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Singh S, Shi X, Haddox S, Elfman J, Ahmad SB, Lynch S, Manley T, Piczak C, Phung C, Sun Y, Sharma A, Li H. RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data. Brief Bioinform 2024; 25:bbae251. [PMID: 38796690 PMCID: PMC11128028 DOI: 10.1093/bib/bbae251] [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: 11/15/2023] [Revised: 03/30/2024] [Accepted: 05/09/2024] [Indexed: 05/28/2024] Open
Abstract
Read-through chimeric RNAs are being recognized as a means to expand the functional transcriptome and contribute to cancer tumorigenesis when mis-regulated. However, current software tools often fail to predict them. We have developed RTCpredictor, utilizing a fast ripgrep tool to search for all possible exon-exon combinations of parental gene pairs. We also added exonic variants allowing searches containing common SNPs. To our knowledge, it is the first read-through chimeric RNA specific prediction method that also provides breakpoint coordinates. Compared with 10 other popular tools, RTCpredictor achieved high sensitivity on a simulated and three real datasets. In addition, RTCpredictor has less memory requirements and faster execution time, making it ideal for applying on large datasets.
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Affiliation(s)
- Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Xinrui Shi
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Justin Elfman
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Syed Basil Ahmad
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Sarah Lynch
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Tommy Manley
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Claire Piczak
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Christopher Phung
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Yunan Sun
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Aadi Sharma
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, United States
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2
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Casuso A, Benavente BP, Leal Y, Carrera-Naipil C, Valenzuela-Muñoz V, Gallardo-Escárate C. Sex-Biased Transcription Expression of Vitellogenins Reveals Fusion Gene and MicroRNA Regulation in the Sea Louse Caligus rogercresseyi. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:243-260. [PMID: 38294574 DOI: 10.1007/s10126-024-10291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
The caligid ectoparasite, Caligus rogercresseyi, is one of the main concerns in the Chilean salmon industry. The molecular mechanisms displayed by the parasite during the reproductive process represent an opportunity for developing novel control strategies. Vitellogenin is a multifunctional protein recognized as a critical player in several crustaceans' biological processes, including reproduction, embryonic development, and immune response. This study aimed to characterize the C. rogercresseyi vitellogenins, including discovering novel transcripts and regulatory mechanisms associated with microRNAs. Herein, vitellogenin genes were identified by homology analysis using the reference sea louse genome, transcriptome database, and arthropods vitellogenin-protein database. The validation of expression transcripts was conducted by RNA nanopore sequencing technology. Moreover, fusion gene profiling, miRNA target analysis, and functional validation were performed using luciferase assay. Six putative vitellogenin genes were identified in the C. rogercresseyi genome with high homology with other copepods vitellogenins. Furthermore, miR-996 showed a putative role in regulating the Cr_Vitellogenin1 gene, which is highly expressed in females. Moreover, vitellogenin-fusion genes were identified in adult stages and highly regulated in males, demonstrating sex-related expression patterns. In females, the identified fusion genes merged with several non-vitellogenin genes involved in biological processes of ribosome assembly, BMP signaling pathway, and biosynthetic processes. This study reports the genome array of vitellogenins in C. rogercresseyi for the first time, revealing the putative role of fusion genes and miRNA regulation in sea lice biology.
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Affiliation(s)
- Antonio Casuso
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Bárbara P Benavente
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Yeny Leal
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Crisleri Carrera-Naipil
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile.
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile.
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3
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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] [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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4
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Shen Y, Jiang H, Canario AV, Chen T, Liu Y, Yang G, Meng X, Zhao J, Chen X. The fusion gene hsf5-rnf43 in Nile tilapia: A potential regulator in the maintenance of testis function and sexual differentiation. iScience 2023; 26:108284. [PMID: 38026183 PMCID: PMC10679895 DOI: 10.1016/j.isci.2023.108284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/27/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
We identified that the genes heat shock transcription factor 5 (hsf5) and ring finger protein 43 (rnf43) happened fusion in Nile tilapia (Oreochromis niloticus), called hsf5-rnf43, and provided the characteristic and functional analysis of hsf5-rnf43 gene in fish for the first time. Analysis of spatiotemporal expression showed that hsf5-rnf43 was specifically expressed in the testis and located in primary spermatocytes of adult Nile tilapia and gradually increased during testis development from 5 to 180 days after hatching. We also found DNA methylation regulated sex-biased expression of hsf5-rnf43 in the early development of Nile tilapia, and was affected by high temperature during the thermosensitive period of Nile tilapia sex differentiation. Therefore, we first reported that the fusion gene hsf5-rnf43 was sex-biased expressed in the testis regulated by DNA methylation and affected by high temperature, which may be involved in the maintenance of testis function and sex differentiation of Nile tilapia.
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Affiliation(s)
- Yawei Shen
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Hewei Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Adelino V.M. Canario
- CCMAR/CIMAR Centre for Marine Sciences, University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal
| | - Tiantian Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yufei Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Guokun Yang
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
| | - Xiaolin Meng
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
| | - Jinliang Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaowu Chen
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
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5
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Sridhar A, More AS, Jadhav AR, Patil K, Mavlankar A, Dixit VM, Bapat SA. Pattern recognition in the landscape of seemingly random chimeric transcripts. Comput Struct Biotechnol J 2023; 21:5153-5164. [PMID: 37920814 PMCID: PMC10618115 DOI: 10.1016/j.csbj.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
The molecular and functional diversity generated by chimeric transcripts (CTs) that are derived from two genes is indicated to contribute to tumor cell survival. Several gaps yet exist. The present research is a systematic study of the spectrum of CTs identified in RNA sequencing datasets of 160 ovarian cancer samples in the The Cancer Genome Atlas (TCGA) (https://portal.gdc.cancer.gov). Structural annotation revealed complexities emerging from chromosomal localization of partner genes, differential splicing and inclusion of regulatory, untranslated regions. Identification of phenotype-specific associations further resolved a dynamically modulated mesenchymal signature during transformation. On an evolutionary background, protein-coding CTs were indicated to be highly conserved, while non-coding CTs may have evolved more recently. We also realized that the current premise postulating structural alterations or neighbouring gene readthrough generating CTs is not valid in instances wherein the parental genes are genomically distanced. In addressing this lacuna, we identified the essentiality of specific spatiotemporal arrangements mediated gene proximities in 3D space for the generation of CTs. All these features together suggest non-random mechanisms towards increasing the molecular diversity in a cell through chimera formation either in parallel or with cross-talks with the indigenous regulatory network.
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Affiliation(s)
- Aksheetha Sridhar
- Open Health Systems Laboratory, 9601 Medical Centre Drive, Rockville, MD 20850, US
| | - Ankita S. More
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Amruta R. Jadhav
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Komal Patil
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Anuj Mavlankar
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Vaishnavi M. Dixit
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Sharmila A. Bapat
- Open Health Systems Laboratory, 9601 Medical Centre Drive, Rockville, MD 20850, US
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411 007, Maharashtra, India
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6
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Ma H, Wang M, Zhang YE, Tan S. The power of "controllers": Transposon-mediated duplicated genes evolve towards neofunctionalization. J Genet Genomics 2023; 50:462-472. [PMID: 37068629 DOI: 10.1016/j.jgg.2023.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Since the discovery of the first transposon by Dr. Barbara McClintock, the prevalence and diversity of transposable elements (TEs) have been gradually recognized. As fundamental genetic components, TEs drive organismal evolution not only by contributing functional sequences (e.g., regulatory elements or "controllers" as phrased by Dr. McClintock) but also by shuffling genomic sequences. In the latter respect, TE-mediated gene duplications have contributed to the origination of new genes and attracted extensive interest. In response to the development of this field, we herein attempt to provide an overview of TE-mediated duplication by focusing on common rules emerging across duplications generated by different TE types. Specifically, despite the huge divergence of transposition machinery across TEs, we identify three common features of various TE-mediated duplication mechanisms, including end bypass, template switching, and recurrent transposition. These three features lead to one common functional outcome, namely, TE-mediated duplicates tend to be subjected to exon shuffling and neofunctionalization. Therefore, the intrinsic properties of the mutational mechanism constrain the evolutionary trajectories of these duplicates. We finally discuss the future of this field including an in-depth characterization of both the duplication mechanisms and functions of TE-mediated duplicates.
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Affiliation(s)
- Huijing Ma
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengxia Wang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Chinese Institute for Brain Research, Beijing 102206, China.
| | - Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Araki S, Ohori M, Yugami M. Targeting pre-mRNA splicing in cancers: roles, inhibitors, and therapeutic opportunities. Front Oncol 2023; 13:1152087. [PMID: 37342192 PMCID: PMC10277747 DOI: 10.3389/fonc.2023.1152087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/09/2023] [Indexed: 06/22/2023] Open
Abstract
Accumulating evidence has indicated that pre-mRNA splicing plays critical roles in a variety of physiological processes, including development of multiple diseases. In particular, alternative splicing is profoundly involved in cancer progression through abnormal expression or mutation of splicing factors. Small-molecule splicing modulators have recently attracted considerable attention as a novel class of cancer therapeutics, and several splicing modulators are currently being developed for the treatment of patients with various cancers and are in the clinical trial stage. Novel molecular mechanisms modulating alternative splicing have proven to be effective for treating cancer cells resistant to conventional anticancer drugs. Furthermore, molecular mechanism-based combination strategies and patient stratification strategies for cancer treatment targeting pre-mRNA splicing must be considered for cancer therapy in the future. This review summarizes recent progress in the relationship between druggable splicing-related molecules and cancer, highlights small-molecule splicing modulators, and discusses future perspectives of splicing modulation for personalized and combination therapies in cancer treatment.
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Kosik P, Skorvaga M, Belyaev I. Preleukemic Fusion Genes Induced via Ionizing Radiation. Int J Mol Sci 2023; 24:ijms24076580. [PMID: 37047553 PMCID: PMC10095576 DOI: 10.3390/ijms24076580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Although the prevalence of leukemia is increasing, the agents responsible for this increase are not definitely known. While ionizing radiation (IR) was classified as a group one carcinogen by the IARC, the IR-induced cancers, including leukemia, are indistinguishable from those that are caused by other factors, so the risk estimation relies on epidemiological data. Several epidemiological studies on atomic bomb survivors and persons undergoing IR exposure during medical investigations or radiotherapy showed an association between radiation and leukemia. IR is also known to induce chromosomal translocations. Specific chromosomal translocations resulting in preleukemic fusion genes (PFGs) are generally accepted to be the first hit in the onset of many leukemias. Several studies indicated that incidence of PFGs in healthy newborns is up to 100-times higher than childhood leukemia with the same chromosomal aberrations. Because of this fact, it has been suggested that PFGs are not able to induce leukemia alone, but secondary mutations are necessary. PFGs also have to occur in specific cell populations of hematopoetic stem cells with higher leukemogenic potential. In this review, we describe the connection between IR, PFGs, and cancer, focusing on recurrent PFGs where an association with IR has been established.
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Affiliation(s)
- Pavol Kosik
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Milan Skorvaga
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Igor Belyaev
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
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9
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Singh S, Shi X, Ahmad SB, Manley T, Piczak C, Phung C, Sun Y, Lynch S, Sharma A, Li H. RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526869. [PMID: 36778443 PMCID: PMC9915620 DOI: 10.1101/2023.02.02.526869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Read-through chimeric RNAs are gaining attention in cancer and other research fields, yet current tools often fail in predicting them. We have thus developed the first read-through chimeric RNA specific prediction method, RTCpredictor, utilizing a fast ripgrep algorithm to search for all possible exon-exon combinations of parental gene pairs. Compared with other ten popular tools, RTCpredictor achieved top performance on both simulated and real datasets. We randomly selected up to 30 candidate read-through chimeras predicted from each software method and experimentally validated a total of 109 read-throughs and on this set, RTCpredictor outperformed all the other methods. In addition, RTCpredictor ( https://github.com/sandybioteck/RTCpredictor ) has less memory requirements and faster execution time.
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10
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Knowing when to stop: Transcription termination on protein-coding genes by eukaryotic RNAPII. Mol Cell 2023; 83:404-415. [PMID: 36634677 PMCID: PMC7614299 DOI: 10.1016/j.molcel.2022.12.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
Gene expression is controlled in a dynamic and regulated manner to allow for the consistent and steady expression of some proteins as well as the rapidly changing production of other proteins. Transcription initiation has been a major focus of study because it is highly regulated. However, termination of transcription also plays an important role in controlling gene expression. Transcription termination on protein-coding genes is intimately linked with 3' end cleavage and polyadenylation of transcripts, and it generally results in the production of a mature mRNA that is exported from the nucleus. Termination on many non-coding genes can also result in the production of a mature transcript. Termination is dynamically regulated-premature termination and transcription readthrough occur in response to a number of cellular signals, and these can have varied consequences on gene expression. Here, we review eukaryotic transcription termination by RNA polymerase II (RNAPII), focusing on protein-coding genes.
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Kiyose H, Nakagawa H, Ono A, Aikata H, Ueno M, Hayami S, Yamaue H, Chayama K, Shimada M, Wong JH, Fujimoto A. Comprehensive analysis of full-length transcripts reveals novel splicing abnormalities and oncogenic transcripts in liver cancer. PLoS Genet 2022; 18:e1010342. [PMID: 35926060 PMCID: PMC9380957 DOI: 10.1371/journal.pgen.1010342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/16/2022] [Accepted: 07/14/2022] [Indexed: 12/24/2022] Open
Abstract
Genes generate transcripts of various functions by alternative splicing. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used, leaving full-length transcripts unobserved directly. Although long-reads sequencing technologies would enable the sequencing of full-length transcripts, the data analysis is difficult. In this study, we developed an analysis pipeline named SPLICE and analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC) and matched non-cancerous livers with an Oxford Nanopore sequencer. Our analysis detected 46,663 transcripts from the protein-coding genes in the HCCs and the matched non-cancerous livers, of which 5,366 (11.5%) were novel. A comparison of expression levels identified 9,933 differentially expressed transcripts (DETs) in 4,744 genes. Interestingly, 746 genes with DETs, including the LINE1-MET transcript, were not found by a gene-level analysis. We also found that fusion transcripts of transposable elements and hepatitis B virus (HBV) were overexpressed in HCCs. In vitro experiments on DETs showed that LINE1-MET and HBV-human transposable elements promoted cell growth. Furthermore, fusion gene detection showed novel recurrent fusion events that were not detected in the short-reads. These results suggest the efficiency of full-length transcriptome studies and the importance of splicing variants in carcinogenesis. Genes generate transcripts of various functions by alternative splicing. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used, leaving full-length transcripts unobserved directly. In this study, we developed an analysis pipeline named SPLICE for long-read transcriptome sequencing and analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC), and matched non-cancerous livers with an Oxford Nanopore sequencer. Our analysis detected 5,366 novel transcripts and 9,933 differentially expressed transcripts in 4,744 genes between HCCs and non-cancerous livers. An analysis of hepatitis B virus (HBV) transcripts showed that fusion transcripts of the HBV gene and human transposable elements were overexpressed in HBV-infected HCCs. We also identified fusion genes that were not found in the short-reads. These results suggest that long-reads sequencing technologies provide a fuller understanding of cancer transcripts and that our method contributes to the analysis of transcriptome sequences by such technologies.
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Affiliation(s)
- Hiroki Kiyose
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Ono
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masaki Ueno
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Shinya Hayami
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Hiroki Yamaue
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Kazuaki Chayama
- Collaborative Research Laboratory of Medical Innovation, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Research Center for Hepatology and Gastroenterology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mihoko Shimada
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jing Hao Wong
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail:
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12
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Song L, Yu M, Jin R, Gu M, Wang Z, Hou D, Xu S, Wang J, Ma T. Long-Read Sequencing Annotation of the Transcriptome in DNA-PK Inactivated Cells. Front Oncol 2022; 12:941638. [PMID: 35992789 PMCID: PMC9382581 DOI: 10.3389/fonc.2022.941638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/23/2022] [Indexed: 12/22/2022] Open
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) with a Ku70/Ku80 heterodimer constitutes the intact DNA-PK kinase, which is an upstream component of the DNA repair machinery that signals the DNA damage, orchestrates the DNA repair, and serves to maintain genome integrity. Beyond its role in DNA damage repair, the DNA-PK kinase is also implicated in transcriptional regulation and RNA metabolism, with an illuminated impact on tumor progression and therapeutic responses. However, the efforts to identify DNA-PK regulated transcriptomes are limited by short-read sequencing to resolve the full complexity of the transcriptome. Therefore, we leveraged the PacBio Single Molecule, Real-Time (SMRT) Sequencing platform to study the transcriptome after DNA-PK inactivation to further underscore the importance of its role in diseases. Our analysis revealed additional novel transcriptome and complex gene structures in the DNA-PK inactivated cells, identifying 8,355 high-confidence new isoforms from 3,197 annotated genes and 523 novel genes. Among them, 380 lncRNAs were identified. We validated these findings using computational approaches and confirmatory transcript quantification with short-read sequencing. Several novel isoforms representing distinct splicing events have been validated through PCR experiments. Our analyses provide novel insights into DNA-PK function in transcriptome regulation and RNA metabolism.
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Affiliation(s)
- Liwei Song
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Mengjun Yu
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Renjing Jin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Meng Gu
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Ziyu Wang
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Dailun Hou
- Department of Radiology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shaofa Xu
- Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- *Correspondence: Shaofa Xu, ; Jinghui Wang, ; Teng Ma,
| | - Jinghui Wang
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- *Correspondence: Shaofa Xu, ; Jinghui Wang, ; Teng Ma,
| | - Teng Ma
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- *Correspondence: Shaofa Xu, ; Jinghui Wang, ; Teng Ma,
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13
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Zhang L, Wang D, Han X, Guo X, Cao Y, Xia Y, Gao D. Novel read-through fusion transcript Bcl2l2-Pabpn1 in glioblastoma cells. J Cell Mol Med 2022; 26:4686-4697. [PMID: 35894779 PMCID: PMC9443946 DOI: 10.1111/jcmm.17481] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/11/2022] [Accepted: 06/19/2022] [Indexed: 11/29/2022] Open
Abstract
Read‐through fusion transcripts have recently been identified as chimeric RNAs and have since been linked to tumour growth in some cases. Many fusion genes generated by chromosomal rearrangements have been described in glioblastoma. However, read‐through fusion transcripts between neighbouring genes in glioblastoma remain unexplored. We performed paired‐end RNA‐seq of rat C6 glioma cells and normal cells and discovered a read‐through fusion transcript Bcl2l2‐Pabpn1 in which exon 3 of Bcl‐2‐like protein 2 (Bcl2l2) fused to exon 2 of Polyadenylate‐binding protein 1 (Pabpn1). This fusion transcript was found in both human glioblastoma and normal cells. Unlike other fusions reported in glioblastoma, Bcl2l2‐Pabpn1 appeared to result from RNA processing rather than genomic rearrangement. Bcl2l2‐Pabpn1 fusion transcript encoded a fusion protein with BH4, BCL and RRM domains. Functionally, Bcl2l2‐Pabpn1 knockdown by targeting its fusion junction decreased its expression, and suppressed cell proliferation, migration and invasion in vitro. Mechanistically, Bcl2l2‐Pabpn1 blocked Bax activity and activated PI3K/AKT pathway to promote glioblastoma progression. Together, our work characterized a glioblastoma‐associated Bcl2l2‐Pabpn1 fusion transcript shared by humans and rats.
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Affiliation(s)
- Lin Zhang
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China.,School of Nursing, Xuzhou Medical University, Xuzhou, China
| | - Dan Wang
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Xiao Han
- Nanjing Medical University, Nanjing, China
| | - Xiaoxiao Guo
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Yuanyuan Cao
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Ying Xia
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China
| | - Dianshuai Gao
- Department of Neurobiology and Anatomy, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, China
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14
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CircRNA: An emerging star in the progression of glioma. Biomed Pharmacother 2022; 151:113150. [PMID: 35623170 DOI: 10.1016/j.biopha.2022.113150] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/12/2022] [Accepted: 05/15/2022] [Indexed: 11/21/2022] Open
Abstract
Circular RNAs (circRNAs), a class of single-stranded noncoding RNAs with a covalently closed loop structure, are recognized as promising biomarkers and targets for diagnosing and treating dozens of diseases, especially cancers. CircRNAs are extremely stable, abundant and conserved and have tissue- or developmental stage-specific expression. Currently, the biogenesis and biological functions of circRNAs have been increasingly revealed with deep sequencing and bioinformatics. Studies have indicated that circRNAs are frequently expressed in brain tissues and that their expression levels change in different stages of neural development, suggesting that circRNAs may play an important role in diseases of the nervous system, such as glioma. However, because the biogenesis and functions of circRNAs do not depend on a single mechanism but are coregulated by multiple factors, it is necessary to further explore the underlying mechanisms. In this review, we summarized the classification, mechanisms of biogenesis and biological functions of circRNAs. Meanwhile, we emphatically expounded on the process of abnormal expression of circRNAs, methods used in circRNA research, and their effects on the malignant biological capabilities of glioma.
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15
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Zhou Y, Zhang C, Zhang L, Ye Q, Liu N, Wang M, Long G, Fan W, Long M, Wing RA. Gene fusion as an important mechanism to generate new genes in the genus Oryza. Genome Biol 2022; 23:130. [PMID: 35706016 PMCID: PMC9199173 DOI: 10.1186/s13059-022-02696-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown. Results We conduct genome-wide interrogations of four Oryza genomes by designing and implementing novel pipelines to detect fusion genes. Based on the phylogeny of ten plant species, we detect 310 fusion genes across four Oryza species. The estimated rate of origination of fusion genes in the Oryza genus is as high as 63 fusion genes per species per million years, which is fixed at 16 fusion genes per species per million years and much higher than that in flies. By RNA sequencing analysis, we find more than 44% of the fusion genes are expressed and 90% of gene pairs show strong signals of purifying selection. Further analysis of CRISPR/Cas9 knockout lines indicates that newly formed fusion genes regulate phenotype traits including seed germination, shoot length and root length, suggesting the functional significance of these genes. Conclusions We detect new fusion genes that may drive phenotype evolution in Oryza. This study provides novel insights into the genome evolution of Oryza. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02696-w.
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Affiliation(s)
- Yanli Zhou
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Chengjun Zhang
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China. .,Department of Ecology and Evolution, The University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA.
| | - Li Zhang
- Department of Ecology and Evolution, The University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA.,Chinese Institute for Brain Research, (CIBR), Beijing, 102206, China
| | - Qiannan Ye
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Ningyawen Liu
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Muhua Wang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Guangqiang Long
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Wei Fan
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA.
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA. .,Center for Desert Agriculture, King Abdullah University of Science & Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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16
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Sun Y, Li H. Chimeric RNAs Discovered by RNA Sequencing and Their Roles in Cancer and Rare Genetic Diseases. Genes (Basel) 2022; 13:genes13050741. [PMID: 35627126 PMCID: PMC9140685 DOI: 10.3390/genes13050741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 12/30/2022] Open
Abstract
Chimeric RNAs are transcripts that are generated by gene fusion and intergenic splicing events, thus comprising nucleotide sequences from different parental genes. In the past, Northern blot analysis and RT-PCR were used to detect chimeric RNAs. However, they are low-throughput and can be time-consuming, labor-intensive, and cost-prohibitive. With the development of RNA-seq and transcriptome analyses over the past decade, the number of chimeric RNAs in cancer as well as in rare inherited diseases has dramatically increased. Chimeric RNAs may be potential diagnostic biomarkers when they are specifically expressed in cancerous cells and/or tissues. Some chimeric RNAs can also play a role in cell proliferation and cancer development, acting as tools for cancer prognosis, and revealing new insights into the cell origin of tumors. Due to their abilities to characterize a whole transcriptome with a high sequencing depth and intergenically identify spliced chimeric RNAs produced with the absence of chromosomal rearrangement, RNA sequencing has not only enhanced our ability to diagnose genetic diseases, but also provided us with a deeper understanding of these diseases. Here, we reviewed the mechanisms of chimeric RNA formation and the utility of RNA sequencing for discovering chimeric RNAs in several types of cancer and rare inherited diseases. We also discussed the diagnostic, prognostic, and therapeutic values of chimeric RNAs.
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Affiliation(s)
- Yunan Sun
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA;
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA;
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence:
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17
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Wang Y, Li C, Gong X, Chen X, Liu C, Zhang H, Li S, Luo Y. Single-Cell Transcriptomics Reveals Splicing Features of Adult Neural Stem Cells in the Subventricular Zone. Front Cell Dev Biol 2022; 10:822934. [PMID: 35300421 PMCID: PMC8921602 DOI: 10.3389/fcell.2022.822934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/03/2022] [Indexed: 11/30/2022] Open
Abstract
The central nervous system has enormously complex cellular diversity with hundreds of distinct cell types, yet alternative splicing features in single cells of important cell types at neurogenic regions are not well understood. By employing in silico analysis, we systematically identified 3,611 alternative splicing events from 1,908 genes in 28 single-cell transcriptomic data of adult mouse ependymal and subependymal regions, and found that single-cell RNA-seq has the advantage in uncovering rare splicing isoforms compared to bulk RNA-seq at the population level. We uncovered that the simultaneous presence of multiple isoforms from the same gene in a single cell is prevalent, and quiescent stem cells, activated stem cells, and neuroblast cells exhibit high heterogeneity of splicing variants. Furthermore, we also demonstrated the existence of novel bicistronic transcripts in quiescent stem cells.
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Affiliation(s)
- Yanlu Wang
- Human Aging Research Institute and School of Life Science, Nanchang University, Nanchang, China
| | - Chun Li
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xi Gong
- Human Aging Research Institute and School of Life Science, Nanchang University, Nanchang, China
| | - Xiao Chen
- College of Architectural Engineering, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Chenming Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hailei Zhang
- Novogene Bioinformatics Technology Co., Ltd., Beijing, China
| | - Siguang Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuping Luo
- Human Aging Research Institute and School of Life Science, Nanchang University, Nanchang, China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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18
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Characterization of a Read-through Fusion Transcript, BCL2L2-PABPN1, Involved in Porcine Adipogenesis. Genes (Basel) 2022; 13:genes13030445. [PMID: 35327999 PMCID: PMC8955228 DOI: 10.3390/genes13030445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 12/29/2022] Open
Abstract
cis-Splicing of adjacent genes (cis-SAGe) has been involved in multiple physiological and pathological processes in humans. However, to the best of our knowledge, there is no report of cis-SAGe in adipogenic regulation. In this study, a cis-SAGe product, BCL2L2–PABPN1 (BP), was characterized in fat tissue of pigs with RT-PCR and RACE method. BP is an in-frame fusion product composed of 333 aa and all the functional domains of both parents. BP is highly conserved among species and rich in splicing variants. BP was found to promote proliferation and inhibit differentiation of primary porcine preadipocytes. A total of 3074/44 differentially expressed mRNAs (DEmRs)/known miRNAs (DEmiRs) were identified in porcine preadipocytes overexpressing BP through RNA-Seq analysis. Both DEmRs and target genes of DEmiRs were involved in various fat-related pathways with MAPK and PI3K-Akt being the top enriched. PPP2CB, EGFR, Wnt5A and EHHADH were hub genes among the fat-related pathways identified. Moreover, ssc-miR-339-3p was found to be critical for BP regulating adipogenesis through integrated analysis of mRNA and miRNA data. The results highlight the role of cis-SAGe in adipogenesis and contribute to further revealing the mechanisms underlying fat deposition, which will be conductive to human obesity control.
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19
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Hedges DJ. RNA-seq Fusion Detection in Clinical Oncology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:163-175. [DOI: 10.1007/978-3-030-91836-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Cutler CP, Murray D, Ojo T, Harmon S, MacIver B, Cramb G, Zeidel ML. Aquaporin (AQP) channels in the spiny dogfish, Squalus acanthias I: Characterization of AQP3 and AQP15 function and expression, and localization of the proteins in gill and spiral valve intestine. Comp Biochem Physiol B Biochem Mol Biol 2021; 258:110702. [PMID: 34856346 DOI: 10.1016/j.cbpb.2021.110702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 01/27/2023]
Abstract
Complementary DNAs (cDNAs) for two aquaporin water channel genes (AQP3 and AQP15) were amplified cloned and sequenced to initiate this study. Northern blot analysis was carried out to confirm the mRNA sizes of these AQP genes with AQP3 mRNA bands exhibiting sizes of 1.2 and 1.6 k bases and AQP15 had a mRNA band of 2.1 k bases. Northern blot analysis was also performed on kidney and esophagus total RNA samples from fish acclimated to 75%, 100% or 120% seawater (SW). The level of AQP15 mRNA expression was shown to significantly decrease following salinity acclimation from 100 to 120% SW. An opposite but non-significantly different trend was observed for AQP3 mRNA levels. Full length cDNAs were then used to generate AQP3 and AQP15 mRNAs for microinjection into Xenopus oocytes. Both AQP3- and AQP15- microinjected oocytes exhibited significantly elevated apparent water permeability compared to control oocytes at neutral pH. The apparent water permeability was mercury-inhibitable, significantly so in the case of AQP3. AQP3 microinjected oocytes showed pH sensitivity in their apparent water permeability, showing a lack of permeability at acidic pH values. The Carboxyl-terminal derived amino acid sequences of AQP3 and AQP15 were used to generate rabbit affinity-purified polyclonal antibodies. Western blots with the antibodies showed a band of 31.3 kDa for AQP3 in the kidney, with minor bands at 26, 24 and 21 kDa. For AQP15 a band of 26 kDa was seen in gill and kidney. Fainter bands at 28 and 24 kDa were also seen in the kidney. There was also some higher molecular weight banding. None of the bands were seen when the antibodies were pre- blocked with their peptide antigens. Immunohistochemical localization studies were also performed in the gill and spiral valve intestine. In the gill, AQP15 antibody staining was seen sporadically in the membranes of surface epithelial cells of the secondary lamellae. Tyramide amplification of signals was employed in the spiral valve intestine. Tyramide-amplified AQP3 antibody staining was observed in the basal membrane of the invaginated epithelial cell layer of secondary intestinal folds in luminal surface of either the side wall of the spiral valve intestine or in internal valve tissue 'flaps'. For the AQP15 antibody, tyramide-amplified staining was instead found on the apical and to a lesser extent the lateral membranes of the same invaginated epithelial cell layer. The localization of AQP3 and AQP15 in the spiral valve intestine suggests that a trans-cellular water absorption pathway may exist in this tissue.
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Affiliation(s)
- Christopher P Cutler
- Department of Biology, Georgia Southern University, Statesboro, GA, USA; Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA.
| | - Debra Murray
- Department of Biology, Georgia Southern University, Statesboro, GA, USA; Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Tolulope Ojo
- Department of Biology, Georgia Southern University, Statesboro, GA, USA
| | - Sheena Harmon
- Department of Biology, Georgia Southern University, Statesboro, GA, USA; Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Bryce MacIver
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Gordon Cramb
- School of Medicine, University of St Andrews, Fife, Scotland, UK
| | - Mark L Zeidel
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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21
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Ohori M, Nakayama Y, Ogasawara-Shimizu M, Toyoshiba H, Nakanishi A, Aparicio S, Araki S. Gene regulatory network analysis defines transcriptome landscape with alternative splicing of human umbilical vein endothelial cells during replicative senescence. BMC Genomics 2021; 22:869. [PMID: 34856941 PMCID: PMC8641155 DOI: 10.1186/s12864-021-08185-x] [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: 01/05/2021] [Accepted: 11/18/2021] [Indexed: 01/10/2023] Open
Abstract
Background Endothelial cell senescence is the state of permanent cell cycle arrest and plays a critical role in the pathogenesis of age-related diseases. However, a comprehensive understanding of the gene regulatory network, including genome-wide alternative splicing machinery, involved in endothelial cell senescence is lacking. Results We thoroughly described the transcriptome landscape of replicative senescent human umbilical vein endothelial cells. Genes with high connectivity showing a monotonic expression increase or decrease with the culture period were defined as hub genes in the co-expression network. Computational network analysis of these genes led to the identification of canonical and non-canonical senescence pathways, such as E2F and SIRT2 signaling, which were down-regulated in lipid metabolism, and chromosome organization processes pathways. Additionally, we showed that endothelial cell senescence involves alternative splicing. Importantly, the first and last exon types of splicing, as observed in FLT1 and ACACA, were preferentially altered among the alternatively spliced genes during endothelial senescence. We further identified novel microexons in PRUNE2 and PSAP, each containing 9 nt, which were altered within the specific domain during endothelial senescence. Conclusions These findings unveil the comprehensive transcriptome pathway and novel signaling regulated by RNA processing, including gene expression and splicing, in replicative endothelial senescence. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08185-x.
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Affiliation(s)
- Momoko Ohori
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.
| | - Yusuke Nakayama
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.,Present address: Discovery Technology Research Laboratories, Tsukuba Research Institute, Ono Pharmaceutical Co., Ltd, 17-2 Wadai, 300-4247, Tsukuba, Ibaraki, Japan
| | - Mari Ogasawara-Shimizu
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan
| | - Hiroyoshi Toyoshiba
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.,Present address: Life Science AI, FRONTEO Healthcare Inc., 2-12-23 Konan, Minato-ku, 108-0075, Tokyo, Japan
| | - Atsushi Nakanishi
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan
| | - Samuel Aparicio
- Molecular Oncology, BC Cancer Agency, 675 W10th Avenue, V5Z 1L3, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, V6T 2B5, Vancouver, BC, Canada
| | - Shinsuke Araki
- Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.
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22
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Leung SK, Jeffries AR, Castanho I, Jordan BT, Moore K, Davies JP, Dempster EL, Bray NJ, O'Neill P, Tseng E, Ahmed Z, Collier DA, Jeffery ED, Prabhakar S, Schalkwyk L, Jops C, Gandal MJ, Sheynkman GM, Hannon E, Mill J. Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing. Cell Rep 2021; 37:110022. [PMID: 34788620 PMCID: PMC8609283 DOI: 10.1016/j.celrep.2021.110022] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 07/30/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022] Open
Abstract
Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community. There is widespread transcript diversity in the cortex and many novel transcripts Some genes display big differences in isoform number between human and mouse cortex There is evidence of differential transcript usage between human fetal and adult cortex There are many novel isoforms of genes associated with human brain disease
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Key Words
- isoform, transcript, expression, brain, cortex, mouse, human, adult, fetal, long-read sequencing, alternative splicing
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Affiliation(s)
| | | | - Isabel Castanho
- University of Exeter, Exeter, UK; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ben T Jordan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | | | | | | | | | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore
| | | | - Connor Jops
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; UVA Cancer Center, University of Virginia, Charlottesville, VA, USA
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23
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Mukherjee S, Detroja R, Balamurali D, Matveishina E, Medvedeva Y, Valencia A, Gorohovski A, Frenkel-Morgenstern M. Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells. NAR Genom Bioinform 2021; 3:lqab074. [PMID: 34458728 PMCID: PMC8386243 DOI: 10.1093/nargab/lqab074] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/02/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
Many human genes are transcribed from both strands and produce sense-antisense gene pairs. Sense-antisense (SAS) chimeric transcripts are produced upon the coalescing of exons/introns from both sense and antisense transcripts of the same gene. SAS chimera was first reported in prostate cancer cells. Subsequently, numerous SAS chimeras have been reported in the ChiTaRS-2.1 database. However, the landscape of their expression in human cells and functional aspects are still unknown. We found that longer palindromic sequences are a unique feature of SAS chimeras. Structural analysis indicates that a long hairpin-like structure formed by many consecutive Watson-Crick base pairs appears because of these long palindromic sequences, which possibly play a similar role as double-stranded RNA (dsRNA), interfering with gene expression. RNA-RNA interaction analysis suggested that SAS chimeras could significantly interact with their parental mRNAs, indicating their potential regulatory features. Here, 267 SAS chimeras were mapped in RNA-seq data from 16 healthy human tissues, revealing their expression in normal cells. Evolutionary analysis suggested the positive selection favoring sense-antisense fusions that significantly impacted the evolution of their function and structure. Overall, our study provides detailed insight into the expression landscape of SAS chimeras in human cells and identifies potential regulatory features.
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Affiliation(s)
- Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Deepak Balamurali
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Elena Matveishina
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russian Federation
- Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russian Federation
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russian Federation
- Department of Biomedical Physics, Moscow Institute of Technology, Dolgoprudny 141701, Russian Federation
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), C/ Jordi Girona 29, 08034, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Alessandro Gorohovski
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
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24
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Yu H, Guo Y, Yang Z, Zhang Q, Xu J, Yang Q, Qu Y, Tan R, Li L, He Y, Li C, Zhang S, Luo B, Gao Y. Regulatory variation within 3’UTR of STAT5A correlates with sudden cardiac death in Chinese populations. Forensic Sci Res 2021; 7:726-735. [PMID: 37101540 PMCID: PMC9976584 DOI: 10.1080/20961790.2021.1895410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Definitive diagnosis to sudden cardiac death (SCD) is often challenging since the postmortem examination on SCD victims could hardly demonstrate an adequate cause of death. It is therefore important to uncover the inherited risk component to SCD. Signal transducer and activators of transcription 5 A (STAT5A) is a member of the STAT family and a transcription factor that is activated by many cell ligands and associated with various cardiovascular processes. In this study, we performed a systematic variant screening on the STAT5A to filter potential functional genetic variations. Based on the screening results, an insertion/deletion polymorphism (rs3833144) in 3'UTR of STAT5A was selected as the candidate variant. A total of 159 SCD cases and 668 SCD matched healthy controls was enrolled to perform a case-control study and evaluate the association between rs3833144 and SCD susceptibility in Chinese populations. Logistic regression analysis showed that the deletion allele of rs3833144 had significantly increased the SCD risk (odds ratio (OR) = 1.54; 95% confidence interval (CI) = 1.18-2.01; P = 0.000955). Further genotype-expression eQTL analysis showed that samples with deletion allele appeared to lower expression of STAT5A, and in silico prediction suggested the local 3 D structure changes of STAT5A mRNA caused by the variant. On the other hand, the bioinformatic analysis presented that promoters of RARA and PTGES3L-AARSD1 could interact with rs3833144, and eQTL analysis showed the higher expression of both genes in samples with deletion allele. Dual-luciferase activity assays also suggested the significant regulatory role of rs3833144 in gene transcription. Our current data thus suggested a possible involvement of rs3833144 to SCD predisposition in Chinese populations and rs3833144 with potential function roles may become a candidate marker for SCD diagnosis and prevention.
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Affiliation(s)
- Huan Yu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Zhenzhen Yang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Qing Zhang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Jiabin Xu
- Public Security Bureau of Taixing, Taizhou, China
| | - Qi Yang
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yiling Qu
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Rui Tan
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Lijuan Li
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yan He
- Department of Epidemiology, Medical College of Soochow University, Suzhou, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Bin Luo
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
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25
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Parker MT, Knop K, Zacharaki V, Sherwood AV, Tomé D, Yu X, Martin PGP, Beynon J, Michaels SD, Barton GJ, Simpson GG. Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. eLife 2021; 10:e65537. [PMID: 33904405 PMCID: PMC8116057 DOI: 10.7554/elife.65537] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here, we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, thereby controlling their functional expression and impacting immunity. Using long-read Nanopore direct RNA sequencing, we resolved the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.
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Affiliation(s)
- Matthew T Parker
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Katarzyna Knop
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | | | - Anna V Sherwood
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Daniel Tomé
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Xuhong Yu
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Pascal GP Martin
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Jim Beynon
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Scott D Michaels
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | | | - Gordon G Simpson
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
- The James Hutton InstituteInvergowrieUnited Kingdom
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26
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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics 2021; 18:167-196. [PMID: 33893073 DOI: 10.21873/cgp.20251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas, solid malignancies as well as benign tumors. Knowledge about fusion genes is crucial not only for our understanding of tumorigenesis, but also for the diagnosis, prognostication, and treatment of cancer. Balanced chromosomal rearrangements, in particular translocations and inversions, are the most frequent genetic events leading to the generation of fusion genes. In the present review, we summarize the existing knowledge on chromosome deletions as a mechanism for fusion gene formation. Such deletions are mostly submicroscopic and, hence, not detected by cytogenetic analyses but by array comparative genome hybridization (aCGH) and/or high throughput sequencing (HTS). They are found across the genome in a variety of neoplasias. As tumors are increasingly analyzed using aCGH and HTS, it is likely that more interstitial deletions giving rise to fusion genes will be found, significantly impacting our understanding and treatment of cancer.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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27
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Matsumoto Y, Tsukamoto T, Chinen Y, Shimura Y, Sasaki N, Nagoshi H, Sato R, Adachi H, Nakano M, Horiike S, Kuroda J, Taki T, Tashiro K, Taniwaki M. Detection of novel and recurrent conjoined genes in non-Hodgkin B-cell lymphoma. J Clin Exp Hematop 2021; 61:71-77. [PMID: 33883344 PMCID: PMC8265495 DOI: 10.3960/jslrt.20033] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
For this study, we investigated comprehensive expression of conjoined genes (CGs) in
non-Hodgkin B-cell lymphoma (B-NHL) cell line KPUM-UH1 by using paired-end RNA sequencing.
Furthermore, we analyzed the expression of these transcripts in an additional 21 cell lines, 37
primary samples of various malignancies and peripheral blood mononuclear cells of four normal
individuals. Seventeen CGs were detected in KPUM-UH1: CTBS-GNG5,
SRP9-EPHX1, RMND5A-ANAPC, OTX1-EHBP1,
ATF2-CHN1, PRKAA1-TTC33, LARP1-MRPL22,
LOC105379697-BAK1, TIAM2-SCAF8,
SPAG1-VPS13B, WBP1L-CNNM2, NARS2-GAB2,
CTSC-RAB38, VAMP1-CD27-AS1, LRRC37A2-NSF,
UBA2-WTIP and ZNF600-ZNF611. To our knowledge, 10 of these
genes have not been previously reported. The various characteristics of the CGs included in-
and out-of-frame fusions, chimeras involving non-coding RNA and transcript variants. A finding
of note was that LARP1-MRPL2 was characterized as in-frame fusion and was
recurrently expressed in B-NHL samples. In this study, variety of CGs was expressed both in
malignant and normal cells, some of which might be specific to lymphoma.
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Affiliation(s)
- Yosuke Matsumoto
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Hematology, Fukuchiyama City Hospital, Fukuchiyama, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Nana Sasaki
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Hisao Nagoshi
- Department of Hematology and Oncology, Hiroshima University, Hiroshima, Japan
| | - Ryuichi Sato
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroko Adachi
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomohiko Taki
- Department of Medical Technology, Kyorin University Faculty of Health Science, Tokyo, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto, Japan
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28
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Shi Y, Yuan J, Rraklli V, Maxymovitz E, Cipullo M, Liu M, Li S, Westerlund I, Bedoya-Reina OC, Bullova P, Rorbach J, Juhlin CC, Stenman A, Larsson C, Kogner P, O’Sullivan MJ, Schlisio S, Holmberg J. Aberrant splicing in neuroblastoma generates RNA-fusion transcripts and provides vulnerability to spliceosome inhibitors. Nucleic Acids Res 2021; 49:2509-2521. [PMID: 33555349 PMCID: PMC7969022 DOI: 10.1093/nar/gkab054] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 01/14/2021] [Accepted: 01/21/2021] [Indexed: 11/12/2022] Open
Abstract
The paucity of recurrent mutations has hampered efforts to understand and treat neuroblastoma. Alternative splicing and splicing-dependent RNA-fusions represent mechanisms able to increase the gene product repertoire but their role in neuroblastoma remains largely unexplored. Here we investigate the presence and possible roles of aberrant splicing and splicing-dependent RNA-fusion transcripts in neuroblastoma. In addition, we attend to establish whether the spliceosome can be targeted to treat neuroblastoma. Through analysis of RNA-sequenced neuroblastoma we show that elevated expression of splicing factors is a strong predictor of poor clinical outcome. Furthermore, we identified >900 primarily intrachromosomal fusions containing canonical splicing sites. Fusions included transcripts from well-known oncogenes, were enriched for proximal genes and in chromosomal regions commonly gained or lost in neuroblastoma. As a proof-of-principle that these fusions can generate altered gene products, we characterized a ZNF451-BAG2 fusion, producing a truncated BAG2-protein which inhibited retinoic acid induced differentiation. Spliceosome inhibition impeded neuroblastoma fusion expression, induced apoptosis and inhibited xenograft tumor growth. Our findings elucidate a splicing-dependent mechanism generating altered gene products in neuroblastoma and show that the spliceosome is a potential target for clinical intervention.
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Affiliation(s)
- Yao Shi
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Juan Yuan
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Vilma Rraklli
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Eva Maxymovitz
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE-171-65 Solna, Sweden
| | - Mingzhi Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Shuijie Li
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Isabelle Westerlund
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
| | - Oscar C Bedoya-Reina
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Petra Bullova
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, SE-171-65 Solna, Sweden
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Adam Stenman
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Catharina Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska (CCK), Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Per Kogner
- Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Maureen J O’Sullivan
- Department of Histopathology, Our Lady's Children's Hospital, Dublin, Ireland
- Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Susanne Schlisio
- Department of Microbiology, Tumor- and Cellbiology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Stockholm, Sweden
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29
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Maspero D, Dassano A, Pintarelli G, Noci S, De Cecco L, Incarbone M, Tosi D, Santambrogio L, Dragani TA, Colombo F. Read-through transcripts in lung: germline genetic regulation and correlation with the expression of other genes. Carcinogenesis 2021; 41:918-926. [PMID: 32157280 DOI: 10.1093/carcin/bgaa020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 01/24/2020] [Accepted: 03/06/2020] [Indexed: 11/14/2022] Open
Abstract
Transcripts originating from the transcriptional read through of two adjacent, similarly oriented genes have been identified in normal and neoplastic tissues, but their functional role and the mechanisms that regulate their expression are mostly unknown. Here, we investigated whether the expression of read-through transcripts previously identified in the non-involved lung tissue of lung adenocarcinoma patients was genetically regulated. Data on genome-wide single nucleotide variant genotypes and expression levels of 10 read-through transcripts in 201 samples of lung tissue were combined to identify expression quantitative trait loci (eQTLs). Then, to identify genes whose expression levels correlated with the 10 read-through transcripts, we used whole transcriptome profiles available for 154 patients. For 8 read-though transcripts, we identified 60 eQTLs (false discovery rate <0.05), including 17 cis-eQTLs and 43 trans-eQTLs. These eQTLs did not maintain their behavior on the 'parental' genes involved in the read-through transcriptional event. The expression levels of 7 read-through transcripts were found to correlate with the expression of other genes: CHIA-PIFO and CTSC-RAB38 correlated with CHIA and RAB38, respectively, while 5 other read-through transcripts correlated with 43 unique non-parental transcripts; thus offering indications about the molecular processes in which these chimeric transcripts may be involved. We confirmed 9 eQTLs (for 4 transcripts) in the non-involved lung tissue from an independent series of 188 lung adenocarcinoma patients. Therefore, this study indicates that the expression of four read-through transcripts in normal lung tissue is under germline genetic regulation, and that this regulation is independent of that of the genes involved in the read-through event.
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Affiliation(s)
- Davide Maspero
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
| | - Alice Dassano
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giulia Pintarelli
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Noci
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Incarbone
- Department of Surgery, IRCCS Multimedica, Sesto S. Giovanni, Milan, Italy
| | - Davide Tosi
- Department of Surgery, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Luigi Santambrogio
- Department of Surgery, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Tommaso A Dragani
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Colombo
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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30
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Van Buren S, Sarkar H, Srivastava A, Rashid NU, Patro R, Love MI. Compression of quantification uncertainty for scRNA-seq counts. Bioinformatics 2021; 37:1699-1707. [PMID: 33471073 PMCID: PMC8289386 DOI: 10.1093/bioinformatics/btab001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/16/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Motivation Quantification estimates of gene expression from single-cell RNA-seq (scRNA-seq) data have inherent uncertainty due to reads that map to multiple genes. Many existing scRNA-seq quantification pipelines ignore multi-mapping reads and therefore underestimate expected read counts for many genes. alevin accounts for multi-mapping reads and allows for the generation of ‘inferential replicates’, which reflect quantification uncertainty. Previous methods have shown improved performance when incorporating these replicates into statistical analyses, but storage and use of these replicates increases computation time and memory requirements. Results We demonstrate that storing only the mean and variance from a set of inferential replicates (‘compression’) is sufficient to capture gene-level quantification uncertainty, while reducing disk storage to as low as 9% of original storage, and memory usage when loading data to as low as 6%. Using these values, we generate ‘pseudo-inferential’ replicates from a negative binomial distribution and propose a general procedure for incorporating these replicates into a proposed statistical testing framework. When applying this procedure to trajectory-based differential expression analyses, we show false positives are reduced by more than a third for genes with high levels of quantification uncertainty. We additionally extend the Swish method to incorporate pseudo-inferential replicates and demonstrate improvements in computation time and memory usage without any loss in performance. Lastly, we show that discarding multi-mapping reads can result in significant underestimation of counts for functionally important genes in a real dataset. Availability and implementation makeInfReps and splitSwish are implemented in the R/Bioconductor fishpond package available at https://bioconductor.org/packages/fishpond. Analyses and simulated datasets can be found in the paper’s GitHub repo at https://github.com/skvanburen/scUncertaintyPaperCode. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Scott Van Buren
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Hirak Sarkar
- Department of Computer Science, University of Maryland College Park, MD 20742, USA.,Center for Bioinformatics and Computational Biology, University of Maryland College Park, MD 20742, USA
| | - Avi Srivastava
- New York Genome Center, New York, NY 10013, USA.,Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Naim U Rashid
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.,Lineberger Comprehensive Cancer Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rob Patro
- Department of Computer Science, University of Maryland College Park, MD 20742, USA.,Center for Bioinformatics and Computational Biology, University of Maryland College Park, MD 20742, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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31
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Vidal AF. Read-through circular RNAs reveal the plasticity of RNA processing mechanisms in human cells. RNA Biol 2020; 17:1823-1826. [PMID: 32783578 PMCID: PMC7714478 DOI: 10.1080/15476286.2020.1805233] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 01/22/2023] Open
Abstract
In the human genome, there are several genes whose primary transcripts are both canonically and non-canonically spliced to generate mRNAs and RNA circles, respectively. These RNA circles are a novel class of long non-coding RNAs that became known as circular RNAs (circRNAs). Recently, a new type of circRNA was discovered and called read-through circRNAs (rt-circRNAs). They are hybrid circles that include coding exons from two adjacent and similarly oriented genes. The function of rt-circRNAs, as well as the impact of read-through transcription in our transcriptome, remains to be elucidated. Although we have just begun to scratch it, here I discussed some insights that these fascinating circRNAs are already giving us about the plasticity of RNA processing in our cells.
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Affiliation(s)
- Amanda F. Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Brazil
- Graduate Program of Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
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32
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Wang J, Li B, Marques S, Steinmetz LM, Wei W, Pelechano V. TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes. Nucleic Acids Res 2020; 48:e104. [PMID: 32816037 PMCID: PMC7544212 DOI: 10.1093/nar/gkaa691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/17/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic transcriptomes are complex, involving thousands of overlapping transcripts. The interleaved nature of the transcriptomes limits our ability to identify regulatory regions, and in some cases can lead to misinterpretation of gene expression. To improve the understanding of the overlapping transcriptomes, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5' and 3' ends of individual RNA molecules at single-nucleotide resolution. We investigated the transcriptome of a well characterized human cell line (K562) and identified thousands of unannotated transcript isoforms. By focusing on transcripts which are challenging to be investigated with RNA-Seq, we accurately defined boundaries of lowly expressed unannotated and read-through transcripts putatively encoding fusion genes. We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic myeloid leukaemia patient samples. Taking the advantage of TIF-Seq2, we explored transcription regulation among overlapping units and investigated their crosstalk. We show that most overlapping upstream transcripts use poly(A) sites within the first 2 kb of the downstream transcription units. Our work shows that, by paring the 5' and 3' end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitate accurate assignment of promoters to genes and easily identify transcriptionally fused genes.
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Affiliation(s)
- Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Sueli Marques
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Wu Wei
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Biomedical Informatics, Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
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Colemon A, Harris TM, Ramanathan S. DNA hypomethylation drives changes in MAGE-A gene expression resulting in alteration of proliferative status of cells. Genes Environ 2020; 42:24. [PMID: 32760472 PMCID: PMC7392716 DOI: 10.1186/s41021-020-00162-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
Melanoma Antigen Genes (MAGEs) are a family of genes that have piqued the interest of scientists for their unique expression pattern. A subset of MAGEs (Type I) are expressed in spermatogonial cells and in no other somatic tissue, and then re-expressed in many cancers. Type I MAGEs are often referred to as cancer-testis antigens due to this expression pattern, while Type II MAGEs are more ubiquitous in expression. This study determines the cause and consequence of the aberrant expression of the MAGE-A subfamily of cancer-testis antigens. We have discovered that MAGE-A genes are regulated by DNA methylation, as revealed by treatment with 5-azacytidine, an inhibitor of DNA methyltransferases. Furthermore, bioinformatics analysis of existing methylome sequencing data also corroborates our findings. The consequence of expressing certain MAGE-A genes is an increase in cell proliferation and colony formation and resistance to chemo-therapeutic agent 5-fluorouracil and DNA damaging agent sodium arsenite. Taken together, these data indicate that DNA methylation plays a crucial role in regulating the expression of MAGE-A genes which then act as drivers of cell proliferation, anchorage-independent growth and chemo-resistance that is critical for cancer-cell survival.
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Affiliation(s)
- Ashley Colemon
- Fisk-Vanderbilt Masters-to-PhD Bridge Program, Fisk University, Nashville, TN USA
| | - Taylor M Harris
- Department of Life and Physical Sciences, Fisk University, Nashville, TN USA
| | - Saumya Ramanathan
- Department of Life and Physical Sciences, Fisk University, Nashville, TN USA.,Department of Pharmacology, Vanderbilt University, Nashville, TN USA
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34
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Elfman J, Pham LP, Li H. The relationship between chimeric RNAs and gene fusions: Potential implications of reciprocity in cancer. J Genet Genomics 2020; 47:341-348. [PMID: 33008771 DOI: 10.1016/j.jgg.2020.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/09/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Justin Elfman
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA
| | - Lam-Phong Pham
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA
| | - Hui Li
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22904 USA.
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35
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Abstract
Chimeric RNAs are hybrid transcripts containing exons from two separate genes. Chimeric RNAs are traditionally considered to be transcribed from fusion genes caused by chromosomal rearrangement. These canonical chimeric RNAs are well characterized to be expressed in a cancer-unique pattern and/or act as oncogene products. However, benefited by the development of advanced deep sequencing technologies, novel types of non-canonical chimeric RNAs have been discovered to be generated from intergenic splicing without genomic aberrations. They can be formed through trans-splicing or cis-splicing between adjacent genes (cis-SAGe) mechanisms. Non-canonical chimeric RNAs are widely detected in normal physiology, although several have been shown to have a cancer-specific expression pattern. Further studies have indicated that some of them play fundamental roles in controlling cell growth and motility, and may have functions independent of the parental genes. These discoveries are unveiling a new layer of the functional transcriptome and are also raising the possibility of utilizing non-canonical chimeric RNAs as cancer diagnostic markers and therapeutic targets. In this chapter, we will overview different categories of chimeric RNAs and their expression in various types of cancerous and normal samples. Acknowledging that chimeric RNAs are not unique to cancer, we will discuss both bioinformatic and biological methods to identify credible cancer-specific chimeric RNAs. Furthermore, we will describe downstream methods to explore their molecular processing mechanisms and potential functions. A better understanding of the biogenesis mechanisms and functional products of cancer-specific chimeric RNAs will pave ways for the development of novel cancer biomarkers and therapeutic targets.
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Affiliation(s)
- Xinrui Shi
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Emily Lin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Hui Li
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, United States; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States.
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36
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McCartney AM, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez-Rodriguez J, Prado-Martinez J, Creevey CJ, Aspden JL, McInerney JO, Marques-Bonet T, O'Connell MJ. Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human. Genome Biol Evol 2020; 11:2678-2690. [PMID: 31400206 PMCID: PMC6764479 DOI: 10.1093/gbe/evz163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 12/14/2022] Open
Abstract
Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products.
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Affiliation(s)
- Ann M McCartney
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
| | - Edel M Hyland
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Institute for Global Food Security, Queens University Belfast, United Kingdom
| | - Paul Cormican
- Teagasc Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland
| | - Raymond J Moran
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland
| | - Kate D Lee
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,School of Biological Sciences, University of Auckland, New Zealand.,School of Fundamental Sciences, Massey University, New Zealand
| | | | - Javier Prado-Martinez
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Christopher J Creevey
- Institute for Global Food Security, Queens University Belfast, United Kingdom.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
| | - James O McInerney
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL, United Kingdom.,School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, NG7 2RD, United Kingdom
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.,NAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom.,School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, NG7 2RD, United Kingdom
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37
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Oliver GR, Jenkinson G, Klee EW. Computational Detection of Known Pathogenic Gene Fusions in a Normal Tissue Database and Implications for Genetic Disease Research. Front Genet 2020; 11:173. [PMID: 32180803 PMCID: PMC7059617 DOI: 10.3389/fgene.2020.00173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/13/2020] [Indexed: 11/13/2022] Open
Abstract
Several recent studies have demonstrated the utility of RNA-Seq in the diagnosis of rare inherited disease. Diagnostic rates 35% higher than those previously achievable with DNA-Seq alone have been attained. These studies have primarily profiled gene expression and splicing defects, however, some have also shown that fusion transcripts are diagnostic or phenotypically relevant in patients with constitutional disorders. Fusion transcripts have traditionally been studied as oncogenic phenomena, with relevance only to cancer testing. Consequently, fusion detection algorithms were biased toward the detection of well-known oncogenic fusions, hindering their application to rare Mendelian genetic disease studies. A recent methodology published by the authors successfully tailored a traditional algorithm to the detection of pathogenic fusion events in inherited disease. A key mechanism of decreasing false positive or biologically benign events was comparison to a database of events detected in normal tissues. This approach is akin to population frequency-based filtering of genetic variants. It is predicated on the idea that pathogenic fusion transcripts are absent from normal tissue. We report on an analysis of RNA-Seq data from the genotype-tissue expression (GTEx) project in which known pathogenic fusions are computationally detected at low levels in normal tissues unassociated with the disease phenotype. Examples include archetypal cancer fusion transcripts, as well as fusions responsible for rare inherited disease. We consider potential explanations for the detectability of such transcripts and discuss the bearing such results have on the future profiling of genetic disease patients for pathogenic gene fusions.
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Affiliation(s)
- Gavin Robert Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Garrett Jenkinson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
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38
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Fusion transcripts in normal human cortex increase with age and show distinct genomic features for single cells and tissues. Sci Rep 2020; 10:1368. [PMID: 31992760 PMCID: PMC6987184 DOI: 10.1038/s41598-020-58165-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/24/2019] [Indexed: 01/24/2023] Open
Abstract
Fusion transcripts can contribute to diversity of molecular networks in the human cortex. In this study, we explored the occurrence of fusion transcripts in normal human cortex along with single neurons and astrocytes. We identified 1305 non-redundant fusion events from 388 transcriptomes representing 59 human cortices and 329 single cells. Our results indicate while the majority of fusion transcripts in human cortex are intra-chromosomal (85%), events found in single neurons and astrocytes were primarily inter-chromosomal (80%). The number of fusions in single neurons was significantly higher than that in single astrocytes (p < 0.05), indicating fusion as a possible contributor towards transcriptome diversity in neuronal cells. The identified fusions were largely private and 4 specific recurring events were found both in cortex and in single neurons but not in astrocytes. We found a significant increase in the number of fusion transcripts in human brain with increasing age both in single cells and whole cortex (p < 0.0005 and < 0.005, respectively). This is likely one of the many possible contributors for the inherent plasticity of the adult brain. The fusion transcripts in fetal brain were enriched for genes for long-term depression; while those in adult brain involved genes enriched for long-term potentiation pathways. Our findings demonstrate fusion transcripts are naturally occurring phenomenon spanning across the health-disease continuum, and likely contribute to the diverse molecular network of human brain.
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Balamurali D, Gorohovski A, Detroja R, Palande V, Raviv-Shay D, Frenkel-Morgenstern M. ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps. Nucleic Acids Res 2020; 48:D825-D834. [PMID: 31747015 PMCID: PMC7145514 DOI: 10.1093/nar/gkz1025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/18/2019] [Accepted: 10/26/2019] [Indexed: 12/11/2022] Open
Abstract
Chimeric RNA transcripts are formed when exons from two genes fuse together, often due to chromosomal translocations, transcriptional errors or trans-splicing effect. While these chimeric RNAs produce functional proteins only in certain cases, they play a significant role in disease phenotyping and progression. ChiTaRS 5.0 (http://chitars.md.biu.ac.il/) is the latest and most comprehensive chimeric transcript repository, with 111 582 annotated entries from eight species, including 23 167 known human cancer breakpoints. The database includes unique information correlating chimeric breakpoints with 3D chromatin contact maps, generated from public datasets of chromosome conformation capture techniques (Hi-C). In this update, we have added curated information on druggable fusion targets matched with chimeric breakpoints, which are applicable to precision medicine in cancers. The introduction of a new section that lists chimeric RNAs in various cell-lines is another salient feature. Finally, using text-mining techniques, novel chimeras in Alzheimer's disease, schizophrenia, dyslexia and other diseases were collected in ChiTaRS. Thus, this improved version is an extensive catalogue of chimeras from multiple species. It extends our understanding of the evolution of chimeric transcripts in eukaryotes and contributes to the analysis of 3D genome conformational changes and the functional role of chimeras in the etiopathogenesis of cancers and other complex diseases.
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Affiliation(s)
- Deepak Balamurali
- Laboratory of Cancer Genomics and Biocomputing of Complex Diseases, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Alessandro Gorohovski
- Laboratory of Cancer Genomics and Biocomputing of Complex Diseases, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Rajesh Detroja
- Laboratory of Cancer Genomics and Biocomputing of Complex Diseases, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Vikrant Palande
- Laboratory of Cancer Genomics and Biocomputing of Complex Diseases, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Dorith Raviv-Shay
- Laboratory of Cancer Genomics and Biocomputing of Complex Diseases, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Milana Frenkel-Morgenstern
- Laboratory of Cancer Genomics and Biocomputing of Complex Diseases, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
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40
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Frenkel-Morgenstern M. Identification of Chimeric RNAs Using RNA-Seq Reads and Protein-Protein Interactions of Translated Chimeras. Methods Mol Biol 2020; 2079:27-40. [PMID: 31728960 DOI: 10.1007/978-1-4939-9904-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chimeric RNA moieties typically consist of exons from two genes expressed from different genomic locations and produced by chromosomal translocations, trans-splicing or transcription errors. Recent advances in next-generation sequencing procedures have opened new horizons for identification of novel chimeric transcripts in various diseases in a personalized manner. Here we describe the detailed computational procedures to identify chimeric transcripts using RNA-seq reads. Moreover, we elaborate on the domain-domain co-occurrence method to detect alterations in chimeric protein-protein interaction (ChiPPI) networks produced by chimeric RNA that are translated to chimeric proteins.
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41
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Abstract
Chimeric RNAs can be formed by trans-splicing from different transcripts or cis-splicing of adjacent genes (cis-SAGe). Cis-SAGe results from read-through transcription of two neighbor genes. To investigate the mechanisms underlying intergenic splicing of adjacent genes, it is important to develop an assay to detect transcriptional read-through. Here, we describe a general RT-PCR based method to confirm the process for cis-SAGe candidates. In this method, we use PCR to amplify cDNA that is reverse transcribed from the read-through precursor mRNA. The result provides a foundation for further downstream mechanistic studies.
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42
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Barresi V, Cosentini I, Scuderi C, Napoli S, Di Bella V, Spampinato G, Condorelli DF. Fusion Transcripts of Adjacent Genes: New Insights into the World of Human Complex Transcripts in Cancer. Int J Mol Sci 2019; 20:ijms20215252. [PMID: 31652751 PMCID: PMC6862657 DOI: 10.3390/ijms20215252] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/18/2019] [Accepted: 10/20/2019] [Indexed: 12/12/2022] Open
Abstract
The awareness of genome complexity brought a radical approach to the study of transcriptome, opening eyes to single RNAs generated from two or more adjacent genes according to the present consensus. This kind of transcript was thought to originate only from chromosomal rearrangements, but the discovery of readthrough transcription opens the doors to a new world of fusion RNAs. In the last years many possible intergenic cis-splicing mechanisms have been proposed, unveiling the origins of transcripts that contain some exons of both the upstream and downstream genes. In some cases, alternative mechanisms, such as trans-splicing and transcriptional slippage, have been proposed. Five databases, containing validated and predicted Fusion Transcripts of Adjacent Genes (FuTAGs), are available for the scientific community. A comparative analysis revealed that two of them contain the majority of the results. A complete analysis of the more widely characterized FuTAGs is provided in this review, including their expression pattern in normal tissues and in cancer. Gene structure, intergenic splicing patterns and exon junction sequences have been determined and here reported for well-characterized FuTAGs. The available functional data and the possible roles in cancer progression are discussed.
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Affiliation(s)
- Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy.
| | - Ilaria Cosentini
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy.
| | - Chiara Scuderi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy.
| | - Salvatore Napoli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy.
| | - Virginia Di Bella
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy.
| | - Giorgia Spampinato
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy.
| | - Daniele Filippo Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy.
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43
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Oliver GR, Tang X, Schultz-Rogers LE, Vidal-Folch N, Jenkinson WG, Schwab TL, Gaonkar K, Cousin MA, Nair A, Basu S, Chanana P, Oglesbee D, Klee EW. A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PLoS One 2019; 14:e0223337. [PMID: 31577830 PMCID: PMC6774566 DOI: 10.1371/journal.pone.0223337] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND RNA sequencing has been proposed as a means of increasing diagnostic rates in studies of undiagnosed rare inherited disease. Recent studies have reported diagnostic improvements in the range of 7.5-35% by profiling splicing, gene expression quantification and allele specific expression. To-date however, no study has systematically assessed the presence of gene-fusion transcripts in cases of germline disease. Fusion transcripts are routinely identified in cancer studies and are increasingly recognized as having diagnostic, prognostic or therapeutic relevance. Isolated reports exist of fusion transcripts being detected in cases of developmental and neurological phenotypes, and thus, systematic application of fusion detection to germline conditions may further increase diagnostic rates. However, current fusion detection methods are unsuited to the investigation of germline disease due to performance biases arising from their development using tumor, cell-line or in-silico data. METHODS We describe a tailored approach to fusion candidate identification and prioritization in a cohort of 47 undiagnosed, suspected inherited disease patients. We modify an existing fusion transcript detection algorithm by eliminating its cell line-derived filtering steps, and instead, prioritize candidates using a custom workflow that integrates genomic and transcriptomic sequence alignment, biological and technical annotations, customized categorization logic, and phenotypic prioritization. RESULTS We demonstrate that our approach to fusion transcript identification and prioritization detects genuine fusion events excluded by standard analyses and efficiently removes phenotypically unimportant candidates and false positive events, resulting in a reduced candidate list enriched for events with potential phenotypic relevance. We describe the successful genetic resolution of two previously undiagnosed disease cases through the detection of pathogenic fusion transcripts. Furthermore, we report the experimental validation of five additional cases of fusion transcripts with potential phenotypic relevance. CONCLUSIONS The approach we describe can be implemented to enable the detection of phenotypically relevant fusion transcripts in studies of rare inherited disease. Fusion transcript detection has the potential to increase diagnostic rates in rare inherited disease and should be included in RNA-based analytical pipelines aimed at genetic diagnosis.
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Affiliation(s)
- Gavin R. Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Xiaojia Tang
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Laura E. Schultz-Rogers
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Noemi Vidal-Folch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - W. Garrett Jenkinson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Tanya L. Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Krutika Gaonkar
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Margot A. Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Asha Nair
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Shubham Basu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Pritha Chanana
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Eric W. Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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44
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Wu H, Singh S, Shi X, Xie Z, Lin E, Li X, Li H. Functional heritage: the evolution of chimeric RNA into a gene. RNA Biol 2019; 17:125-134. [PMID: 31566065 DOI: 10.1080/15476286.2019.1670038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Once believed to be unique features of neoplasia, chimeric RNAs are now being discovered in normal physiology. We speculated that some chimeric RNAs may be functional precursors of genes, and that forming chimeric RNA at the transcriptional level may be a 'trial' mechanism before the functional element is fixed into the genome. Supporting this idea, we identified a chimeric RNA, HNRNPA1L2-SUGT1 (H-S), whose sequence is highly similar to that of a 'pseudogene' MRPS31P5. Sequence analysis revealed that MRPS31P5 transcript is more similar to H-S chimeric RNA than its 'parent' gene, MRPS31. Evolutionarily, H-S precedes MRPS31P5, as it can be detected bioinformatically and experimentally in marmosets, which do not yet possess MRPS31P5 in their genome. Conversely, H-S is minimally expressed in humans, while instead, MRPS31P5 is abundantly expressed. Silencing H-S in marmoset cells resulted in similar phenotype as silencing MRPS31P5 in human cells. In addition, whole transcriptome analysis and candidate downstream target validation revealed common signalling pathways shared by the two transcripts. Interestingly, H-S failed to rescue the phenotype caused by silencing MPRS31P5 in human and rhesus cells, whereas MRPS31P5 can at least partially rescue the phenotype caused by silencing H-S in marmoset cells, suggesting that MRPS31P5 may have further evolved into a distinct entity. Thus, multiple lines of evidence support that MRPS31P5 is not truly a pseudogene of MRPS31, but a likely functional descendent of H-S chimera. Instead being a gene fusion product, H-S is a product of cis-splicing between adjacent genes, while MRPS31P5 is likely produced by genome rearrangement.
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Affiliation(s)
- Hao Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China.,Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Xinrui Shi
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Emily Lin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
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45
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Chwalenia K, Qin F, Singh S, Li H. A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes. Nucleic Acids Res 2019; 47:e24. [PMID: 30590765 PMCID: PMC6393300 DOI: 10.1093/nar/gky1288] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 11/14/2018] [Accepted: 12/14/2018] [Indexed: 12/14/2022] Open
Abstract
Chimeric RNAs generated by cis-splicing between adjacent genes (cis-SAGe) are increasingly recognized as a widespread phenomenon. These chimeric messenger RNAs are present in normal human cells, and are also detected in various cancers. The mechanisms for how this group of chimeras is formed are not yet clear, in part due to the lack of a tractable system for their experimental investigation. Here we developed a fast, easy and versatile cell-based reporter system to identify regulators of cis-SAGe. The reporter, consisting of four main cassettes, simultaneously measures the effects of a candidate regulator on cis-SAGe and canonical splicing. Using this cell-based assay, we screened 102 candidate factors involved in RNA pol II cleavage and termination, elongation, splicing, alternative splicing and R-loop formation. We discovered that two factors, SRRM1 and SF3B1, affect not only cis-SAGe chimeras, but also other types of chimeric RNAs in a genome-wide fashion. This system can be used for studying trans-acting factors and cis-acting sequence elements and factors, as well as for screening small molecule inhibitors.
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Affiliation(s)
- Katarzyna Chwalenia
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Sandeep Singh
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
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46
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Tang Y, Ma S, Wang X, Xing Q, Huang T, Liu H, Li Q, Zhang Y, Zhang K, Yao M, Yang GL, Li H, Zang X, Yang B, Guan F. Identification of chimeric RNAs in human infant brains and their implications in neural differentiation. Int J Biochem Cell Biol 2019; 111:19-26. [DOI: 10.1016/j.biocel.2019.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/06/2019] [Accepted: 03/30/2019] [Indexed: 02/07/2023]
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47
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Haney RA, Matte T, Forsyth FS, Garb JE. Alternative Transcription at Venom Genes and Its Role as a Complementary Mechanism for the Generation of Venom Complexity in the Common House Spider. Front Ecol Evol 2019; 7. [PMID: 31431897 PMCID: PMC6700725 DOI: 10.3389/fevo.2019.00085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The complex composition of venom, a proteinaceous secretion used by
diverse animal groups for predation or defense, is typically viewed as being
driven by gene duplication in conjunction with positive selection, leading to
large families of diversified toxins with selective venom gland expression. Yet,
the production of alternative transcripts at venom genes is often overlooked as
another potentially important process that could contribute proteins to venom,
and requires comprehensive datasets integrating genome and transcriptome
sequences together with proteomic characterization of venom to be fully
documented. In the common house spider, Parasteatoda
tepidariorum, we used RNA sequencing of four tissue types in
conjunction with the sequenced genome to provide a comprehensive transcriptome
annotation. We also used mass spectrometry to identify a minimum of 99 distinct
proteins in P tepidariorum venom, including at least 33
latrotoxins, pore-forming neurotoxins shared with the confamilial black widow.
We found that venom proteins are much more likely to come from multiple
transcript genes, whose transcripts produced distinct protein sequences. The
presence of multiple distinct proteins in venom from transcripts at individual
genes was confirmed for eight loci by mass spectrometry, and is possible at 21
others. Alternative transcripts from the same gene, whether encoding or not
encoding a protein found in venom, showed a range of expression patterns, but
were not necessarily restricted to the venom gland. However, approximately half
of venom protein encoding transcripts were found among the 1,318 transcripts
with strongly venom gland biased expression. Our findings revealed an important
role for alternative transcription in generating venom protein complexity and
expanded the traditional model of venom evolution.
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Affiliation(s)
- Robert A Haney
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Taylor Matte
- Center for Regenerative Medicine, Boston University, Medical, Boston, MA, United States
| | - FitzAnthony S Forsyth
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
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Chibon F, Lesluyes T, Valentin T, Le Guellec S. CINSARC signature as a prognostic marker for clinical outcome in sarcomas and beyond. Genes Chromosomes Cancer 2019; 58:124-129. [PMID: 30387235 DOI: 10.1002/gcc.22703] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022] Open
Abstract
Prognostication is a key issue for sarcoma patients' care as it triggers the therapeutic approach including chemotherapy, which is still not standard for localized patients. Current prognostic evaluation, based on the FNCLCC grading system, has recently been improved by the CINSARC signature outperforming histology-based grading system by identifying high-risk patients in every grade, even in those considered as low. CINSARC is an expression-based signature related to mitosis and chromosome integrity with prognostic value in a wide range of cancers additional to sarcoma. First developed with frozen material, CINSARC is now coupled with NanoString technology allowing evaluation from FFPE blocks used in clinical practice. Consequently, CINSARC is currently evaluated in clinical trials with a dual objective of demonstrating the benefit of chemotherapy in sarcoma patients and testing its response prediction. Considering its overarching value in oncology, its development is welcome in any cancers where the prognostication needs to be improved.
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Affiliation(s)
- Frederic Chibon
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.,Department of Pathology, Institut Claudius Regaud, Toulouse, France
| | - Tom Lesluyes
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.,University of Bordeaux, Bordeaux, France.,Institut Claudius Regaud, Toulouse, France
| | - Thibaud Valentin
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.,Department of Medical Oncology, Institut Claudius Regaud, Toulouse, France
| | - Sophie Le Guellec
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.,Department of Pathology, Institut Claudius Regaud, Toulouse, France
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49
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Vo JN, Cieslik M, Zhang Y, Shukla S, Xiao L, Zhang Y, Wu YM, Dhanasekaran SM, Engelke CG, Cao X, Robinson DR, Nesvizhskii AI, Chinnaiyan AM. The Landscape of Circular RNA in Cancer. Cell 2019; 176:869-881.e13. [PMID: 30735636 PMCID: PMC6601354 DOI: 10.1016/j.cell.2018.12.021] [Citation(s) in RCA: 1041] [Impact Index Per Article: 208.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/05/2018] [Accepted: 12/12/2018] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are an intriguing class of RNA due to their covalently closed structure, high stability, and implicated roles in gene regulation. Here, we used an exome capture RNA sequencing protocol to detect and characterize circRNAs across >2,000 cancer samples. When compared against Ribo-Zero and RNase R, capture sequencing significantly enhanced the enrichment of circRNAs and preserved accurate circular-to-linear ratios. Using capture sequencing, we built the most comprehensive catalog of circRNA species to date: MiOncoCirc, the first database to be composed primarily of circRNAs directly detected in tumor tissues. Using MiOncoCirc, we identified candidate circRNAs to serve as biomarkers for prostate cancer and were able to detect circRNAs in urine. We further detected a novel class of circular transcripts, termed read-through circRNAs, that involved exons originating from different genes. MiOncoCirc will serve as a valuable resource for the development of circRNAs as diagnostic or therapeutic targets across cancer types.
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Affiliation(s)
- Josh N Vo
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin Cieslik
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yajia Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sudhanshu Shukla
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, 580011, India
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carl G Engelke
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Arul M Chinnaiyan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA.
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50
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Matsumura K, Imai H, Go Y, Kusuhara M, Yamaguchi K, Shirai T, Ohshima K. Transcriptional activation of a chimeric retrogene PIPSL in a hominoid ancestor. Gene 2018; 678:318-323. [PMID: 30096459 DOI: 10.1016/j.gene.2018.08.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/05/2018] [Accepted: 08/07/2018] [Indexed: 01/09/2023]
Abstract
Retrogenes are a class of functional genes derived from the mRNA of various intron-containing genes. PIPSL was created through a unique mechanism, whereby distinct genes were assembled at the RNA level, and the resulting chimera was then reverse transcribed and integrated into the genome by the L1 retrotransposon. Expression of PIPSL RNA via its transcription start sites (TSSs) has been confirmed in the testes of humans and chimpanzee. Here, we demonstrated that PIPSL RNA is expressed in the testis of the white-handed gibbon. The 5'-end positions of gibbon RNAs were confined to a narrow range upstream of the PIPSL start codon and overlapped with those of orangutan and human, suggesting that PIPSL TSSs are similar among hominoid species. Reporter assays using a luciferase gene and the flanking sequences of human PIPSL showed that an upstream sequence exhibits weak promoter activity in human cells. Our findings suggest that PIPSL might have acquired a promoter at an early stage of hominoid evolution before the divergence of gibbons and ultimately retained similar TSSs in all of the lineages. Moreover, the upstream sequence derived from the phosphatidylinositol-4-phosphate 5-kinase, type I, alpha 5' untranslated region and/or neighboring repetitive sequences in the genome possibly exhibits promoter activity. Furthermore, we observed that a TATA-box-like sequence has emerged by nucleotide substitution in a lineage leading to humans, with this possibly responsible for a broader distribution of the human PIPSL TSSs.
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Affiliation(s)
- Kenya Matsumura
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan; Shizuoka Cancer Center Research Institute, Sunto, Shizuoka, Japan
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yasuhiro Go
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Physiological Sciences, National Institute for Physiological Sciences, Okazaki, Aichi, Japan; School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | | | - Ken Yamaguchi
- Shizuoka Cancer Center Research Institute, Sunto, Shizuoka, Japan
| | - Tsuyoshi Shirai
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Kazuhiko Ohshima
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan.
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