1
|
Boyd-Shiwarski CR, Shiwarski DJ, Subramanya AR. A New Phase for WNK Kinase Signaling Complexes as Biomolecular Condensates. Physiology (Bethesda) 2024; 39:0. [PMID: 38624245 DOI: 10.1152/physiol.00013.2024] [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: 02/22/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
The purpose of this review is to highlight transformative advances that have been made in the field of biomolecular condensates, with special emphasis on condensate material properties, physiology, and kinases, using the With-No-Lysine (WNK) kinases as a prototypical example. To convey how WNK kinases illustrate important concepts for biomolecular condensates, we start with a brief history, focus on defining features of biomolecular condensates, and delve into some examples of how condensates are implicated in cellular physiology (and pathophysiology). We then highlight how WNK kinases, through the action of "WNK droplets" that ubiquitously regulate intracellular volume and kidney-specific "WNK bodies" that are implicated in distal tubule salt reabsorption and potassium homeostasis, exemplify many of the defining features of condensates. Finally, this review addresses the controversies within this emerging field and questions to address.
Collapse
Affiliation(s)
- Cary R Boyd-Shiwarski
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Pittsburgh Heart, Lung, Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Daniel J Shiwarski
- Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Arohan R Subramanya
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Pittsburgh Heart, Lung, Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, United States
| |
Collapse
|
2
|
Kodavati M, Maloji Rao VH, Provasek VE, Hegde ML. Regulation of DNA damage response by RNA/DNA-binding proteins: Implications for neurological disorders and aging. Ageing Res Rev 2024; 100:102413. [PMID: 39032612 DOI: 10.1016/j.arr.2024.102413] [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: 06/03/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024]
Abstract
RNA-binding proteins (RBPs) are evolutionarily conserved across most forms of life, with an estimated 1500 RBPs in humans. Traditionally associated with post-transcriptional gene regulation, RBPs contribute to nearly every known aspect of RNA biology, including RNA splicing, transport, and decay. In recent years, an increasing subset of RBPs have been recognized for their DNA binding properties and involvement in DNA transactions. We refer to these RBPs with well-characterized DNA binding activity as RNA/DNA binding proteins (RDBPs), many of which are linked to neurological diseases. RDBPs are associated with both nuclear and mitochondrial DNA repair. Furthermore, the presence of intrinsically disordered domains in RDBPs appears to be critical for regulating their diverse interactions and plays a key role in controlling protein aggregation, which is implicated in neurodegeneration. In this review, we discuss the emerging roles of common RDBPs from the heterogeneous nuclear ribonucleoprotein (hnRNP) family, such as TAR DNA binding protein-43 (TDP43) and fused in sarcoma (FUS) in controlling DNA damage response (DDR). We also explore the implications of RDBP pathology in aging and neurodegenerative diseases and provide a prospective on the therapeutic potential of targeting RDBP pathology mediated DDR defects for motor neuron diseases and aging.
Collapse
Affiliation(s)
- Manohar Kodavati
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA.
| | - Vikas H Maloji Rao
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA
| | - Vincent E Provasek
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA; School of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Muralidhar L Hegde
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA; School of Medicine, Texas A&M University, College Station, TX 77843, USA; Department of Neurosurgery, Weill Medical College, New York, NY 10065, USA.
| |
Collapse
|
3
|
Byrne A, Le D, Sereti K, Menon H, Vaidya S, Patel N, Lund J, Xavier-Magalhães A, Shi M, Liang Y, Sterne-Weiler T, Modrusan Z, Stephenson W. Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer. Nat Commun 2024; 15:6916. [PMID: 39134520 PMCID: PMC11319652 DOI: 10.1038/s41467-024-51252-6] [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: 07/27/2023] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
Single-cell RNA sequencing predominantly employs short-read sequencing to characterize cell types, states and dynamics; however, it is inadequate for comprehensive characterization of RNA isoforms. Long-read sequencing technologies enable single-cell RNA isoform detection but are hampered by lower throughput and unintended sequencing of artifacts. Here we develop Single-cell Targeted Isoform Long-Read Sequencing (scTaILoR-seq), a hybridization capture method which targets over a thousand genes of interest, improving the median number of on-target transcripts per cell by 29-fold. We use scTaILoR-seq to identify and quantify RNA isoforms from ovarian cancer cell lines and primary tumors, yielding 10,796 single-cell transcriptomes. Using long-read variant calling we reveal associations of expressed single nucleotide variants (SNVs) with alternative transcript structures. Phasing of SNVs across transcripts enables the measurement of allelic imbalance within distinct cell populations. Overall, scTaILoR-seq is a long-read targeted RNA sequencing method and analytical framework for exploring transcriptional variation at single-cell resolution.
Collapse
Affiliation(s)
- Ashley Byrne
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA
| | - Daniel Le
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA
| | - Kostianna Sereti
- Department of Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - Hari Menon
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA
| | - Samir Vaidya
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA
| | - Neha Patel
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA
| | - Jessica Lund
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA
| | - Ana Xavier-Magalhães
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA
| | - Minyi Shi
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA
| | - Yuxin Liang
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA
| | - Timothy Sterne-Weiler
- Department of Discovery Oncology, Genentech, South San Francisco, CA, USA
- Department of Oncology Bioinformatics, Genentech, South San Francisco, CA, USA
| | - Zora Modrusan
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
| | - William Stephenson
- Department of Proteomic and Genomic Technologies, Genentech, South San Francisco, CA, USA.
| |
Collapse
|
4
|
Song Y, Parada G, Lee JTH, Hemberg M. Mining alternative splicing patterns in scRNA-seq data using scASfind. Genome Biol 2024; 25:197. [PMID: 39075577 PMCID: PMC11285346 DOI: 10.1186/s13059-024-03323-6] [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: 08/17/2023] [Accepted: 06/26/2024] [Indexed: 07/31/2024] Open
Abstract
Single-cell RNA-seq (scRNA-seq) is widely used for transcriptome profiling, but most analyses focus on gene-level events, with less attention devoted to alternative splicing. Here, we present scASfind, a novel computational method to allow for quantitative analysis of cell type-specific splicing events using full-length scRNA-seq data. ScASfind utilizes an efficient data structure to store the percent spliced-in value for each splicing event. This makes it possible to exhaustively search for patterns among all differential splicing events, allowing us to identify marker events, mutually exclusive events, and events involving large blocks of exons that are specific to one or more cell types.
Collapse
Affiliation(s)
- Yuyao Song
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Guillermo Parada
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | | | - Martin Hemberg
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
5
|
Jones EF, Howton TC, Flanary VL, Clark AD, Lasseigne BN. Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage. Mol Brain 2024; 17:40. [PMID: 38902764 PMCID: PMC11188239 DOI: 10.1186/s13041-024-01112-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/08/2024] [Indexed: 06/22/2024] Open
Abstract
Alternative splicing (AS) contributes to the biological heterogeneity between species, sexes, tissues, and cell types. Many diseases are either caused by alterations in AS or by alterations to AS. Therefore, measuring AS accurately and efficiently is critical for assessing molecular phenotypes, including those associated with disease. Long-read sequencing enables more accurate quantification of differentially spliced isoform expression than short-read sequencing approaches, and third-generation platforms facilitate high-throughput experiments. To assess differences in AS across the cerebellum, cortex, hippocampus, and striatum by sex, we generated and analyzed Oxford Nanopore Technologies (ONT) long-read RNA sequencing (lrRNA-Seq) C57BL/6J mouse brain cDNA libraries. From > 85 million reads that passed quality control metrics, we calculated differential gene expression (DGE), differential transcript expression (DTE), and differential transcript usage (DTU) across brain regions and by sex. We found significant DGE, DTE, and DTU across brain regions and that the cerebellum had the most differences compared to the other three regions. Additionally, we found region-specific differential splicing between sexes, with the most sex differences in DTU in the cortex and no DTU in the hippocampus. We also report on two distinct patterns of sex DTU we observed, sex-divergent and sex-specific, that could potentially help explain sex differences in the prevalence and prognosis of various neurological and psychiatric disorders in future studies. Finally, we built a Shiny web application for researchers to explore the data further. Our study provides a resource for the community; it underscores the importance of AS in biological heterogeneity and the utility of long-read sequencing to better understand AS in the brain.
Collapse
Affiliation(s)
- Emma F Jones
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Timothy C Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Victoria L Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Amanda D Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Brittany N Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America.
| |
Collapse
|
6
|
Brandão-Teles C, Antunes ASLM, de Moraes Vrechi TA, Martins-de-Souza D. The Roles of hnRNP Family in the Brain and Brain-Related Disorders. Mol Neurobiol 2024; 61:3578-3595. [PMID: 37999871 DOI: 10.1007/s12035-023-03747-4] [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: 08/31/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) belong to a complex family of RNA-binding proteins that are essential to control alternative splicing, mRNA trafficking, synaptic plasticity, stress granule formation, cell cycle regulation, and axonal transport. Over the past decade, hnRNPs have been associated with different brain disorders such as Alzheimer's disease, multiple sclerosis, and schizophrenia. Given their essential role in maintaining cell function and integrity, it is not surprising that dysregulated hnRNP levels lead to neurological implications. This review aims to explore the primary functions of hnRNPs in neurons, oligodendrocytes, microglia, and astrocytes, and their roles in brain disorders. We also discuss proteomics and other technologies and their potential for studying and evaluating hnRNPs in brain disorders, including the discovery of new therapeutic targets and possible pharmacological interventions.
Collapse
Affiliation(s)
- Caroline Brandão-Teles
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
| | - André S L M Antunes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Talita Aparecida de Moraes Vrechi
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, 13083-862, Brazil.
- INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil.
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, Instituto Nacional de Biomarcadores em Neuropsiquiatria, São Paulo, Brazil.
| |
Collapse
|
7
|
Jones EF, Haldar A, Oza VH, Lasseigne BN. Quantifying transcriptome diversity: a review. Brief Funct Genomics 2024; 23:83-94. [PMID: 37225889 DOI: 10.1093/bfgp/elad019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/14/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
Following the central dogma of molecular biology, gene expression heterogeneity can aid in predicting and explaining the wide variety of protein products, functions and, ultimately, heterogeneity in phenotypes. There is currently overlapping terminology used to describe the types of diversity in gene expression profiles, and overlooking these nuances can misrepresent important biological information. Here, we describe transcriptome diversity as a measure of the heterogeneity in (1) the expression of all genes within a sample or a single gene across samples in a population (gene-level diversity) or (2) the isoform-specific expression of a given gene (isoform-level diversity). We first overview modulators and quantification of transcriptome diversity at the gene level. Then, we discuss the role alternative splicing plays in driving transcript isoform-level diversity and how it can be quantified. Additionally, we overview computational resources for calculating gene-level and isoform-level diversity for high-throughput sequencing data. Finally, we discuss future applications of transcriptome diversity. This review provides a comprehensive overview of how gene expression diversity arises, and how measuring it determines a more complete picture of heterogeneity across proteins, cells, tissues, organisms and species.
Collapse
Affiliation(s)
- Emma F Jones
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anisha Haldar
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishal H Oza
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brittany N Lasseigne
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| |
Collapse
|
8
|
Jones EF, Howton TC, Flanary VL, Clark AD, Lasseigne BN. Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575219. [PMID: 38260631 PMCID: PMC10802568 DOI: 10.1101/2024.01.11.575219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alternative splicing (AS) contributes to the biological heterogeneity between species, sexes, tissues, and cell types. Many diseases are either caused by alterations in AS or by alterations to AS. Therefore, measuring AS accurately and efficiently is critical for assessing molecular phenotypes, including those associated with disease. Long-read sequencing enables more accurate quantification of differentially spliced isoform expression than short-read sequencing approaches, and third-generation platforms facilitate high-throughput experiments. To assess differences in AS across the cerebellum, cortex, hippocampus, and striatum by sex, we generated and analyzed Oxford Nanopore Technologies (ONT) long-read RNA sequencing (lrRNA-Seq) C57BL/6J mouse brain cDNA libraries. From >85 million reads that passed quality control metrics, we calculated differential gene expression (DGE), differential transcript expression (DTE), and differential transcript usage (DTU) across brain regions and by sex. We found significant DGE, DTE, and DTU across brain regions and that the cerebellum had the most differences compared to the other three regions. Additionally, we found region-specific differential splicing between sexes, with the most sex differences in DTU in the cortex and no DTU in the hippocampus. We also report on two distinct patterns of sex DTU we observed, sex-divergent and sex-specific, that could potentially help explain sex differences in the prevalence and prognosis of various neurological and psychiatric disorders in future studies. Finally, we built a Shiny web application for researchers to explore the data further. Our study provides a resource for the community; it underscores the importance of AS in biological heterogeneity and the utility of long-read sequencing to better understand AS in the brain.
Collapse
Affiliation(s)
- Emma F. Jones
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Victoria L. Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| |
Collapse
|
9
|
Zhang M, Wang H, Han J, Wang H, Jia Y, Hong W, Tang F, Li Z. Specific recognition and sensitive quantification of mRNA splice variants via one-pot ligation-dependent loop-mediated isothermal amplification. Analyst 2023; 148:5605-5611. [PMID: 37818948 DOI: 10.1039/d3an01382k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Specific recognition and sensitive quantification of mRNA alternative splice variants have been a necessity for exploring the regulatory mechanism of RNA splicing and revealing the association between pre-mRNA splicing and transcriptome function, as well as disease diagnosis. However, their wide abundance range and high sequence homology pose enormous challenges for high sensitivity and selectivity quantification of splice variants. Herein, taking advantage of the excellent specificity of ligation and the powerful nucleic acid replication feature of loop-mediated isothermal amplification (LAMP), we developed a one-pot method (termed one-pot ligation-LAMP) for specific recognition and sensitive quantification of mRNA splicing variants based on two splicing junction-specific stem-loop DNA probe ligation and the subsequently initiating LAMP. The one-pot ligation-LAMP can specifically detect as low as 100 aM mRNA splice variants without any nonspecific signals and quantify them with a wide dynamics range spanning at least six orders of magnitude. We have demonstrated that the one-pot ligation-LAMP is a versatile and practical strategy for accurately quantifying different splicing variants in complex biological samples with high sensitivity all in one tube within 90 min, thereby providing an attractive tool for mRNA splice variant-related studies.
Collapse
Affiliation(s)
- Mai Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Jun Han
- National Textile and Leather Product Quality Inspection and Testing Centre, 15 Xili-Balizhuang, Chaoyang District, Beijing 100025, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Yuting Jia
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Weixiang Hong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| | - Fu Tang
- School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China.
| |
Collapse
|
10
|
Weber AI, Parthasarathy S, Borisova E, Epifanova E, Preußner M, Rusanova A, Ambrozkiewicz MC, Bessa P, Newman A, Müller L, Schaal H, Heyd F, Tarabykin V. Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression. Nucleic Acids Res 2023; 51:10218-10237. [PMID: 37697438 PMCID: PMC10602877 DOI: 10.1093/nar/gkad703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 09/13/2023] Open
Abstract
The seat of higher-order cognitive abilities in mammals, the neocortex, is a complex structure, organized in several layers. The different subtypes of principal neurons are distributed in precise ratios and at specific positions in these layers and are generated by the same neural progenitor cells (NPCs), steered by a spatially and temporally specified combination of molecular cues that are incompletely understood. Recently, we discovered that an alternatively spliced isoform of the TrkC receptor lacking the kinase domain, TrkC-T1, is a determinant of the corticofugal projection neuron (CFuPN) fate. Here, we show that the finely tuned balance between TrkC-T1 and the better known, kinase domain-containing isoform, TrkC-TK+, is cell type-specific in the developing cortex and established through the antagonistic actions of two RNA-binding proteins, Srsf1 and Elavl1. Moreover, our data show that Srsf1 promotes the CFuPN fate and Elavl1 promotes the callosal projection neuron (CPN) fate in vivo via regulating the distinct ratios of TrkC-T1 to TrkC-TK+. Taken together, we connect spatio-temporal expression of Srsf1 and Elavl1 in the developing neocortex with the regulation of TrkC alternative splicing and transcript stability and neuronal fate choice, thus adding to the mechanistic and functional understanding of alternative splicing in vivo.
Collapse
Affiliation(s)
- A Ioana Weber
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Srinivas Parthasarathy
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Ekaterina Borisova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Ekaterina Epifanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Marco Preußner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Alexandra Rusanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Mateusz C Ambrozkiewicz
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Paraskevi Bessa
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Andrew G Newman
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Lisa Müller
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Heiner Schaal
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Victor Tarabykin
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia
| |
Collapse
|
11
|
Engelhard CA, Khani S, Derdak S, Bilban M, Kornfeld JW. Nanopore sequencing unveils the complexity of the cold-activated murine brown adipose tissue transcriptome. iScience 2023; 26:107190. [PMID: 37564700 PMCID: PMC10410515 DOI: 10.1016/j.isci.2023.107190] [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: 01/30/2023] [Revised: 04/28/2023] [Accepted: 06/16/2023] [Indexed: 08/12/2023] Open
Abstract
Alternative transcription increases transcriptome complexity by expression of multiple transcripts per gene. Annotation and quantification of transcripts using short-read sequencing is non-trivial. Long-read sequencing aims at overcoming these problems by sequencing full-length transcripts. Activation of brown adipose tissue (BAT) thermogenesis involves major transcriptomic remodeling and positively affects metabolism via increased energy expenditure. We benchmark Oxford Nanopore Technology (ONT) long-read sequencing protocols to Illumina short-read sequencing assessing alignment characteristics, gene and transcript detection and quantification, differential gene and transcript expression, transcriptome reannotation, and differential transcript usage (DTU). We find ONT sequencing is superior to Illumina for transcriptome reassembly, reducing the risk of false-positive events by unambiguously mapping reads to transcripts. We identified novel isoforms of genes undergoing DTU in cold-activated BAT including Cars2, Adtrp, Acsl5, Scp2, Aldoa, and Pde4d, validated by real-time PCR. The reannotated murine BAT transcriptome established here provides a framework for future investigations into the regulation of BAT.
Collapse
Affiliation(s)
- Christoph Andreas Engelhard
- Department for Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Sajjad Khani
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Sophia Derdak
- Core Facilities, Medical University of Vienna, Lazarettgasse 14, 1090 Vienna, Austria
| | - Martin Bilban
- Department of Laboratory Medicine & Core Facilities, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Jan-Wilhelm Kornfeld
- Department for Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| |
Collapse
|
12
|
Sun Y, Bae YE, Zhu J, Zhang Z, Zhong H, Yu J, Wu C, Wu L. A splicing transcriptome-wide association study identifies novel altered splicing for Alzheimer's disease susceptibility. Neurobiol Dis 2023:106209. [PMID: 37354922 DOI: 10.1016/j.nbd.2023.106209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/26/2023] [Accepted: 06/19/2023] [Indexed: 06/26/2023] Open
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disease in aging individuals. Alternative splicing is reported to be relevant to AD development while their roles in etiology of AD remain largely elusive. We performed a comprehensive splicing transcriptome-wide association study (spTWAS) using intronic excision expression genetic prediction models of 12 brain tissues developed through three modelling strategies, to identify candidate susceptibility splicing introns for AD risk. A total of 111,326 (46,828 proxy) cases and 677,663 controls of European ancestry were studied. We identified 343 associations of 233 splicing introns (143 genes) with AD risk after Bonferroni correction (0.05/136,884 = 3.65 × 10-7). Fine-mapping analyses supported 155 likely causal associations corresponding to 83 splicing introns of 55 genes. Eighteen causal splicing introns of 15 novel genes (EIF2D, WDR33, SAP130, BYSL, EPHB6, MRPL43, VEGFB, PPP1R13B, TLN2, CLUHP3, LRRC37A4P, CRHR1, LINC02210, ZNF45-AS1, and XPNPEP3) were identified for the first time to be related to AD susceptibility. Our study identified novel genes and splicing introns associated with AD risk, which can improve our understanding of the etiology of AD.
Collapse
Affiliation(s)
- Yanfa Sun
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian 364012, PR China; Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Ye Eun Bae
- Department of Statistics, Florida State University, Tallahassee, FL 32304, USA
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Zichen Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32304, USA
| | - Hua Zhong
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Jie Yu
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian 364012, PR China
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
| |
Collapse
|
13
|
Pan L, Zheng C, Yang Z, Pawitan Y, Vu TN, Shen X. Hidden Genetic Regulation of Human Complex Traits via Brain Isoforms. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:217-227. [PMID: 37325708 PMCID: PMC10260721 DOI: 10.1007/s43657-023-00100-6] [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: 08/17/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 06/17/2023]
Abstract
Alternative splicing exists in most multi-exonic genes, and exploring these complex alternative splicing events and their resultant isoform expressions is essential. However, it has become conventional that RNA sequencing results have often been summarized into gene-level expression counts mainly due to the multiple ambiguous mapping of reads at highly similar regions. Transcript-level quantification and interpretation are often overlooked, and biological interpretations are often deduced based on combined transcript information at the gene level. Here, for the most variable tissue of alternative splicing, the brain, we estimate isoform expressions in 1,191 samples collected by the Genotype-Tissue Expression (GTEx) Consortium using a powerful method that we previously developed. We perform genome-wide association scans on the isoform ratios per gene and identify isoform-ratio quantitative trait loci (irQTL), which could not be detected by studying gene-level expressions alone. By analyzing the genetic architecture of the irQTL, we show that isoform ratios regulate educational attainment via multiple tissues including the frontal cortex (BA9), cortex, cervical spinal cord, and hippocampus. These tissues are also associated with different neuro-related traits, including Alzheimer's or dementia, mood swings, sleep duration, alcohol intake, intelligence, anxiety or depression, etc. Mendelian randomization (MR) analysis revealed 1,139 pairs of isoforms and neuro-related traits with plausible causal relationships, showing much stronger causal effects than on general diseases measured in the UK Biobank (UKB). Our results highlight essential transcript-level biomarkers in the human brain for neuro-related complex traits and diseases, which could be missed by merely investigating overall gene expressions. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00100-6.
Collapse
Affiliation(s)
- Lu Pan
- Biostatistics Group, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 China
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177 Sweden
| | - Chenqing Zheng
- Biostatistics Group, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhijian Yang
- Biostatistics Group, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177 Sweden
| | - Trung Nghia Vu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177 Sweden
| | - Xia Shen
- Biostatistics Group, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 China
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177 Sweden
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458 China
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG UK
| |
Collapse
|
14
|
Misra CS, Sousa AGG, Barros PM, Kermanov A, Becker JD. Cell-type-specific alternative splicing in the Arabidopsis germline. PLANT PHYSIOLOGY 2023; 192:85-101. [PMID: 36515615 PMCID: PMC10152659 DOI: 10.1093/plphys/kiac574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 09/30/2022] [Accepted: 11/23/2022] [Indexed: 05/03/2023]
Abstract
During sexual reproduction in flowering plants, the two haploid sperm cells (SCs) embedded within the cytoplasm of a growing pollen tube are carried to the embryo sac for double fertilization. Pollen development in flowering plants is a dynamic process that encompasses changes at transcriptome and epigenome levels. While the transcriptome of pollen and SCs in Arabidopsis (Arabidopsis thaliana) is well documented, previous analyses have mostly been based on gene-level expression. In-depth transcriptome analysis, particularly the extent of alternative splicing (AS) at the resolution of SC and vegetative nucleus (VN), is still lacking. Therefore, we performed RNA-seq analysis to generate a spliceome map of Arabidopsis SCs and VN isolated from mature pollen grains. Based on our de novo transcriptome assembly, we identified 58,039 transcripts, including 9,681 novel transcripts, of which 2,091 were expressed in SCs and 3,600 in VN. Four hundred and sixty-eight genes were regulated both at gene and splicing levels, with many having functions in mRNA splicing, chromatin modification, and protein localization. Moreover, a comparison with egg cell RNA-seq data uncovered sex-specific regulation of transcription and splicing factors. Our study provides insights into a gamete-specific AS landscape at unprecedented resolution.
Collapse
Affiliation(s)
- Chandra Shekhar Misra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | | | - Pedro M Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Anton Kermanov
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| |
Collapse
|
15
|
Kameda-Smith MM, Zhu H, Luo EC, Suk Y, Xella A, Yee B, Chokshi C, Xing S, Tan F, Fox RG, Adile AA, Bakhshinyan D, Brown K, Gwynne WD, Subapanditha M, Miletic P, Picard D, Burns I, Moffat J, Paruch K, Fleming A, Hope K, Provias JP, Remke M, Lu Y, Reya T, Venugopal C, Reimand J, Wechsler-Reya RJ, Yeo GW, Singh SK. Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma. Nat Commun 2022; 13:7506. [PMID: 36473869 PMCID: PMC9726987 DOI: 10.1038/s41467-022-35118-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open
Abstract
Pediatric medulloblastoma (MB) is the most common solid malignant brain neoplasm, with Group 3 (G3) MB representing the most aggressive subgroup. MYC amplification is an independent poor prognostic factor in G3 MB, however, therapeutic targeting of the MYC pathway remains limited and alternative therapies for G3 MB are urgently needed. Here we show that the RNA-binding protein, Musashi-1 (MSI1) is an essential mediator of G3 MB in both MYC-overexpressing mouse models and patient-derived xenografts. MSI1 inhibition abrogates tumor initiation and significantly prolongs survival in both models. We identify binding targets of MSI1 in normal neural and G3 MB stem cells and then cross referenced these data with unbiased large-scale screens at the transcriptomic, translatomic and proteomic levels to systematically dissect its functional role. Comparative integrative multi-omic analyses of these large datasets reveal cancer-selective MSI1-bound targets sharing multiple MYC associated pathways, providing a valuable resource for context-specific therapeutic targeting of G3 MB.
Collapse
Affiliation(s)
- Michelle M. Kameda-Smith
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON Canada
| | - Helen Zhu
- grid.419890.d0000 0004 0626 690XComputational Biology Program, Ontario Institute for Cancer Research, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Medical Biophysics, University of Toronto, Toronto, Canada ,grid.231844.80000 0004 0474 0428University Health Network, Toronto, ON Canada ,grid.494618.6Vector Institute Toronto, Toronto, ON Canada
| | - En-Ching Luo
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Stem Cell Program, University of California San Diego, La Jolla, CA USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA USA
| | - Yujin Suk
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Michael G DeGroote School of Medicine, McMaster University, Hamilton, Canada
| | - Agata Xella
- grid.479509.60000 0001 0163 8573Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA
| | - Brian Yee
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Stem Cell Program, University of California San Diego, La Jolla, CA USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA USA
| | - Chirayu Chokshi
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Sansi Xing
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Frederick Tan
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Stem Cell Program, University of California San Diego, La Jolla, CA USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA USA
| | - Raymond G. Fox
- grid.266100.30000 0001 2107 4242Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, Sanford Consortium for Regenerative Medicine, La Jolla, CA USA
| | - Ashley A. Adile
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - David Bakhshinyan
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Kevin Brown
- grid.17063.330000 0001 2157 2938Donnelly Centre, Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - William D. Gwynne
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Minomi Subapanditha
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada
| | - Petar Miletic
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Daniel Picard
- grid.14778.3d0000 0000 8922 7789Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Ian Burns
- grid.25073.330000 0004 1936 8227Michael G DeGroote School of Medicine, McMaster University, Hamilton, Canada
| | - Jason Moffat
- grid.17063.330000 0001 2157 2938Donnelly Centre, Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Kamil Paruch
- grid.10267.320000 0001 2194 0956Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.483343.bInternational Clinical Research Center, St. Anne’s University Hospital in Brno, 602 00 Brno, Czech Republic
| | - Adam Fleming
- grid.25073.330000 0004 1936 8227McMaster University, Departments of Pediatrics, Hematology and Oncology Division, Hamilton, Canada
| | - Kristin Hope
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - John P. Provias
- grid.25073.330000 0004 1936 8227McMaster University, Departments of Neuropathology, Hamilton, Canada
| | - Marc Remke
- grid.14778.3d0000 0000 8922 7789Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Yu Lu
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Tannishtha Reya
- grid.266100.30000 0001 2107 4242Departments of Pharmacology and Medicine, University of California San Diego School of Medicine, Sanford Consortium for Regenerative Medicine, La Jolla, CA USA ,grid.239585.00000 0001 2285 2675Present Address: Herbert Irving Comprehensive Cancer Center, Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY USA
| | - Chitra Venugopal
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON Canada
| | - Jüri Reimand
- grid.419890.d0000 0004 0626 690XComputational Biology Program, Ontario Institute for Cancer Research, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Medical Biophysics, University of Toronto, Toronto, Canada ,grid.17063.330000 0001 2157 2938Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Robert J. Wechsler-Reya
- grid.479509.60000 0001 0163 8573Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA ,grid.239585.00000 0001 2285 2675Present Address: Herbert Irving Comprehensive Cancer Center, Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY USA
| | - Gene W. Yeo
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Stem Cell Program, University of California San Diego, La Jolla, CA USA ,grid.468218.10000 0004 5913 3393Sanford Consortium for Regenerative Medicine, La Jolla, CA USA
| | - Sheila K. Singh
- grid.25073.330000 0004 1936 8227Centre for Discovery in Cancer Research (CDCR), McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227Surgery, Faculty of Health Sciences, McMaster University, Hamilton, ON Canada ,grid.25073.330000 0004 1936 8227McMaster University, Department of Pediatrics, Hamilton, Canada
| |
Collapse
|
16
|
Aubol BE, Adams JA. SRPK1 regulates RNA binding in a pre-spliceosomal complex using a catalytic bypass mechanism. FEBS J 2022; 289:7428-7445. [PMID: 35730996 DOI: 10.1111/febs.16560] [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: 02/15/2022] [Revised: 05/10/2022] [Accepted: 06/21/2022] [Indexed: 01/14/2023]
Abstract
Serine-arginine protein kinase 1 (SRPK1) phosphorylates serine-arginine (SR) proteins in the cytoplasm, directing them to the nucleus for splicing function. SRPK1 has also been detected in the nucleus but its function here is still not fully understood. We now demonstrate that nuclear SRPK1 can regulate U1-70K, a protein component of the uridine-rich 1 small nuclear ribonucleoprotein (U1 snRNP) that binds SR proteins and facilitates 5' splice-site selection in precursor mRNA. We found that SRPK1 uses a large, disordered domain to bind U1-70K, regulating the interaction of an exonic splicing enhancer (ESE) to the associated SR protein. Surprisingly, the catalytic activity of SRPK1 is not required for this phenomenon. Instead, SRPK1 associates directly with the N-terminus of U1-70K and alters the regulatory function of the distal C-terminus, modifying interactions between the U1-70K:SR protein complex and the ESE. Disruption of SRPK1 binding to this complex affects the alternative splicing of genes modulated by the C-terminus of U1-70K. Such findings suggest that, in addition to operating as a traditional serine-modifying catalyst, SRPK1 can also bypass this intrinsic activity to regulate RNA contacts in an early pre-spliceosomal complex.
Collapse
Affiliation(s)
- Brandon E Aubol
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Joseph A Adams
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
17
|
The Role of Alternative Splicing Factors hnRNP G and Fox-2 in the Progression and Prognosis of Esophageal Cancer. DISEASE MARKERS 2022; 2022:3043737. [DOI: 10.1155/2022/3043737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 08/10/2022] [Accepted: 10/08/2022] [Indexed: 11/24/2022]
Abstract
Aim. Alternative splicing (AS) has been widely demonstrated in the occurrence and progression of many cancers. Nevertheless, the involvement of cancer-associated splicing factors in the development of esophageal carcinoma (ESCA) remains to be explored. Method. RNA-Seq data and the corresponding clinical information of the ESCA cohort were downloaded from The Cancer Genome Atlas database. Bioinformatics methods were used to further analyzed the differently expressed AS (DEAS) events and their splicing network. Kaplan–Meier, Cox regression, and unsupervised cluster analyses were used to assess the association between AS events and clinical characteristics of ESCA patients. The splicing factors screened out were verified in vitro at the cellular level. Results. A total of 50,342 AS events were identified, of which 3,988 were DEAS events and 46 of these were associated with overall survival (OS) of ESCA patients, with a 5-year OS rate of 0.941. By constructing a network of AS events with survival-related splicing factors, the AS factors related to prognosis can be further identified. In vitro experiments and database analysis confirmed that the high expression of hnRNP G in ESCA is related to the high invasion ability of ESCA cells and the poor prognosis of ESCA patients. In contrast, the low expression of fox-2 in esophageal cancer is related to a better prognosis. Conclusion. ESCA-associated AS factors hnRNP G and Fox-2 are of great value in deciphering the underlying mechanisms of AS in ESCA and providing clues for therapeutic goals for further validation.
Collapse
|
18
|
Lin X, Liu F, Meng K, Liu H, Zhao Y, Chen Y, Hu W, Luo D. Comprehensive Transcriptome Analysis Reveals Sex-Specific Alternative Splicing Events in Zebrafish Gonads. Life (Basel) 2022; 12:life12091441. [PMID: 36143477 PMCID: PMC9501657 DOI: 10.3390/life12091441] [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: 08/29/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/21/2022] Open
Abstract
Alternative splicing is an important way of regulating gene functions in eukaryotes. Several key genes involved in sex determination and gonadal differentiation, such as nr5a1 and ddx4, have sex-biased transcripts between males and females, suggesting a potential regulatory role of alternative splicing in gonads. Currently, the sex-specific alternative splicing events and genes have not been comprehensively studied at the genome-wide level in zebrafish. In this study, through global splicing analysis on three independent sets of RNA-seq data from matched zebrafish testes and ovaries, we identified 120 differentially spliced genes shared by the three datasets, most of which haven’t been reported before. Functional enrichment analysis showed that the GO terms of mRNA processing, mRNA metabolism and microtubule-based process were strongly enriched. The testis- and ovary-biased alternative splicing genes were identified, and part of them (tp53bp1, tpx2, mapre1a, kif2c, and ncoa5) were further validated by RT-PCR. Sequence characteristics analysis suggested that the lengths, GC contents, and splice site strengths of the alternative exons or introns may have different influences in different types of alternative splicing events. Interestingly, we identified an unexpected high proportion (over 70%) of non-frameshift exon-skipping events, suggesting that in these cases the two protein isoforms derived from alternative splicing may both have functions. Furthermore, as a representative example, we found that the alternative splicing of ncoa5 causes the loss of a conserved RRM domain in the short transcript predominantly produced in testes. Our study discovers novel sex-specific alternative splicing events and genes with high reliabilities in zebrafish testes and ovaries, which would provide attractive targets for follow-up studies to reveal the biological significances of alternative splicing events and genes in sex determination and gonadal differentiation.
Collapse
Affiliation(s)
- Xing Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (F.L.); (D.L.)
| | - Kaifeng Meng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, China
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Hairong Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, China
| | - Yuanli Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, China
| | - Yuanyuan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang 524088, China
| | - Daji Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang 524088, China
- Correspondence: (F.L.); (D.L.)
| |
Collapse
|
19
|
The Post-Translational Modification Networking in WNK-Centric Hypertension Regulation and Electrolyte Homeostasis. Biomedicines 2022; 10:biomedicines10092169. [PMID: 36140271 PMCID: PMC9496095 DOI: 10.3390/biomedicines10092169] [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: 07/19/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022] Open
Abstract
The with-no-lysine (WNK) kinase family, comprising four serine-threonine protein kinases (WNK1-4), were first linked to hypertension due to their mutations in association with pseudohypoaldosteronism type II (PHAII). WNK kinases regulate crucial blood pressure regulators, SPAK/OSR1, to mediate the post-translational modifications (PTMs) of their downstream ion channel substrates, such as sodium chloride co-transporter (NCC), epithelial sodium chloride (ENaC), renal outer medullary potassium channel (ROMK), and Na/K/2Cl co-transporters (NKCCs). In this review, we summarize the molecular pathways dysregulating the WNKs and their downstream target renal ion transporters. We summarize each of the genetic variants of WNK kinases and the small molecule inhibitors that have been discovered to regulate blood pressure via WNK-triggered PTM cascades.
Collapse
|
20
|
Chen M, Zhu R, Zhang F, Zhu L. Screening and Identification of Survival-Associated Splicing Factors in Lung Squamous Cell Carcinoma. Front Genet 2022; 12:803606. [PMID: 35126467 PMCID: PMC8811261 DOI: 10.3389/fgene.2021.803606] [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: 10/28/2021] [Accepted: 12/27/2021] [Indexed: 11/17/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is a disease with high morbidity and mortality. Many studies have shown that aberrant alternative splicing (AS) can lead to tumorigenesis, and splicing factors (SFs) serve as an important function during AS. In this research, we propose an analysis method based on synergy to screen key factors that regulate the initiation and progression of LUSC. We first screened alternative splicing events (ASEs) associated with survival in LUSC patients by bivariate Cox regression analysis. Then an association network consisting of OS-ASEs, SFs, and their targeting relationship was constructed to identify key SFs. Finally, 10 key SFs were selected in terms of degree centrality. The validation on TCGA and cross-platform GEO datasets showed that some SFs were significantly differentially expressed in cancer and paracancer tissues, and some of them were associated with prognosis, indicating that our method is valid and accurate. It is expected that our method would be applied to a wide range of research fields and provide new insights in the future.
Collapse
Affiliation(s)
- Min Chen
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Rui Zhu
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Fangzhou Zhang
- School of Materials Science and Engineering, Institute of Materials, Shanghai University, Shanghai, China
- Shaoxing Institute of Technology, Shanghai University, Shanghai, China
- *Correspondence: Fangzhou Zhang , ; Liucun Zhu ,
| | - Liucun Zhu
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Fangzhou Zhang , ; Liucun Zhu ,
| |
Collapse
|
21
|
Desai J, Francis C, Longo K, Hoss A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3128-3141. [PMID: 35286381 PMCID: PMC8989546 DOI: 10.1093/nar/gkac155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 02/14/2022] [Accepted: 02/26/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is frequently involved in the diversification of protein function and can also be modulated for therapeutic purposes. Here we develop a predictive model, called Exon ByPASS (predicting Exon skipping Based on Protein amino acid SequenceS), to assess the criticality of exon inclusion based solely on information contained in the amino acid sequence upstream and downstream of the exon junctions. By focusing on protein sequence, Exon ByPASS predicts exon skipping independent of tissue and species in the absence of any intronic information. We validate model predictions using transcriptomic and proteomic data and show that the model can capture exon skipping in different tissues and species. Additionally, we reveal potential therapeutic opportunities by predicting synthetically skippable exons and neo-junctions arising in cancer cells.
Collapse
Affiliation(s)
- Jigar Desai
- To whom correspondence should be addressed. Tel: +1 704 214 7914;
| | | | | | - Andrew Hoss
- Wave Life Sciences, Cambridge, MA 02138, USA
| |
Collapse
|
22
|
Shields EJ, Sorida M, Sheng L, Sieriebriennikov B, Ding L, Bonasio R. Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain. BMC Biol 2021; 19:254. [PMID: 34838024 PMCID: PMC8626913 DOI: 10.1186/s12915-021-01188-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/10/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Functional genomic analyses rely on high-quality genome assemblies and annotations. Highly contiguous genome assemblies have become available for a variety of species, but accurate and complete annotation of gene models, inclusive of alternative splice isoforms and transcription start and termination sites, remains difficult with traditional approaches. RESULTS Here, we utilized full-length isoform sequencing (Iso-Seq), a long-read RNA sequencing technology, to obtain a comprehensive annotation of the transcriptome of the ant Harpegnathos saltator. The improved genome annotations include additional splice isoforms and extended 3' untranslated regions for more than 4000 genes. Reanalysis of RNA-seq experiments using these annotations revealed several genes with caste-specific differential expression and tissue- or caste-specific splicing patterns that were missed in previous analyses. The extended 3' untranslated regions afforded great improvements in the analysis of existing single-cell RNA-seq data, resulting in the recovery of the transcriptomes of 18% more cells. The deeper single-cell transcriptomes obtained with these new annotations allowed us to identify additional markers for several cell types in the ant brain, as well as genes differentially expressed across castes in specific cell types. CONCLUSIONS Our results demonstrate that Iso-Seq is an efficient and effective approach to improve genome annotations and maximize the amount of information that can be obtained from existing and future genomic datasets in Harpegnathos and other organisms.
Collapse
Affiliation(s)
- Emily J Shields
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Urology and Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Masato Sorida
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lihong Sheng
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Bogdan Sieriebriennikov
- Department of Biology, New York University, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Long Ding
- Department of Biology, New York University, New York, NY, USA
| | - Roberto Bonasio
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
23
|
Verdile V, Guizzo G, Ferrante G, Paronetto MP. RNA Targeting in Inherited Neuromuscular Disorders: Novel Therapeutic Strategies to Counteract Mis-Splicing. Cells 2021; 10:cells10112850. [PMID: 34831073 PMCID: PMC8616048 DOI: 10.3390/cells10112850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 01/14/2023] Open
Abstract
Neuromuscular disorders represent multifaceted abnormal conditions, with little or no cure, leading to patient deaths from complete muscle wasting and atrophy. Despite strong efforts in the past decades, development of effective treatments is still urgently needed. Advent of next-generation sequencing technologies has allowed identification of novel genes and mutations associated with neuromuscular pathologies, highlighting splicing defects as essential players. Deciphering the significance and relative contributions of defective RNA metabolism will be instrumental to address and counteract these malignancies. We review here recent progress on the role played by alternative splicing in ensuring functional neuromuscular junctions (NMJs), and its involvement in the pathogenesis of NMJ-related neuromuscular disorders, with particular emphasis on congenital myasthenic syndromes and muscular dystrophies. We will also discuss novel strategies based on oligonucleotides designed to bind their cognate sequences in the RNA or targeting intermediary of mRNA metabolism. These efforts resulted in several chemical classes of RNA molecules that have recently proven to be clinically effective, more potent and better tolerated than previous strategies.
Collapse
Affiliation(s)
- Veronica Verdile
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143 Rome, Italy; (V.V.); (G.G.); (G.F.)
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 6, 00135 Rome, Italy
| | - Gloria Guizzo
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143 Rome, Italy; (V.V.); (G.G.); (G.F.)
| | - Gabriele Ferrante
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143 Rome, Italy; (V.V.); (G.G.); (G.F.)
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143 Rome, Italy; (V.V.); (G.G.); (G.F.)
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 6, 00135 Rome, Italy
- Correspondence:
| |
Collapse
|
24
|
Gagné M, Deshaies JE, Sidibé H, Benchaar Y, Arbour D, Dubinski A, Litt G, Peyrard S, Robitaille R, Sephton CF, Vande Velde C. hnRNP A1B, a Splice Variant of HNRNPA1, Is Spatially and Temporally Regulated. Front Neurosci 2021; 15:724307. [PMID: 34630013 PMCID: PMC8498194 DOI: 10.3389/fnins.2021.724307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/30/2021] [Indexed: 11/28/2022] Open
Abstract
RNA binding proteins (RBPs) play a key role in cellular growth, homoeostasis and survival and are tightly regulated. A deep understanding of their spatiotemporal regulation is needed to understand their contribution to physiology and pathology. Here, we have characterized the spatiotemporal expression pattern of hnRNP A1 and its splice variant hnRNP A1B in mice. We have found that hnRNP A1B expression is more restricted to the CNS compared to hnRNP A1, and that it can form an SDS-resistant dimer in the CNS. Also, hnRNP A1B expression becomes progressively restricted to motor neurons in the ventral horn of the spinal cord, compared to hnRNP A1 which is more broadly expressed. We also demonstrate that hnRNP A1B is present in neuronal processes, while hnRNP A1 is absent. This finding supports a hypothesis that hnRNP A1B may have a cytosolic function in neurons that is not shared with hnRNP A1. Our results demonstrate that both isoforms are differentially expressed across tissues and have distinct localization profiles, suggesting that the two isoforms may have specific subcellular functions that can uniquely contribute to disease progression.
Collapse
Affiliation(s)
- Myriam Gagné
- Department of Biochemistry, Université de Montréal, Montréal, QC, Canada.,Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Jade-Emmanuelle Deshaies
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Hadjara Sidibé
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Yousri Benchaar
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Danielle Arbour
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Alicia Dubinski
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Gurleen Litt
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Sarah Peyrard
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Richard Robitaille
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Chantelle F Sephton
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Christine Vande Velde
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| |
Collapse
|
25
|
Alternative Splicing in Cardiovascular Disease-A Survey of Recent Findings. Genes (Basel) 2021; 12:genes12091457. [PMID: 34573439 PMCID: PMC8469243 DOI: 10.3390/genes12091457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/11/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing, a driver of posttranscriptional variance, differs from canonical splicing by arranging the introns and exons of an immature pre-mRNA transcript in a multitude of different ways. Although alternative splicing was discovered almost half a century ago, estimates of the proportion of genes that undergo alternative splicing have risen drastically over the last two decades. Deep sequencing methods and novel bioinformatic algorithms have led to new insights into the prevalence of spliced variants, tissue-specific splicing patterns and the significance of alternative splicing in development and disease. Thus far, the role of alternative splicing has been uncovered in areas ranging from heart development, the response to myocardial infarction to cardiac structural disease. Circular RNAs, a product of alternative back-splicing, were initially discovered in 1976, but landmark publications have only recently identified their regulatory role, tissue-specific expression, and transcriptomic abundance, spurring a renewed interest in the topic. The aim of this review is to provide a brief insight into some of the available findings on the role of alternative splicing in cardiovascular disease, with a focus on atherosclerosis, myocardial infarction, heart failure, dilated cardiomyopathy and circular RNAs in myocardial infarction.
Collapse
|
26
|
Naftaly AS, Pau S, White MA. Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish. Genome Res 2021; 31:1486-1497. [PMID: 34131005 PMCID: PMC8327910 DOI: 10.1101/gr.274282.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/15/2021] [Indexed: 01/07/2023]
Abstract
Alternate isoforms are important contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full-length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five organs in threespine stickleback fish (Gasterosteus aculeatus), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly in which gene annotations are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq-predicted transcription start sites were more accurate and verified through ATAC-seq. We also detected many alternative splicing events between sexes and across organs. We found a substantial number of genes in both somatic and gonadal samples that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish.
Collapse
Affiliation(s)
- Alice S Naftaly
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Shana Pau
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Biology, University of Texas Arlington, Arlington, Texas 76019, USA
| | - Michael A White
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
27
|
Sena RM, Twiss JL, Gardiner AS, Dell’Orco M, Linsenbardt DN, Perrone-Bizzozero NI. The RNA-Binding Protein HuD Regulates Alternative Splicing and Alternative Polyadenylation in the Mouse Neocortex. Molecules 2021; 26:2836. [PMID: 34064652 PMCID: PMC8151252 DOI: 10.3390/molecules26102836] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022] Open
Abstract
The neuronal Hu/ELAV-like proteins HuB, HuC and HuD are a class of RNA-binding proteins that are crucial for proper development and maintenance of the nervous system. These proteins bind to AU-rich elements (AREs) in the untranslated regions (3'-UTRs) of target mRNAs regulating mRNA stability, transport and translation. In addition to these cytoplasmic functions, Hu proteins have been implicated in alternative splicing and alternative polyadenylation in the nucleus. The purpose of this study was to identify transcriptome-wide effects of HuD deletion on both of these nuclear events using RNA sequencing data obtained from the neocortex of Elavl4-/- (HuD KO) mice. HuD KO affected alternative splicing of 310 genes, including 17 validated HuD targets such as Cbx3, Cspp1, Snap25 and Gria2. In addition, deletion of HuD affected polyadenylation of 53 genes, with the majority of significantly altered mRNAs shifting towards usage of proximal polyadenylation signals (PAS), resulting in shorter 3'-UTRs. None of these genes overlapped with those showing alternative splicing events. Overall, HuD KO had a greater effect on alternative splicing than polyadenylation, with many of the affected genes implicated in several neuronal functions and neuropsychiatric disorders.
Collapse
Affiliation(s)
- Rebecca M. Sena
- Department Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (R.M.S.); (A.S.G.); (M.D.)
| | - Jeffery L. Twiss
- Department Biological Sciences, University of South Carolina, Columbia, SC 29208, USA;
| | - Amy S. Gardiner
- Department Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (R.M.S.); (A.S.G.); (M.D.)
- Department Cell Biology and Physiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | - Michela Dell’Orco
- Department Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (R.M.S.); (A.S.G.); (M.D.)
| | - David N. Linsenbardt
- Department Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (R.M.S.); (A.S.G.); (M.D.)
| | - Nora I. Perrone-Bizzozero
- Department Neurosciences, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA; (R.M.S.); (A.S.G.); (M.D.)
| |
Collapse
|
28
|
Arzalluz-Luque Á, Cabrera JL, Skottman H, Benguria A, Bolinches-Amorós A, Cuenca N, Lupo V, Dopazo A, Tarazona S, Delás B, Carballo M, Pascual B, Hernan I, Erceg S, Lukovic D. Mutant PRPF8 Causes Widespread Splicing Changes in Spliceosome Components in Retinitis Pigmentosa Patient iPSC-Derived RPE Cells. Front Neurosci 2021; 15:636969. [PMID: 33994920 PMCID: PMC8116631 DOI: 10.3389/fnins.2021.636969] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is a rare, progressive disease that affects photoreceptors and retinal pigment epithelial (RPE) cells with blindness as a final outcome. Despite high medical and social impact, there is currently no therapeutic options to slow down the progression of or cure the disease. The development of effective therapies was largely hindered by high genetic heterogeneity, inaccessible disease tissue, and unfaithful model organisms. The fact that components of ubiquitously expressed splicing factors lead to the retina-specific disease is an additional intriguing question. Herein, we sought to correlate the retinal cell-type-specific disease phenotype with the splicing profile shown by a patient with autosomal recessive RP, caused by a mutation in pre-mRNA splicing factor 8 (PRPF8). In order to get insight into the role of PRPF8 in homeostasis and disease, we capitalize on the ability to generate patient-specific RPE cells and reveal differentially expressed genes unique to RPE cells. We found that spliceosomal complex and ribosomal functions are crucial in determining cell-type specificity through differential expression and alternative splicing (AS) and that PRPF8 mutation causes global changes in splice site selection and exon inclusion that particularly affect genes involved in these cellular functions. This finding corroborates the hypothesis that retinal tissue identity is conferred by a specific splicing program and identifies retinal AS events as a framework toward the design of novel therapeutic opportunities.
Collapse
Affiliation(s)
- Ángeles Arzalluz-Luque
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, València, Spain
| | - Jose Luis Cabrera
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC). Madrid, Spain
| | - Heli Skottman
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alberto Benguria
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC). Madrid, Spain
| | - Arantxa Bolinches-Amorós
- Stem Cells Therapies in Neurodegenerative Diseases Lab, Research Center Principe Felipe, Valencia, Spain
- National Stem Cell Bank-Valencia Node, Research Center Principe Felipe, Valencia, Spain
| | - Nicolás Cuenca
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Vincenzo Lupo
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
- Rare Diseases Joint Units, IIS La Fe-CIPF, Valencia, Spain
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC). Madrid, Spain
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, València, Spain
| | - Bárbara Delás
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Miguel Carballo
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Beatriz Pascual
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Imma Hernan
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Slaven Erceg
- Stem Cells Therapies in Neurodegenerative Diseases Lab, Research Center Principe Felipe, Valencia, Spain
- National Stem Cell Bank-Valencia Node, Research Center Principe Felipe, Valencia, Spain
- Rare Diseases Joint Units, IIS La Fe-CIPF, Valencia, Spain
- Department of Neuroregeneration, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
| | - Dunja Lukovic
- Rare Diseases Joint Units, IIS La Fe-CIPF, Valencia, Spain
- Retinal Degeneration Lab, Research Centre Principe Felipe, Valencia, Spain
| |
Collapse
|
29
|
Lu H, Zhang J, Chen YE, Garcia-Barrio MT. Integration of Transformative Platforms for the Discovery of Causative Genes in Cardiovascular Diseases. Cardiovasc Drugs Ther 2021; 35:637-654. [PMID: 33856594 DOI: 10.1007/s10557-021-07175-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2021] [Indexed: 12/11/2022]
Abstract
Cardiovascular diseases are the leading cause of morbidity and mortality worldwide. Genome-wide association studies (GWAS) are powerful epidemiological tools to find genes and variants associated with cardiovascular diseases while follow-up biological studies allow to better understand the etiology and mechanisms of disease and assign causality. Improved methodologies and reduced costs have allowed wider use of bulk and single-cell RNA sequencing, human-induced pluripotent stem cells, organoids, metabolomics, epigenomics, and novel animal models in conjunction with GWAS. In this review, we feature recent advancements relevant to cardiovascular diseases arising from the integration of genetic findings with multiple enabling technologies within multidisciplinary teams to highlight the solidifying transformative potential of this approach. Well-designed workflows integrating different platforms are greatly improving and accelerating the unraveling and understanding of complex disease processes while promoting an effective way to find better drug targets, improve drug design and repurposing, and provide insight towards a more personalized clinical practice.
Collapse
Affiliation(s)
- Haocheng Lu
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA
| | - Jifeng Zhang
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA.,Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, 48109, USA
| | - Y Eugene Chen
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA. .,Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, 48109, USA.
| | - Minerva T Garcia-Barrio
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA.
| |
Collapse
|
30
|
An extended catalogue of tandem alternative splice sites in human tissue transcriptomes. PLoS Comput Biol 2021; 17:e1008329. [PMID: 33826604 PMCID: PMC8055015 DOI: 10.1371/journal.pcbi.1008329] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 04/19/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Tandem alternative splice sites (TASS) is a special class of alternative splicing events that are characterized by a close tandem arrangement of splice sites. Most TASS lack functional characterization and are believed to arise from splicing noise. Based on the RNA-seq data from the Genotype Tissue Expression project, we present an extended catalogue of TASS in healthy human tissues and analyze their tissue-specific expression. The expression of TASS is usually dominated by one major splice site (maSS), while the expression of minor splice sites (miSS) is at least an order of magnitude lower. Among 46k miSS with sufficient read support, 9k (20%) are significantly expressed above the expected noise level, and among them 2.5k are expressed tissue-specifically. We found significant correlations between tissue-specific expression of RNA-binding proteins (RBP), tissue-specific expression of miSS, and miSS response to RBP inactivation by shRNA. In combination with RBP profiling by eCLIP, this allowed prediction of novel cases of tissue-specific splicing regulation including a miSS in QKI mRNA that is likely regulated by PTBP1. The analysis of human primary cell transcriptomes suggested that both tissue-specific and cell-type-specific factors contribute to the regulation of miSS expression. More than 20% of tissue-specific miSS affect structured protein regions and may adjust protein-protein interactions or modify the stability of the protein core. The significantly expressed miSS evolve under the same selection pressure as maSS, while other miSS lack signatures of evolutionary selection and conservation. Using mixture models, we estimated that not more than 15% of maSS and not more than 54% of tissue-specific miSS are noisy, while the proportion of noisy splice sites among non-significantly expressed miSS is above 63%. Pre-mRNA splicing is an important step in the processing of the genomic information during gene expression. During splicing, introns are excised from a gene transcript, and the remaining exons are ligated. Our work concerns one its particular subtype, which involves the so-called tandem alternative splice sites, a group of closely located exon borders that are used alternatively. We analyzed RNA-seq measurements of gene expression provided by the Genotype-Tissue Expression (GTEx) project, the largest to-date collection of such measurements in healthy human tissues, and constructed a detailed catalogue of tandem alternative splice sites. Within this catalogue, we characterized patterns of tissue-specific expression, regulation, impact on protein structure, and evolutionary selection acting on tandem alternative splice sites. In a number of genes, we predicted regulatory mechanisms that could be responsible for choosing one of many tandem alternative splice sites. The results of this study provide an invaluable resource for molecular biologists studying alternative splicing.
Collapse
|
31
|
Ducret V, Richards AJ, Videlier M, Scalvenzi T, Moore KA, Paszkiewicz K, Bonneaud C, Pollet N, Herrel A. Transcriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri. BMC Genomics 2021; 22:204. [PMID: 33757428 PMCID: PMC7986297 DOI: 10.1186/s12864-021-07517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and performance trade-offs remains poorly understood. In this study we identify the genes, signaling pathways, and regulatory processes possibly responsible for the trade-off between burst performance and endurance observed in Xenopus allofraseri, using a transcriptomic approach. RESULTS We obtained a total of about 121 million paired-end reads from Illumina RNA sequencing and analyzed 218,541 transcripts obtained from a de novo assembly. We identified 109 transcripts with a significant differential expression between endurant and burst performant individuals (FDR ≤ 0.05 and logFC ≥2), and blast searches resulted in 103 protein-coding genes. We found major differences between endurant and burst-performant individuals in the expression of genes involved in the polymerization and ATPase activity of actin filaments, cellular trafficking, proteoglycans and extracellular proteins secreted, lipid metabolism, mitochondrial activity and regulators of signaling cascades. Remarkably, we revealed transcript isoforms of key genes with functions in metabolism, apoptosis, nuclear export and as a transcriptional corepressor, expressed in either burst-performant or endurant individuals. Lastly, we find two up-regulated transcripts in burst-performant individuals that correspond to the expression of myosin-binding protein C fast-type (mybpc2). This suggests the presence of mybpc2 homoeologs and may have been favored by selection to permit fast and powerful locomotion. CONCLUSION These results suggest that the differential expression of genes belonging to the pathways of calcium signaling, endoplasmic reticulum stress responses and striated muscle contraction, in addition to the use of alternative splicing and effectors of cellular activity underlie locomotor performance trade-offs. Ultimately, our transcriptomic analysis offers new perspectives for future analyses of the role of single nucleotide variants, homoeology and alternative splicing in the evolution of locomotor performance trade-offs.
Collapse
Affiliation(s)
- Valérie Ducret
- UMR 7179 MECADEV, C.N.R.S/M.N.H.N., Département Adaptations du Vivant, 55 Rue Buffon, 75005, Paris, France.
| | - Adam J Richards
- Station d'Ecologie Expérimentale du CNRS, USR 2936, 09200, Moulis, France
| | - Mathieu Videlier
- Functional Ecology Lab, Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada
| | - Thibault Scalvenzi
- Evolution, Génomes, Comportement & Ecologie, Université Paris-Saclay, CNRS, IRD, 91198, Gif-sur-Yvette, France
| | - Karen A Moore
- Exeter Sequencing Service, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Konrad Paszkiewicz
- Exeter Sequencing Service, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Camille Bonneaud
- Station d'Ecologie Expérimentale du CNRS, USR 2936, 09200, Moulis, France
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, UK
| | - Nicolas Pollet
- Evolution, Génomes, Comportement & Ecologie, Université Paris-Saclay, CNRS, IRD, 91198, Gif-sur-Yvette, France
| | - Anthony Herrel
- Station d'Ecologie Expérimentale du CNRS, USR 2936, 09200, Moulis, France
- Evolutionary Morphology of Vertebrates, Ghent University, B-9000, Ghent, Belgium
| |
Collapse
|
32
|
Li J, Liu F, Lv Y, Sun K, Zhao Y, Reilly J, Zhang Y, Tu J, Yu S, Liu X, Qin Y, Huang Y, Gao P, Jia D, Chen X, Han Y, Shu X, Luo D, Tang Z, Liu M. Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing. Nucleic Acids Res 2021; 49:2027-2043. [PMID: 33476374 PMCID: PMC7913766 DOI: 10.1093/nar/gkab003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 01/01/2021] [Accepted: 01/05/2021] [Indexed: 12/23/2022] Open
Abstract
Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis, especially in neural tissues. Mutations in pre-mRNAs processing factor 31 (PRPF31) cause autosomal dominant retinitis pigmentosa, a progressive retinal degeneration disease. The transcriptome-wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here, we showed that the differentiation and viability of retinal progenitor cells (RPCs) are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level, significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild-type human PRPF31 rather than the disease-associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak 5′ splicing site. Moreover, genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events, which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis.
Collapse
Affiliation(s)
- Jingzhen Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Fei Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuexia Lv
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuntong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Science, Wuhan 430072, PR China
| | - Jamas Reilly
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, Scotland, UK
| | - Yangjun Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Shanshan Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xiliang Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yayun Qin
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Xinhua Shu
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, Scotland, UK
| | - Daji Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Science, Wuhan 430072, PR China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
| |
Collapse
|
33
|
Ghiasi SM, Rutter GA. Consequences for Pancreatic β-Cell Identity and Function of Unregulated Transcript Processing. Front Endocrinol (Lausanne) 2021; 12:625235. [PMID: 33763030 PMCID: PMC7984428 DOI: 10.3389/fendo.2021.625235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/26/2021] [Indexed: 12/25/2022] Open
Abstract
Mounting evidence suggests a role for alternative splicing (AS) of transcripts in the normal physiology and pathophysiology of the pancreatic β-cell. In the apparent absence of RNA repair systems, RNA decay pathways are likely to play an important role in controlling the stability, distribution and diversity of transcript isoforms in these cells. Around 35% of alternatively spliced transcripts in human cells contain premature termination codons (PTCs) and are targeted for degradation via nonsense-mediated decay (NMD), a vital quality control process. Inflammatory cytokines, whose levels are increased in both type 1 (T1D) and type 2 (T2D) diabetes, stimulate alternative splicing events and the expression of NMD components, and may or may not be associated with the activation of the NMD pathway. It is, however, now possible to infer that NMD plays a crucial role in regulating transcript processing in normal and stress conditions in pancreatic β-cells. In this review, we describe the possible role of Regulated Unproductive Splicing and Translation (RUST), a molecular mechanism embracing NMD activity in relationship to AS and translation of damaged transcript isoforms in these cells. This process substantially reduces the abundance of non-functional transcript isoforms, and its dysregulation may be involved in pancreatic β-cell failure in diabetes.
Collapse
Affiliation(s)
- Seyed M. Ghiasi
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
34
|
Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021. [PMID: 33565261 DOI: 10.1002/wrna.1643.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
Collapse
Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
| |
Collapse
|
35
|
Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1643. [PMID: 33565261 DOI: 10.1002/wrna.1643] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
Collapse
Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
| |
Collapse
|
36
|
Li Z, Zhang Y, Bush SJ, Tang C, Chen L, Zhang D, Urrutia AO, Lin JW, Chen L. MeDAS: a Metazoan Developmental Alternative Splicing database. Nucleic Acids Res 2021; 49:D144-D150. [PMID: 33084905 PMCID: PMC7779033 DOI: 10.1093/nar/gkaa886] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/24/2020] [Accepted: 10/07/2020] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing is widespread throughout eukaryotic genomes and greatly increases transcriptomic diversity. Many alternative isoforms have functional roles in developmental processes and are precisely temporally regulated. To facilitate the study of alternative splicing in a developmental context, we created MeDAS, a Metazoan Developmental Alternative Splicing database. MeDAS is an added-value resource that re-analyses publicly archived RNA-seq libraries to provide quantitative data on alternative splicing events as they vary across the time course of development. It has broad temporal and taxonomic scope and is intended to assist the user in identifying trends in alternative splicing throughout development. To create MeDAS, we re-analysed a curated set of 2232 Illumina polyA+ RNA-seq libraries that chart detailed time courses of embryonic and post-natal development across 18 species with a taxonomic range spanning the major metazoan lineages from Caenorhabditis elegans to human. MeDAS is freely available at https://das.chenlulab.com both as raw data tables and as an interactive browser allowing searches by species, tissue, or genomic feature (gene, transcript or exon ID and sequence). Results will provide details on alternative splicing events identified for the queried feature and can be visualised at the gene-, transcript- and exon-level as time courses of expression and inclusion levels, respectively.
Collapse
Affiliation(s)
- Zhidan Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, China
| | - Yiming Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, China
| | - Stephen J Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, UK
| | - Chao Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, China
| | - Li Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, China
| | - Dan Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, China
| | - Araxi O Urrutia
- Instituto de Ecologia, UNAM, Ciudad de Mexico 04510, Mexico.,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Jing-Wen Lin
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
37
|
Koterniak B, Pilaka PP, Gracida X, Schneider LM, Pritišanac I, Zhang Y, Calarco JA. Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans. Genome Res 2020; 30:1766-1780. [PMID: 33127752 PMCID: PMC7706725 DOI: 10.1101/gr.267328.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/28/2020] [Indexed: 12/27/2022]
Abstract
Alternative splicing plays a major role in shaping tissue-specific transcriptomes. Among the broad tissue types present in metazoans, the central nervous system contains some of the highest levels of alternative splicing. Although many documented examples of splicing differences between broad tissue types exist, there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. By using translating ribosome affinity purification coupled with deep-sequencing (TRAP-seq) in Caenorhabditis elegans, we have obtained high coverage profiles of ribosome-associated mRNA for three broad tissue classes (nervous system, muscle, and intestine) and two neuronal subtypes (dopaminergic and serotonergic neurons). We have identified hundreds of splice junctions that exhibit distinct splicing patterns between tissue types or within the nervous system. Alternative splicing events differentially regulated between tissues are more often frame-preserving, are more highly conserved across Caenorhabditis species, and are enriched in specific cis regulatory motifs, when compared with other types of exons. By using this information, we have identified a likely mechanism of splicing repression by the RNA-binding protein UNC-75/CELF via interactions with cis elements that overlap a 5′ splice site. Alternatively spliced exons also overlap more frequently with intrinsically disordered peptide regions than constitutive exons. Moreover, regulated exons are often shorter than constitutive exons but are flanked by longer intron sequences. Among these tissue-regulated exons are several highly conserved microexons <27 nt in length. Collectively, our results indicate a rich layer of tissue-specific gene regulation at the level of alternative splicing in C. elegans that parallels the evolutionary forces and constraints observed across metazoa.
Collapse
Affiliation(s)
- Bina Koterniak
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Pallavi P Pilaka
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Xicotencatl Gracida
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Lisa-Marie Schneider
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.,Department of Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Iva Pritišanac
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.,Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Yun Zhang
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - John A Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| |
Collapse
|
38
|
Jung H, Han S, Lee Y. Transcriptome analysis of alternative splicing in the pathogen life cycle in human foreskin fibroblasts infected with Trypanosoma cruzi. Sci Rep 2020; 10:17481. [PMID: 33060827 PMCID: PMC7566602 DOI: 10.1038/s41598-020-74540-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/05/2020] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma cruzi is an intracellular protozoan parasite that causes Chagas disease as a zoonotic pathogen. The parasite has been shown to remodel expression in the host transcriptome under different conditions. Although alternative splicing (AS) is involved in virtually every biological function in eukaryotes, including cellular differentiation and responses to immune reactions, host AS events that occur as a result of T. cruzi infection have yet to be explored. In this study, we bioinformatically investigated the transcriptome AS dynamics of T. cruzi (Y strain) infected human foreskin fibroblasts using RNA-Seq data captured over four timepoints (4, 24, 48, and 72 h post infection (hpi)). We identified 1768, 399, 250, and 299 differentially expressed exons (AS exons) at 4, 24, 48, and 72 hpi, respectively, showing that host AS mechanism may have a significant role in the intracellular life cycle of the parasite. We present an exon skipping event in HDAC7, which is a candidate gene that is important in the parasite’s cell cycle. To sum up, this bioinformatics analysis of transcriptome may provide new potential insight into AS regulation in human foreskin fibroblast (HFF) cells infected by T. cruzi and into its implication to the parasite life cycle. Moreover, identified AS genes may provide new potential molecular candidates for improving treatment.
Collapse
Affiliation(s)
- Hyeim Jung
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.
| |
Collapse
|
39
|
Su F, Wang G, Ji J, Zhang P, Wang F, Li Z. Real-time detection of mRNA splicing variants with specifically designed reverse-transcription loop-mediated isothermal amplification. RSC Adv 2020; 10:6271-6276. [PMID: 35495989 PMCID: PMC9049701 DOI: 10.1039/d0ra00591f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 01/31/2020] [Indexed: 01/22/2023] Open
Abstract
Alternative splicing is a ubiquitous and crucial process in cellular processes and has a specific linkage with diseases. To date, developing cost-effective methods with high sensitivity and specificity for detection of splicing variants has been needed. Herein, we report a novel splicing variant assay based on specifically designed reverse-transcription loop-mediated isothermal amplification. After reverse transcribing the splicing variant into cDNA, four DNA primers are specifically designed to recognize six distinct regions. The four DNA primers can hybridize with corresponding sequences for extension and strand displacement DNA synthesis to form stem-loop DNA and then LAMP amplification is started. The proposed method can detect as low as 100 aM splicing variants in real-time fashion with high specificity, showing great potential in biological function and clinical studies. A novel splicing variant assay is developed based on specifically designed reverse-transcription (RT) loop-mediated isothermal amplification.![]()
Collapse
Affiliation(s)
- Fengxia Su
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Guanhao Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Jianing Ji
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Pengbo Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Fangfang Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Zhengping Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| |
Collapse
|
40
|
Global Analysis of Alternative Splicing Difference in Peripheral Immune Organs between Tongcheng Pigs and Large White Pigs Artificially Infected with PRRSV In Vivo. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4045204. [PMID: 32083129 PMCID: PMC7011390 DOI: 10.1155/2020/4045204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/13/2019] [Indexed: 11/17/2022]
Abstract
Alternative splicing (AS) plays a significant role in regulating gene expression at the transcriptional level in eukaryotes. Flexibility and diversity of transcriptome and proteome can be significantly increased through alternative splicing of genes. In the present study, transcriptome data of peripheral immune organs including spleen and inguinal lymph nodes (ILN) were used to identify AS difference between PRRSV-resistant Tongcheng (TC) pigs and PRRSV-susceptible Large White (LW) pigs artificially infected with porcine reproductive and respiratory syndrome virus (PRRSV) in vivo. The results showed that PRRSV infection induced global alternative splicing events (ASEs) with different modes. Among them, 373 genes and 595 genes in the spleen and ILN of TC pigs, while 458 genes and 560 genes in the spleen and ILN of LW pigs had significantly differential ASEs. Alternative splicing was subject to tissue-specific and lineage-specific regulation in response to PRRSV infection. Enriched GO terms and pathways showed that genes with differential ASEs played important roles in transcriptional regulation, immune response, metabolism, and apoptosis. Furthermore, a splicing factor associated with apoptosis, SRSF4, was significantly upregulated in LW pigs. Functional analysis on apoptosis associated genes was validated by RT-PCR and DNA sequencing. These findings revealed different response to PRRSV between PRRSV-resistant TC pigs and PRRSV-susceptible LW pigs at the level of alternative splicing, suggesting the potential relationship between AS and disease resistance to PRRSV.
Collapse
|
41
|
Abstract
Eating more potassium may reduce blood pressure and the occurrence of other cardiovascular diseases by actions on various systems, including the vasculature, the sympathetic nervous system, systemic metabolism, and body fluid volume. Among these, the kidney plays a major role in the potassium-rich diet-mediated blood pressure reduction. PURPOSE OF REVIEW: To provide an overview of recent discoveries about the mechanisms by which a potassium-rich diet leads to natriuresis. RECENT FINDINGS: Although the distal convoluted tubule (DCT) is a short part of the nephron that reabsorbs salt, via the sodium-chloride cotransporter (NCC), it is highly sensitive to changes in plasma potassium concentration. Activation or inhibition of NCC raises or lowers blood pressure. Recent work suggests that extracellular potassium concentration is sensed by the DCT via intracellular chloride concentration which regulates WNK kinases in the DCT. High-potassium diet targets NCC in the DCT, resulting in natriuresis and fluid volume reduction, which are protective from hypertension and other cardiovascular problems.
Collapse
Affiliation(s)
- Xiao-Tong Su
- School of Medicine, Oregon Health and Science University, Portland, OR USA
| | - Chao-Ling Yang
- School of Medicine, Oregon Health and Science University, Portland, OR USA
| | - David H. Ellison
- School of Medicine, Oregon Health and Science University, Portland, OR USA ,Oregon Clinical & Translational Research Institute, SN4N, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239 USA ,Veterans Administration Portland Health Care System, Portland, OR USA
| |
Collapse
|
42
|
Tu Z, Shen Y, Wen S, Zong Y, Li H. Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense. FRONTIERS IN PLANT SCIENCE 2020; 11:578100. [PMID: 33072153 PMCID: PMC7539066 DOI: 10.3389/fpls.2020.578100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/04/2020] [Indexed: 05/11/2023]
Abstract
Alternative splicing (AS) plays pivotal roles in regulating plant growth and development, flowering, biological rhythms, signal transduction, and stress responses. However, no studies on AS have been performed in Liriodendron chinense, a deciduous tree species that has high economic and ecological value. In this study, we used multiple tools and algorithms to analyze transcriptome data derived from seven tissues via hybrid sequencing. Although only 17.56% (8,503/48,408) of genes in L. chinense were alternatively spliced, these AS genes occurred in 37,844 AS events. Among these events, intron retention was the most frequent AS event, producing 1,656 PTC-containing and 3,310 non-PTC-containing transcripts. Moreover, 183 long noncoding RNAs (lncRNAs) also underwent AS events. Furthermore, weighted gene coexpression network analysis (WGCNA) revealed that there were great differences in the activities of transcription and post-transcriptional regulation between pistils and leaves, and AS had an impact on many physiological and biochemical processes in L. chinense, such as photosynthesis, sphingolipid metabolism, fatty acid biosynthesis and metabolism. Moreover, our analysis showed that the features of genes may affect AS, as AS genes and non-AS genes had differences in the exon/intron length, transcript length, and number of exons/introns. In addition, the structure of AS genes may impact the frequencies and types of AS because AS genes with more exons or introns tended to exhibit more AS events, and shorter introns tended to be retained, whereas shorter exons tended to be skipped. Furthermore, eight AS genes were verified, and the results were consistent with our analysis. Overall, this study reveals that AS and gene interaction are mutual-on one hand, AS can affect gene expression and translation, while on the other hand, the structural characteristics of the gene can also affect AS. This work is the first to comprehensively report on AS in L. chinense, and it can provide a reference for further research on AS in L. chinense.
Collapse
Affiliation(s)
- Zhonghua Tu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yufang Shen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shaoying Wen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaxian Zong
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huogen Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Huogen Li,
| |
Collapse
|
43
|
Abstract
Alternative Splicing produces multiple mRNA isoforms of genes which have important diverse roles such as regulation of gene expression, human heritable diseases, and response to environmental stresses. However, little has been done to assign functions at the mRNA isoform level. Functional networks, where the interactions are quantified by their probability of being involved in the same biological process are typically generated at the gene level. We use a diverse array of tissue-specific RNA-seq datasets and sequence information to train random forest models that predict the functional networks. Since there is no mRNA isoform-level gold standard, we use single isoform genes co-annotated to Gene Ontology biological process annotations, Kyoto Encyclopedia of Genes and Genomes pathways, BioCyc pathways and protein-protein interactions as functionally related (positive pair). To generate the non-functional pairs (negative pair), we use the Gene Ontology annotations tagged with "NOT" qualifier. We describe 17 Tissue-spEcific mrNa iSoform functIOnal Networks (TENSION) following a leave-one-tissue-out strategy in addition to an organism level reference functional network for mouse. We validate our predictions by comparing its performance with previous methods, randomized positive and negative class labels, updated Gene Ontology annotations, and by literature evidence. We demonstrate the ability of our networks to reveal tissue-specific functional differences of the isoforms of the same genes. All scripts and data from TENSION are available at: https://doi.org/10.25380/iastate.c.4275191 .
Collapse
Affiliation(s)
- Gaurav Kandoi
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA
| | - Julie A Dickerson
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA.
| |
Collapse
|
44
|
Olthof AM, Hyatt KC, Kanadia RN. Minor intron splicing revisited: identification of new minor intron-containing genes and tissue-dependent retention and alternative splicing of minor introns. BMC Genomics 2019; 20:686. [PMID: 31470809 PMCID: PMC6717393 DOI: 10.1186/s12864-019-6046-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Mutations in minor spliceosome components such as U12 snRNA (cerebellar ataxia) and U4atac snRNA (microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1)) result in tissue-specific symptoms. Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). The current model of inefficient splicing is thought to apply to the regulation of the ~ 500 MIGs identified in the U12DB. However this database was created more than 10 years ago. Therefore, we first wanted to revisit the classification of minor introns in light of the most recent reference genome. We then sought to address specificity of MIG expression, minor intron retention, and alternative splicing (AS) across mouse and human tissues. RESULTS We employed position-weight matrices to obtain a comprehensive updated list of minor introns, consisting of 722 mouse and 770 human minor introns. These can be found in the Minor Intron DataBase (MIDB). Besides identification of 99% of the minor introns found in the U12DB, we also discovered ~ 150 new MIGs. We then analyzed the RNAseq data from eleven different mouse tissues, which revealed tissue-specific MIG expression and minor intron retention. Additionally, many minor introns were efficiently spliced compared to their flanking major introns. Finally, we identified several novel AS events across minor introns in both mouse and human, which were also tissue-dependent. Bioinformatics analysis revealed that several of the AS events could result in the production of novel tissue-specific proteins. Moreover, like the major introns, we found that these AS events were more prevalent in long minor introns, while retention was favoured in shorter introns. CONCLUSION Here we show that minor intron splicing and AS across minor introns is a highly organised process that might be regulated in coordination with the major spliceosome in a tissue-specific manner. We have provided a framework to further study the impact of the minor spliceosome and the regulation of MIG expression. These findings may shed light on the mechanism underlying tissue-specific phenotypes in diseases associated with minor spliceosome inactivation. MIDB can be accessed at https://midb.pnb.uconn.edu .
Collapse
Affiliation(s)
- Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
| | - Katery C. Hyatt
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
- Institute of Systems Genomics, University of Connecticut, Storrs, CT 06269 USA
| |
Collapse
|
45
|
Ling Z, Brockmöller T, Baldwin IT, Xu S. Evolution of Alternative Splicing in Eudicots. FRONTIERS IN PLANT SCIENCE 2019; 10:707. [PMID: 31244865 PMCID: PMC6581728 DOI: 10.3389/fpls.2019.00707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/13/2019] [Indexed: 05/30/2023]
Abstract
Alternative pre-mRNA splicing (AS) is prevalent in plants and is involved in many interactions between plants and environmental stresses. However, the patterns and underlying mechanisms of AS evolution in plants remain unclear. By analyzing the transcriptomes of four eudicot species, we revealed that the divergence of AS is largely due to the gains and losses of AS events among orthologous genes. Furthermore, based on a subset of AS, in which AS can be directly associated with specific transcripts, we found that AS that generates transcripts containing premature termination codons (PTC), are likely more conserved than those that generate non-PTC containing transcripts. This suggests that AS coupled with nonsense-mediated decay (NMD) might play an important role in affecting mRNA levels post-transcriptionally. To understand the mechanisms underlying the divergence of AS, we analyzed the key determinants of AS using a machine learning approach. We found that the presence/absence of alternative splice site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5' donor site and 3' acceptor site among the studied species, suggesting a relatively conserved AS mechanism. The comparative analysis further demonstrated that variations of the identified AS determinants significantly contributed to the AS divergence among closely related species in both Solanaceae and Brassicaceae taxa. Together, these results provide detailed insights into the evolution of AS in plants.
Collapse
Affiliation(s)
- Zhihao Ling
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Ian T. Baldwin
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Shuqing Xu
- Plant Adaptation-in-action Group, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| |
Collapse
|
46
|
Jespersen DS, Schönherz AA, Due H, Bøgsted M, Sondergaard TE, Dybkær K. Expression of NOTCH3 exon 16 differentiates Diffuse Large B-cell Lymphoma into molecular subtypes and is associated with prognosis. Sci Rep 2019; 9:335. [PMID: 30674940 PMCID: PMC6344585 DOI: 10.1038/s41598-018-36680-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease with diverse clinical presentation and outcome. Bio-clinical prognostic models including oncogene expression and cell-of-origin phenotyping has been developed, however, approximately 30% of all patients still die from their disease, illustrating the need for additional prognostic biomarkers associating oncogenesis and phenotypic subclasses. Hence, we tested if alternative splice variations have biomarker potential. Initial alternative splicing analysis of human exon array from clinical DLBCL samples identified candidate genes. Experimental validation by ddPCR was performed in a DLBCL cohort classified into ABC/GCB subclasses, B-cell associated gene signatures (BAGS: naive, centroblast, centrocyte, memory, and plasmablast), and vincristine resistant gene signatures. Prognostic potential was assessed for aberrantly spliced transcripts. Thus, NOTCH3 was identified as alternatively spliced, with differential exon 16 depletion (−exon 16) between differentiation associated BAGS subtypes. Predicted vincristine resistant patients of the GCB subclass had significantly downregulated NOTCH3 −exon 16 transcript expression and tended to display adverse overall survival for R-CHOP treated patients. In conclusion, we have identified a specific alternatively spliced NOTCH3 event that differentiate molecular subtypes of DLBCL and display prognostic and predictive biomarker potential in GCB DLBCL.
Collapse
Affiliation(s)
| | - Anna A Schönherz
- Department of Hematology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Hanne Due
- Department of Hematology, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Hematology, Aalborg University Hospital, Aalborg, Denmark.,Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Karen Dybkær
- Department of Hematology, Aalborg University Hospital, Aalborg, Denmark. .,Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark. .,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
| |
Collapse
|
47
|
Coulson RL, Powell WT, Yasui DH, Dileep G, Resnick J, LaSalle JM. Prader-Willi locus Snord116 RNA processing requires an active endogenous allele and neuron-specific splicing by Rbfox3/NeuN. Hum Mol Genet 2018; 27:4051-4060. [PMID: 30124848 PMCID: PMC6240740 DOI: 10.1093/hmg/ddy296] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/10/2018] [Accepted: 07/03/2018] [Indexed: 12/18/2022] Open
Abstract
Prader-Willi syndrome (PWS), an imprinted neurodevelopmental disorder characterized by metabolic, sleep and neuropsychiatric features, is caused by the loss of paternal SNORD116, containing only non-coding RNAs (ncRNAs). The primary SNORD116 transcript is processed into small nucleolar RNAs (snoRNAs), which localize to nucleoli, and their spliced host gene 116HG, which is retained at its site of transcription. While functional complementation of the SNORD116 ncRNAs is a desirable goal for treating PWS, the mechanistic requirements of SNORD116 RNA processing are poorly understood. Here we developed and tested a novel transgenic mouse which ubiquitously expresses Snord116 on both a wild-type and a Snord116 paternal deletion (Snord116+/-) background. Interestingly, while the Snord116 transgene was ubiquitously expressed in multiple tissues, splicing of the transgene and production of snoRNAs was limited to brain tissues. Knockdown of Rbfox3, encoding neuron-specific splicing factor neuronal nuclei (NeuN) in Snord116+/--derived neurons, reduced splicing of the transgene in neurons. RNA fluorescence in situ hybridization for 116HG revealed a single significantly larger signal in transgenic mice, demonstrating colocalization of transgenic and endogenous 116HG RNAs. Similarly, significantly increased snoRNA levels were detected in transgenic neuronal nucleoli, indicating that transgenic Snord116 snoRNAs were effectively processed and localized. In contrast, neither transgenic 116HG nor snoRNAs were detectable in either non-neuronal tissues or Snord116+/- neurons. Together, these results demonstrate that exogenous expression and neuron-specific splicing of the Snord116 locus are insufficient to rescue the genetic deficiency of Snord116 paternal deletion. Elucidating the mechanisms regulating Snord116 processing and localization is essential to develop effective gene replacement therapies for PWS.
Collapse
Affiliation(s)
- Rochelle L Coulson
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Weston T Powell
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Dag H Yasui
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Gayathri Dileep
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - James Resnick
- Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Janine M LaSalle
- Microbiology and Immunology, Genome Center, and MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| |
Collapse
|
48
|
Redmond AK, Macqueen DJ, Dooley H. Phylotranscriptomics suggests the jawed vertebrate ancestor could generate diverse helper and regulatory T cell subsets. BMC Evol Biol 2018; 18:169. [PMID: 30442091 PMCID: PMC6238376 DOI: 10.1186/s12862-018-1290-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The cartilaginous fishes diverged from other jawed vertebrates ~ 450 million years ago (mya). Despite this key evolutionary position, the only high-quality cartilaginous fish genome available is for the elephant shark (Callorhinchus milii), a chimaera whose ancestors split from the elasmobranch lineage ~ 420 mya. Initial analysis of this resource led to proposals that key components of the cartilaginous fish adaptive immune system, most notably their array of T cell subsets, was primitive compared to mammals. This proposal is at odds with the robust, antigen-specific antibody responses reported in elasmobranchs following immunization. To explore this discrepancy, we generated a multi-tissue transcriptome for small-spotted catshark (Scyliorhinus canicula), a tractable elasmobranch model for functional studies. We searched this, and other newly available sequence datasets, for CD4+ T cell subset-defining genes, aiming to confirm the presence or absence of each subset in cartilaginous fishes. RESULTS We generated a new transcriptome based on a normalised, multi-tissue RNA pool, aiming to maximise representation of tissue-specific and lowly expressed genes. We utilized multiple transcriptomic datasets and assembly variants in phylogenetic reconstructions to unambiguously identify several T cell subset-specific molecules in cartilaginous fishes for the first time, including interleukins, interleukin receptors, and key transcription factors. Our results reveal the inability of standard phylogenetic reconstruction approaches to capture the site-specific evolutionary processes of fast-evolving immune genes but show that site-heterogeneous mixture models can adequately do so. CONCLUSIONS Our analyses reveal that cartilaginous fishes are capable of producing a range of CD4+ T cell subsets comparable to that of mammals. Further, that the key molecules required for the differentiation and functioning of these subsets existed in the jawed vertebrate ancestor. Additionally, we highlight the importance of considering phylogenetic diversity and, where possible, utilizing multiple datasets for individual species, to accurately infer gene presence or absence at higher taxonomic levels.
Collapse
Affiliation(s)
- Anthony K Redmond
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
- Centre for Genome-Enabled Biology & Medicine, University of Aberdeen, Aberdeen, AB24 2TZ, UK
- Present address: Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
| | - Daniel J Macqueen
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Helen Dooley
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Institute of Marine & Environmental Technology, 701 E Pratt St, Baltimore, MD21202, USA.
| |
Collapse
|
49
|
Identification of novel transcripts and peptides in developing murine lens. Sci Rep 2018; 8:11162. [PMID: 30042402 PMCID: PMC6057992 DOI: 10.1038/s41598-018-28727-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/19/2018] [Indexed: 01/09/2023] Open
Abstract
We previously investigated the transcriptome and proteome profiles of the murine ocular lens at six developmental time points including two embryonic (E15 and E18) and four postnatal time points (P0, P3, P6, and P9). Here, we extend our analyses to identify novel transcripts and peptides in developing mouse lens. We identified a total of 9,707 novel transcripts and 325 novel fusion genes in developing mouse lens. Additionally, we identified 13,281 novel alternative splicing (AS) events in mouse lens including 6,990 exon skipping (ES), 2,447 alternative 3' splice site (A3SS), 1,900 alternative 5' splice site (A5SS), 1,771 mutually exclusive exons (MXE), and 173 intron retention (IR). Finally, we integrated our OMIC (Transcriptome and Proteome) datasets identifying 20 novel peptides in mouse lens. All 20 peptides were validated through matching MS/MS spectra of synthetic peptides. To the best of our knowledge, this is the first report integrating OMIC datasets to identify novel peptides in developing murine lens.
Collapse
|
50
|
Wang K, Wu D, Zhang H, Das A, Basu M, Malin J, Cao K, Hannenhalli S. Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases. Sci Rep 2018; 8:10929. [PMID: 30026530 PMCID: PMC6053367 DOI: 10.1038/s41598-018-29086-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/23/2018] [Indexed: 12/31/2022] Open
Abstract
Alternative splicing contributes to phenotypic diversity at multiple biological scales, and its dysregulation is implicated in both ageing and age-associated diseases in human. Cross-tissue variability in splicing further complicates its links to age-associated phenotypes and elucidating these links requires a comprehensive map of age-associated splicing changes across multiple tissues. Here, we generate such a map by analyzing ~8500 RNA-seq samples across 48 tissues in 544 individuals. Employing a stringent model controlling for multiple confounders, we identify 49,869 tissue-specific age-associated splicing events of 7 distinct types. We find that genome-wide splicing profile is a better predictor of biological age than the gene and transcript expression profiles, and furthermore, age-associated splicing provides additional independent contribution to age-associated complex diseases. We show that the age-associated splicing changes may be explained, in part, by concomitant age-associated changes of the upstream splicing factors. Finally, we show that our splicing-based model of age can successfully predict the relative ages of cells in 8 of the 10 paired longitudinal data as well as in 2 sets of cell passage data. Our study presents the first systematic investigation of age-associated splicing changes across tissues, and further strengthening the links between age-associated splicing and age-associated diseases.
Collapse
Affiliation(s)
- Kun Wang
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Di Wu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Haoyue Zhang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Avinash Das
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Mahashweta Basu
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Justin Malin
- Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kan Cao
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA.
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
| |
Collapse
|