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Chang S, Torii S, Inamo J, Ishikawa K, Kochi Y, Shimizu S. Uncovering the Localization and Function of a Novel Read-Through Transcript ' TOMM40-APOE'. Cells 2023; 13:69. [PMID: 38201273 PMCID: PMC10778128 DOI: 10.3390/cells13010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Recent advancements in genome analysis technology have revealed the presence of read-through transcripts in which transcription continues by skipping the polyA signal. We here identified and characterized a new read-through transcript, TOMM40-APOE. With cDNA amplification from THP-1 cells, the TOMM40-APOE3 product was successfully generated. We also generated TOMM40-APOE4, another isoform, by introducing point mutations. Notably, while APOE3 and APOE4 exhibited extracellular secretion, both TOMM40-APOE3 and TOMM40-APOE4 were localized exclusively to the mitochondria. But functionally, they did not affect mitochondrial membrane potential. Cell death induction studies illustrated increased cell death with TOMM40-APOE3 and TOMM40-APOE4, and we did not find any difference in cellular function between the two isoforms. These findings indicated that the new mitochondrial protein TOMM40-APOE has cell toxic ability.
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Affiliation(s)
- Shichen Chang
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan (S.T.)
- Department of Personalized Genomic Medicine for Health, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Satoru Torii
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan (S.T.)
| | - Jun Inamo
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kinya Ishikawa
- Department of Personalized Genomic Medicine for Health, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Shigeomi Shimizu
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan (S.T.)
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Garcia BCB, Mukai Y, Tomonaga K, Horie M. The hidden diversity of ancient bornaviral sequences from X and P genes in vertebrate genomes. Virus Evol 2023; 9:vead038. [PMID: 37360682 PMCID: PMC10288550 DOI: 10.1093/ve/vead038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/10/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
Endogenous bornavirus-like elements (EBLs) are heritable sequences derived from bornaviruses in vertebrate genomes that originate from transcripts of ancient bornaviruses. EBLs have been detected using sequence similarity searches such as tBLASTn, whose technical limitations may hinder the detection of EBLs derived from small and/or rapidly evolving viral X and P genes. Indeed, no EBLs derived from the X and P genes of orthobornaviruses have been detected to date in vertebrate genomes. Here, we aimed to develop a novel strategy to detect such 'hidden' EBLs. To this aim, we focused on the 1.9-kb read-through transcript of orthobornaviruses, which encodes a well-conserved N gene and small and rapidly evolving X and P genes. We show a series of evidence supporting the existence of EBLs derived from orthobornaviral X and P genes (EBLX/Ps) in mammalian genomes. Furthermore, we found that an EBLX/P is expressed as a fusion transcript with the cellular gene, ZNF451, which potentially encodes the ZNF451/EBLP fusion protein in miniopterid bat cells. This study contributes to a deeper understanding of ancient bornaviruses and co-evolution between bornaviruses and their hosts. Furthermore, our data suggest that endogenous viral elements are more abundant than those previously appreciated using BLAST searches alone, and further studies are required to understand ancient viruses more accurately.
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Affiliation(s)
- Bea Clarise B Garcia
- Laboratory of Veterinary Microbiology, Graduate School of Veterinary Science, Osaka Metropolitan University, 1-58 Rinku Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Yahiro Mukai
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogo-in, Sakyo, Kyoto 606-8507, Japan
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, 53 Kawahara-cho, Shogo-in, Sakyo, Kyoto 606-8507, Japan
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogo-in, Sakyo, Kyoto 606-8507, Japan
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, 53 Kawahara-cho, Shogo-in, Sakyo, Kyoto 606-8507, Japan
- Department of Molecular Virology, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogo-in, Sakyo, Kyoto 606-8507, Japan
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Shirai M, Nara T, Takahashi H, Takayama K, Chen Y, Hirose Y, Fujii M, Awazu A, Shimoda N, Kikuchi Y. Identification of aberrant transcription termination at specific gene loci with DNA hypomethylated transcription termination sites caused by DNA methyltransferase deficiency. Gene 2022; 97:139-152. [PMID: 35718462 DOI: 10.1266/ggs.21-00092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
CpG methylation of genomic DNA is a well-known repressive epigenetic marker in eukaryotic transcription, and DNA methylation of promoter regions is correlated with gene silencing. In contrast to the promoter regions, the function of DNA methylation during transcription termination remains to be elucidated. A recent study revealed that mouse DNA methyltransferase 3a (Dnmt3a) mainly functions in de novo methylation in the promoter and gene body regions, including transcription termination sites (TTSs), during development. To investigate the relationship between DNA methylation overlapping the TTSs and transcription termination, we performed bioinformatics analysis using six pre-existing Dnmt-/- mouse cell datasets: four types of neurons (three Dnmt3a-/- and one Dnmt1-/- mutants) and two types of embryonic fibroblasts (MEFs) (Dnmt3a-/- and Dnmt3b-/- mutants). Combined analyses using methylome and transcriptome data revealed that read counts downstream of hypomethylated TTSs were increased in three types of neurons (two Dnmt3a-/- and one Dnmt1-/- mutants). Among these, an increase in chimeric transcripts downstream of the TTSs was observed in Dnmt3a-/- mature olfactory sensory neurons and Dnmt3a-/- agouti-related peptide (protein)-producing neurons, thereby indicating that read-through occurs in hypomethylated TTSs at specific gene loci in these two mutants. Conversely, in Dnmt3a-/- MEFs, we detected reductions in read counts downstream of hypomethylated TTSs. These results indicate that the hypomethylation of TTSs can both positively and negatively regulate transcription termination, dependent on Dnmt and cell types. This study is the first to identify the aberrant termination of transcription at specific gene loci with DNA hypomethylated TTSs attributable to Dnmt deficiency.
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Affiliation(s)
- Masaki Shirai
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima
| | - Takuya Nara
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima
| | - Haruko Takahashi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima
| | - Kazuya Takayama
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima
| | - Yuan Chen
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima
| | - Yudai Hirose
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima
| | - Masashi Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima
| | - Nobuyoshi Shimoda
- Laboratory of Molecular Analysis, Core Facilities, National Center for Geriatrics and Gerontology
| | - Yutaka Kikuchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima
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