data is available at https://data-access.cesgo.org/index.php/s/V97GXxOS66NqTkZ .
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42
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Cheng R, Xu Z, Luo M, Wang P, Cao H, Jin X, Zhou W, Xiao L, Jiang Q. Identification of alternative splicing-derived cancer neoantigens for mRNA vaccine development. Brief Bioinform 2022; 23:bbab553. [PMID: 35279714 DOI: 10.1093/bib/bbab553] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2023] Open
Abstract
Messenger RNA (mRNA) vaccines have shown great potential for anti-tumor therapy due to the advantages in safety, efficacy and industrial production. However, it remains a challenge to identify suitable cancer neoantigens that can be targeted for mRNA vaccines. Abnormal alternative splicing occurs in a variety of tumors, which may result in the translation of abnormal transcripts into tumor-specific proteins. High-throughput technologies make it possible for systematic characterization of alternative splicing as a source of suitable target neoantigens for mRNA vaccine development. Here, we summarized difficulties and challenges for identifying alternative splicing-derived cancer neoantigens from RNA-seq data and proposed a conceptual framework for designing personalized mRNA vaccines based on alternative splicing-derived cancer neoantigens. In addition, several points were presented to spark further discussion toward improving the identification of alternative splicing-derived cancer neoantigens.
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Affiliation(s)
- Rui Cheng
- Harbin Institute of Technology, China
| | | | - Meng Luo
- Harbin Institute of Technology, China
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43
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Miller RM, Jordan BT, Mehlferber MM, Jeffery ED, Chatzipantsiou C, Kaur S, Millikin RJ, Dai Y, Tiberi S, Castaldi PJ, Shortreed MR, Luckey CJ, Conesa A, Smith LM, Deslattes Mays A, Sheynkman GM. Enhanced protein isoform characterization through long-read proteogenomics. Genome Biol 2022; 23:69. [PMID: 35241129 PMCID: PMC8892804 DOI: 10.1186/s13059-022-02624-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/02/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic analysis relies on accurate reference databases that match the sample; neither a subset nor a superset database is ideal. Long-read RNA sequencing (e.g., PacBio or Oxford Nanopore) provides full-length transcripts which can be used to predict full-length protein isoforms. RESULTS We describe here a long-read proteogenomics approach for integrating sample-matched long-read RNA-seq and MS-based proteomics data to enhance isoform characterization. We introduce a classification scheme for protein isoforms, discover novel protein isoforms, and present the first protein inference algorithm for the direct incorporation of long-read transcriptome data to enable detection of protein isoforms previously intractable to MS-based detection. We have released an open-source Nextflow pipeline that integrates long-read sequencing in a proteomic workflow for isoform-resolved analysis. CONCLUSIONS Our work suggests that the incorporation of long-read sequencing and proteomic data can facilitate improved characterization of human protein isoform diversity. Our first-generation pipeline provides a strong foundation for future development of long-read proteogenomics and its adoption for both basic and translational research.
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Affiliation(s)
- Rachel M. Miller
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Ben T. Jordan
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA USA
| | - Madison M. Mehlferber
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA USA ,grid.27755.320000 0000 9136 933XDepartment of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA USA
| | - Erin D. Jeffery
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA USA
| | | | - Simi Kaur
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Robert J. Millikin
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Yunxiang Dai
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Simone Tiberi
- grid.7400.30000 0004 1937 0650Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Peter J. Castaldi
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA USA ,grid.62560.370000 0004 0378 8294Division of General Medicine and Primary Care, Brigham and Women’s Hospital, Boston, MA USA
| | - Michael R. Shortreed
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Chance John Luckey
- grid.27755.320000 0000 9136 933XDepartment of Pathology, University of Virginia, Charlottesville, VA USA
| | - Ana Conesa
- grid.4711.30000 0001 2183 4846Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain ,grid.15276.370000 0004 1936 8091Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL USA
| | - Lloyd M. Smith
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Anne Deslattes Mays
- grid.420089.70000 0000 9635 8082 Office of Data Science and Sharing, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD USA
| | - Gloria M. Sheynkman
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA USA ,grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA ,grid.27755.320000 0000 9136 933XUVA Cancer Center, University of Virginia, Charlottesville, VA USA
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Zenere A, Rundquist O, Gustafsson M, Altafini C. Multi-omics protein-coding units as massively parallel Bayesian networks: empirical validation of causality structure. iScience 2022; 25:104048. [PMID: 35355520 PMCID: PMC8958332 DOI: 10.1016/j.isci.2022.104048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/17/2022] [Accepted: 03/08/2022] [Indexed: 11/29/2022] Open
Abstract
In this article we use high-throughput epigenomics, transcriptomics, and proteomics data to construct fine-graded models of the “protein-coding units” gathering all transcript isoforms and chromatin accessibility peaks associated with more than 4000 genes in humans. Each protein-coding unit has the structure of a directed acyclic graph (DAG) and can be represented as a Bayesian network. The factorization of the joint probability distribution induced by the DAGs imposes a number of conditional independence relationships among the variables forming a protein-coding unit, corresponding to the missing edges in the DAGs. We show that a large fraction of these conditional independencies are indeed verified by the data. Factors driving this verification appear to be the structural and functional annotation of the transcript isoforms, as well as a notion of structural balance (or frustration-free) of the corresponding sample correlation graph, which naturally leads to reduction of correlation (and hence to independence) upon conditioning. Protein coding unit: DAG associated with epigenetic and gene information of a protein DAGs correspond to Bayesian networks Edge absence on a DAG corresponds to conditional independence Multi-omics data (ATAC-seq, RNA-seq and mass-spec) are used for DAG validation
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45
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Singh P, Ahi EP. The importance of alternative splicing in adaptive evolution. Mol Ecol 2022; 31:1928-1938. [DOI: 10.1111/mec.16377] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/06/2022] [Accepted: 01/25/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Pooja Singh
- Department of Biological Sciences University of Calgary Calgary Canada
- Institute of Ecology and Evolution University of Bern Bern Switzerland
- Swiss Federal Institute of Aquatic Science and Technology (EAWAG) Kastanienbaum Switzerland
| | - Ehsan Pashay Ahi
- Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland
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46
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Korsching E, Matschke J, Hotfilder M. Splice variants denote differences between a cancer stem cell side population of EWSR1‑ERG‑based Ewing sarcoma cells, its main population and EWSR1‑FLI‑based cells. Int J Mol Med 2022; 49:39. [PMID: 35088879 PMCID: PMC8815407 DOI: 10.3892/ijmm.2022.5094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/17/2021] [Indexed: 11/06/2022] Open
Abstract
Ewing sarcoma is a challenging cancer entity, which, besides the characteristic presence of a fusion gene, is driven by multiple alternative splicing events. So far, splice variants in Ewing sarcoma cells were mainly analyzed for EWSR1‑FLI1. The present study provided a comprehensive alternative splicing study on CADO‑ES1, an Ewing model cell line for an EWSR1‑ERG fusion gene. Based on a well‑-characterized RNA‑sequencing dataset with extensive control mechanisms across all levels of analysis, the differential spliced genes in Ewing cancer stem cells were ATP13A3 and EPB41, while the main population was defined by ACADVL, NOP58 and TSPAN3. All alternatively spliced genes were further characterized by their Gene Ontology (GO) terms and by their membership in known protein complexes. These results confirm and extend previous studies towards a systematic whole‑transcriptome analysis. A highlight is the striking segregation of GO terms associated with five basic splice events. This mechanistic insight, together with a coherent integration of all observations with prior knowledge, indicates that EWSR1‑ERG is truly a close twin to EWSR1‑FLI1, but still exhibits certain individuality. Thus, the present study provided a measure of variability in Ewing sarcoma, whose understanding is essential both for clinical procedures and basic mechanistic insight.
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Affiliation(s)
- Eberhard Korsching
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, D‑48149 Münster, Germany
| | - Julian Matschke
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, D‑48149 Münster, Germany
| | - Marc Hotfilder
- Department of Pediatric Hematology and Oncology, University Hospital Münster, D‑48149 Münster, Germany
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47
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Reixachs-Solé M, Eyras E. Uncovering the impacts of alternative splicing on the proteome with current omics techniques. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1707. [PMID: 34979593 PMCID: PMC9542554 DOI: 10.1002/wrna.1707] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
Abstract
The high‐throughput sequencing of cellular RNAs has underscored a broad effect of isoform diversification through alternative splicing on the transcriptome. Moreover, the differential production of transcript isoforms from gene loci has been recognized as a critical mechanism in cell differentiation, organismal development, and disease. Yet, the extent of the impact of alternative splicing on protein production and cellular function remains a matter of debate. Multiple experimental and computational approaches have been developed in recent years to address this question. These studies have unveiled how molecular changes at different steps in the RNA processing pathway can lead to differences in protein production and have functional effects. New and emerging experimental technologies open exciting new opportunities to develop new methods to fully establish the connection between messenger RNA expression and protein production and to further investigate how RNA variation impacts the proteome and cell function. This article is categorized under:RNA Processing > Splicing Regulation/Alternative Splicing Translation > Regulation RNA Evolution and Genomics > Computational Analyses of RNA
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Affiliation(s)
- Marina Reixachs-Solé
- The John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.,EMBL Australia Partner Laboratory Network and the Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eduardo Eyras
- The John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.,EMBL Australia Partner Laboratory Network and the Australian National University, Canberra, Australian Capital Territory, Australia.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain.,Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
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48
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Gohr A, Mantica F, Hermoso-Pulido A, Tapial J, Márquez Y, Irimia M. Computational Analysis of Alternative Splicing Using VAST-TOOLS and the VastDB Framework. Methods Mol Biol 2022; 2537:97-128. [PMID: 35895261 DOI: 10.1007/978-1-0716-2521-7_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] [Indexed: 06/15/2023]
Abstract
Alternative splicing (AS) can vastly expand animal transcriptomes and proteomes. Two main open questions in the field are how AS is regulated across cell/tissue types and disease, and what roles different AS events play. To facilitate AS research, we have created the computational VastDB framework, which comprises a series of complementary software and resources that we describe in this chapter. The VastDB framework is especially designed to aid biomedical researchers without a strong computational background. It offers tools and resources to: (a) quantify AS and identify differentially spliced AS events using RNA-seq data (vast-tools), (b) perform multiple genomic and sequence analyses for investigating AS events (Matt), (c) identify AS events with genomic and regulatory conservation among species (ExOrthist), and (d) help with the biological interpretation of the results, and, ultimately, with the identification of interesting AS events to design wet-lab experiments (VastDB and PastDB).
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Affiliation(s)
- André Gohr
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Hermoso-Pulido
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Javier Tapial
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yamile Márquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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49
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Kashkan I, Timofeyenko K, Růžička K. How alternative splicing changes the properties of plant proteins. QUANTITATIVE PLANT BIOLOGY 2022; 3:e14. [PMID: 37077961 PMCID: PMC10095807 DOI: 10.1017/qpb.2022.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 05/03/2023]
Abstract
Most plant primary transcripts undergo alternative splicing (AS), and its impact on protein diversity is a subject of intensive investigation. Several studies have uncovered various mechanisms of how particular protein splice isoforms operate. However, the common principles behind the AS effects on protein function in plants have rarely been surveyed. Here, on the selected examples, we highlight diverse tissue expression patterns, subcellular localization, enzymatic activities, abilities to bind other molecules and other relevant features. We describe how the protein isoforms mutually interact to underline their intriguing roles in altering the functionality of protein complexes. Moreover, we also discuss the known cases when these interactions have been placed inside the autoregulatory loops. This review is particularly intended for plant cell and developmental biologists who would like to gain inspiration on how the splice variants encoded by their genes of interest may coordinately work.
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Affiliation(s)
- Ivan Kashkan
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno62500, Czech Republic
| | - Ksenia Timofeyenko
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno62500, Czech Republic
| | - Kamil Růžička
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Author for correspondence: K. Růžička, E-mail:
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50
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Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 233:329-343. [PMID: 34637542 DOI: 10.1111/nph.17792] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development.
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Affiliation(s)
- Ivan Kashkan
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Mónika Hrtyan
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Katarzyna Retzer
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Jana Humpolíčková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 166 10, Czech Republic
| | - Aswathy Jayasree
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Roberta Filepová
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Zuzana Vondráková
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Sibu Simon
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Debbie Rombaut
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Jan Hejátko
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Jiří Friml
- Institute of Science and Technology (IST Austria), Klosterneuburg, 3400, Austria
| | - Jan Petrášek
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Kamil Růžička
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
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