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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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Yamada M, Suzuki H, Watanabe A, Uehara T, Takenouchi T, Mizuno S, Kosaki K. Role of chimeric transcript formation in the pathogenesis of birth defects. Congenit Anom (Kyoto) 2021; 61:76-81. [PMID: 33118233 DOI: 10.1111/cga.12400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/30/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022]
Abstract
Chimeric transcripts are formed by chromosomal aberrations. Little is known about the role of chimeric transcripts in the pathogenesis of birth defects. We reanalyzed RNA-seq data in alignment map files from the peripheral blood of 56 patients in whom the diagnoses could not be confirmed by standard exome analysis and transcriptome analysis to screen for chimeric transcripts using a dedicated software, ChimPipe. Chimeric analysis led to a diagnosis in two of the 56 patients: (a) the first patient had a chimeric transcript spanning the causative gene ZEB2 and the GTDC1 gene in its neighboring locus. RNA-seq revealed reads spanning exon 5 of ZEB2 and exon 7 of GTDC1. Whole genome sequencing revealed a 436-kb deletion spanning intron 4 of ZEB2 and intron 7 of GTDC1 and the diagnosis of Mowat-Wilson syndrome was made. (b) The second patient had a chimeric transcript spanning the causative gene KCNK9 and the TRAPPC9 gene in its neighboring locus. RNA-seq revealed reads spanning exon 21 of TRAPPC9 and exon 1 of KCNK9. Whole genome sequencing revealed a 186-kb deletion spanning intron 20 of TRAPPC9 and intron 1 of KCNK9 in this patient. KCNK9 gene is a maternally expressed imprinted gene. The diagnosis of Birk-Barel syndrome was made. Thus, both patients had chimeric transcripts that were directly involved in the pathogenesis of the birth defects. The approach reported herein, of detecting chimeric transcripts from RNA-seq data, is unique in that the approach does not rely on any prior information on the presence of genomic deletion.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Akiko Watanabe
- Department of Pediatrics, Juntendo University Urayasu Hospital, Chiba, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.,Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Aichi, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Aichi, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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Subudhi PK, Garcia RS, Coronejo S, De Leon TB. A Novel Mutation of the NARROW LEAF 1 Gene Adversely Affects Plant Architecture in Rice ( Oryza sativa L.). Int J Mol Sci 2020; 21:ijms21218106. [PMID: 33143090 PMCID: PMC7672626 DOI: 10.3390/ijms21218106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/25/2020] [Accepted: 10/26/2020] [Indexed: 11/17/2022] Open
Abstract
Plant architecture is critical for enhancing the adaptability and productivity of crop plants. Mutants with an altered plant architecture allow researchers to elucidate the genetic network and the underlying mechanisms. In this study, we characterized a novel nal1 rice mutant with short height, small panicle, and narrow and thick deep green leaves that was identified from a cross between a rice cultivar and a weedy rice accession. Bulked segregant analysis coupled with genome re-sequencing and cosegregation analysis revealed that the overall mutant phenotype was caused by a 1395-bp deletion spanning over the last two exons including the transcriptional end site of the nal1 gene. This deletion resulted in chimeric transcripts involving nal1 and the adjacent gene, which were validated by a reference-guided assembly of transcripts followed by PCR amplification. A comparative transcriptome analysis of the mutant and the wild-type rice revealed 263 differentially expressed genes involved in cell division, cell expansion, photosynthesis, reproduction, and gibberellin (GA) and brassinosteroids (BR) signaling pathways, suggesting the important regulatory role of nal1. Our study indicated that nal1 controls plant architecture through the regulation of genes involved in the photosynthetic apparatus, cell cycle, and GA and BR signaling pathways.
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Affiliation(s)
- Prasanta K. Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (R.S.G.); (S.C.)
- Correspondence: ; Tel.: +1-225-578-1303
| | - Richard S. Garcia
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (R.S.G.); (S.C.)
| | - Sapphire Coronejo
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (R.S.G.); (S.C.)
| | - Teresa B. De Leon
- California Cooperative Rice Research Foundation, Inc., Biggs, CA 95917, USA;
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Miglio U, Berrino E, Panero M, Ferrero G, Coscujuela Tarrero L, Miano V, Dell'Aglio C, Sarotto I, Annaratone L, Marchiò C, Comoglio PM, De Bortoli M, Pasini B, Venesio T, Sapino A. The expression of LINE1-MET chimeric transcript identifies a subgroup of aggressive breast cancers. Int J Cancer 2018; 143:2838-2848. [PMID: 30144023 DOI: 10.1002/ijc.31831] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/17/2018] [Accepted: 08/15/2018] [Indexed: 01/03/2023]
Abstract
Demethylation of the long interspersed nuclear element (LINE-1; L1) antisense promoter can result in transcription of neighboring sequences as for the L1-MET transcript produced by the L1 placed in the second intron of MET. To define the role of L1-MET, we investigated the sequence and the transcription of L1-MET in vitro models and heterogeneous breast cancers, previously reported to show other L1-derived transcripts. L1-MET expressing cell lines were initially identified in silico and investigated for L1-MET promoter methylation, cDNA sequence and cell fraction mRNA. The transcriptional level of L1-MET and MET were then evaluated in breast specimens, including 9 cancer cell lines, 41 carcinomas of different subtypes, and 11 normal tissues. In addition to a L1-MET transcript ending at MET exon 21, six novel L1-MET splice variants were identified. Normal breast tissues were negative for the L1-MET expression, whereas the triple-negative breast cancer (TNBC) and the high-grade carcinomas were enriched with the L1-MET mRNA (p = 0.005 and p = 0.018, respectively). In cancer cells and tissues the L1-MET expression was associated with its promoter hypomethylation (ρ = -0.8 and -0.9, respectively). No correlation was found between L1-MET and MET mRNA although L1-MET expressing tumors with higher L1-MET/MET ratio were negative for the MET protein expression (p = 0.006). Besides providing the first identification and detailed description of L1-MET in breast cancer, we clearly demonstrate that higher levels of this transcript specifically recognize a subset of more aggressive carcinomas, mainly TNBC. We suggest the possible evaluation of L1-MET in the challenging diagnosis of early TNBCs.
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Affiliation(s)
- Umberto Miglio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Enrico Berrino
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Mara Panero
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy.,Department of Computer Science, University of Turin, Turin, Italy
| | | | - Valentina Miano
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Carmine Dell'Aglio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Ivana Sarotto
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paolo M Comoglio
- Molecular Therapeutics and Exploratory Research Laboratory, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Michele De Bortoli
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Tiziana Venesio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Anna Sapino
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
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Sugimoto T, Tomita A, Abe A, Iriyama C, Kiyoi H, Naoe T. Chimeric antisense RNA derived from chromosomal translocation modulates target gene expression. Haematologica 2012; 97:1278-80. [PMID: 22491739 PMCID: PMC3409828 DOI: 10.3324/haematol.2011.057869] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Takumi Sugimoto
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Hematology and Oncology, Toyohashi Municipal Hospital, Toyohashi, Aichi, Japan
| | - Akihiro Tomita
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Akihiro Abe
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Department of Hematology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Chisako Iriyama
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Tomoki Naoe
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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Lai J, Lehman ML, Dinger ME, Hendy SC, Mercer TR, Seim I, Lawrence MG, Mattick JS, Clements JA, Nelson CC. A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells. RNA 2010; 16:1156-1166. [PMID: 20406994 PMCID: PMC2874168 DOI: 10.1261/rna.2019810] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2009] [Accepted: 02/18/2010] [Indexed: 05/29/2023]
Abstract
In humans, more than 30,000 chimeric transcripts originating from 23,686 genes have been identified. The mechanisms and association of chimeric transcripts arising from chromosomal rearrangements with cancer are well established, but much remains unknown regarding the biogenesis and importance of other chimeric transcripts that arise from nongenomic alterations. Recently, a SLC45A3-ELK4 chimera has been shown to be androgen-regulated, and is overexpressed in metastatic or high-grade prostate tumors relative to local prostate cancers. Here, we characterize the expression of a KLK4 cis sense-antisense chimeric transcript, and show other examples in prostate cancer. Using non-protein-coding microarray analyses, we initially identified an androgen-regulated antisense transcript within the 3' untranslated region of the KLK4 gene in LNCaP cells. The KLK4 cis-NAT was validated by strand-specific linker-mediated RT-PCR and Northern blotting. Characterization of the KLK4 cis-NAT by 5' and 3' rapid amplification of cDNA ends (RACE) revealed that this transcript forms multiple fusions with the KLK4 sense transcript. Lack of KLK4 antisense promoter activity using reporter assays suggests that these transcripts are unlikely to arise from a trans-splicing mechanism. 5' RACE and analyses of deep sequencing data from LNCaP cells treated +/-androgens revealed six high-confidence sense-antisense chimeras of which three were supported by the cDNA databases. In this study, we have shown complex gene expression at the KLK4 locus that might be a hallmark of cis sense-antisense chimeric transcription.
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Affiliation(s)
- John Lai
- Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology and Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
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