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Pasquesi GIM, Allen H, Ivancevic A, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen L, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB. Regulation of human interferon signaling by transposon exonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557241. [PMID: 37745311 PMCID: PMC10515820 DOI: 10.1101/2023.09.11.557241] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Innate immune signaling is essential for clearing pathogens and damaged cells, and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues, and functions as a decoy receptor that potently inhibits interferon signaling including in cells infected with SARS-CoV-2. Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.
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Affiliation(s)
- Giulia Irene Maria Pasquesi
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303
| | - Holly Allen
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Atma Ivancevic
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Olivia Joyner
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - David M. Simpson
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Keala Gapin
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Isabella Horton
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Lily Nguyen
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Qing Yang
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109
| | - Cody J. Warren
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- The Ohio State University College of Veterinary Medicine, Columbus, OH, 43210
| | - Liliana D. Florea
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
| | - Benjamin G. Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Mario L. Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Sara L. Sawyer
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Edward B. Chuong
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303
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Darby MM, Leek JT, Langmead B, Yolken RH, Sabunciyan S. Widespread splicing of repetitive element loci into coding regions of gene transcripts. Hum Mol Genet 2018; 25:4962-4982. [PMID: 28171598 DOI: 10.1093/hmg/ddw321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/22/2016] [Accepted: 09/14/2016] [Indexed: 11/14/2022] Open
Abstract
We performed a thorough characterization of expressed repetitive element loci (RE) in the human orbitofrontal cortex (OFC) using directional RNA sequencing data. Considering only sequencing reads that map uniquely onto the human genome, we discovered that the overwhelming majority of intronic and exonic RE are expressed in the same orientation as the gene in which they reside. Our mapping approach enabled the identification of novel differentially expressed RE transcripts between the OFC and peripheral blood lymphocytes. Further analysis revealed that RE are extensively spliced into coding regions of gene transcripts yielding thousands of novel mRNA variants with altered coding potential. Lower frequency splicing of RE into untranslated regions of gene transcripts was also observed. The same pattern of RE splicing in the brain was also detected for Drosophila, zebrafish, mouse, rat, dog and rabbit. RE splicing occurs largely at canonical GT-AG splice junctions with LINE and SINE elements forming the most RE splice junctions in the human OFC. This type of splicing usually gives rise to a minor splice variant of the endogenous gene and in silico analysis suggests that RE splicing has the potential to introduce novel open reading frames. Reanalysis of previously published sequencing data performed in the mouse cerebellum revealed that thousands of RE splice variants are associated with translating ribosomes. Our results demonstrate that RE expression is more complex than previously envisioned and raise the possibility that RE splicing might generate functional protein isoforms.
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Affiliation(s)
- Miranda M Darby
- Department of Pediatrics, Johns Hopkins University, Baltimore, USA
| | - Jeffrey T Leek
- Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, USA
| | - Ben Langmead
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Center for Computational Biology and Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Robert H Yolken
- Department of Pediatrics, Johns Hopkins University, Baltimore, USA
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De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin. Sci Rep 2016; 6:28199. [PMID: 27618997 PMCID: PMC5020319 DOI: 10.1038/srep28199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 06/01/2016] [Indexed: 01/06/2023] Open
Abstract
Pangolins are scale-covered mammals, containing eight endangered species. Maintaining pangolins in captivity is a significant challenge, in part because little is known about their genetics. Here we provide the first large-scale sequencing of the critically endangered Manis javanica transcriptomes from eight different organs using Illumina HiSeq technology, yielding ~75 Giga bases and 89,754 unigenes. We found some unigenes involved in the insect hormone biosynthesis pathway and also 747 lipids metabolism-related unigenes that may be insightful to understand the lipid metabolism system in pangolins. Comparative analysis between M. javanica and other mammals revealed many pangolin-specific genes significantly over-represented in stress-related processes, cell proliferation and external stimulus, probably reflecting the traits and adaptations of the analyzed pregnant female M. javanica. Our study provides an invaluable resource for future functional works that may be highly relevant for the conservation of pangolins.
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Warren IA, Naville M, Chalopin D, Levin P, Berger CS, Galiana D, Volff JN. Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates. Chromosome Res 2016; 23:505-31. [PMID: 26395902 DOI: 10.1007/s10577-015-9493-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.
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Affiliation(s)
- Ian A Warren
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.,Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA
| | - Perrine Levin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Chloé Suzanne Berger
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Delphine Galiana
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.
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Peng G, Dan W, Jun W, Junjun Y, Tong R, Baoli Z, Yang X. Transcriptome profiling of the cancer and adjacent nontumor tissues from cervical squamous cell carcinoma patients by RNA sequencing. Tumour Biol 2015; 36:3309-17. [PMID: 25586346 DOI: 10.1007/s13277-014-2963-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/08/2014] [Indexed: 01/28/2023] Open
Abstract
Cervical cancer is the third most common cancer and the fourth leading cause of cancer deaths among women in the world. The discovery of vital diagnostic and therapeutic markers against cervical squamous cell carcinoma (CSCC) would broaden our understanding on the molecular basis of CSCC. In this study, we thoroughly analyzed the transcriptome of CSCC and matched adjacent nontumor (ATN) tissue. RNA sequencing was performed to screen the differentially expressed genes (DEGs) of three pairs of CSCC and ATN tissues. Functional enrichment analysis was used to uncover the biological functions of DEGs. Protein interaction network was carried out to reveal interaction of DEGs. Quantitative real-time PCR was conducted to validate the expression of DEGs. Immunohistochemistry was used to detect the relationship between clinicopathological parameters of CSCC and DEGs. There were a total of 347 significantly common DEGs in the three paired examples, including 104 consistent upregulated and 148 consistent downregulated DEGs. The 347 DEGs were categorized into 73 functional categories by Gene Ontology (GO) analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis suggested six significantly signal pathways. The protein interaction network uncovered three important DEGs, including retinol dehydrogenase 12 (RDH12), ubiquitin D (UBD), and serum amyloid A1 (SAA1). We found that RDH12 expression was decreased in 74.5 % of CSCC tissues. RDH12 expression was negatively associated with tumor size and depth of cervical invasion. The UBD was overexpressed in 61.7 % of CSCC tissues and was positively related with tumor size and lymphatic metastasis. The SAA1 protein was overexpressed in 57.4 % of CSCC tissues and was positively related with clinicopathological parameters of tumor size, lymphatic metastasis, and depth of cervical invasion. The RDH12, UBD, and SAA1 genes might participate in the progression of CSCC.
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Affiliation(s)
- Guo Peng
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, No. 1 Shuai Fu Yuan, Wang Fu Jing Street, Beijing, 100730, People's Republic of China
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