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Xu YF, Dang Y, Kong WB, Wang HL, Chen X, Yao L, Zhao Y, Zhang RQ. Regulation of TMEM100 expression by epigenetic modification, effects on proliferation and invasion of esophageal squamous carcinoma. World J Clin Oncol 2024; 15:554-565. [PMID: 38689624 PMCID: PMC11056859 DOI: 10.5306/wjco.v15.i4.554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/01/2024] [Accepted: 03/20/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is a prevalent malignancy with a high morbidity and mortality rate. TMEM100 has been shown to be suppressor gene in a variety of tumors, but there are no reports on the role of TMEM100 in esophageal cancer (EC). AIM To investigate epigenetic regulation of TMEM100 expression in ESCC and the effect of TMEM100 on ESCC proliferation and invasion. METHODS Firstly, we found the expression of TMEM100 in EC through The Cancer Genome Atlas database. The correlation between TMEM100 gene expression and the survival of patients with EC was further confirmed through Kaplan-Meier analysis. We then added the demethylating agent 5-AZA to ESCC cell lines to explore the regulation of TMEM100 expression by epigenetic modification. To observe the effect of TMEM100 expression on tumor proliferation and invasion by overexpressing TMEM100. Finally, we performed gene set enrichment analysis using the Kyoto Encyclopaedia of Genes and Genomes Orthology-Based Annotation System database to look for pathways that might be affected by TMEM100 and verified the effect of TMEM100 expression on the mitogen-activated protein kinases (MAPK) pathway. RESULTS In the present study, by bioinformatic analysis we found that TMEM100 was lowly expressed in EC patients compared to normal subjects. Kaplan-meier survival analysis showed that low expression of TMEM100 was associated with poor prognosis in patients with EC. Then, we found that the demethylating agent 5-AZA resulted in increased expression of TMEM100 in ESCC cells [quantitative real-time PCR (qRT-PCR) and western blotting]. Subsequently, we confirmed that overexpression of TMEM100 leads to its increased expression in ESCC cells (qRT-PCR and western blotting). Overexpression of TMEM100 also inhibited proliferation, invasion and migration of ESCC cells (cell counting kit-8 and clone formation assays). Next, by enrichment analysis, we found that the gene set was significantly enriched in the MAPK signaling pathway. The involvement of TMEM100 in the regulation of MAPK signaling pathway in ESCC cell was subsequently verified by western blotting. CONCLUSION TMEM100 is a suppressor gene in ESCC, and its low expression may lead to aberrant activation of the MAPK pathway. Promoter methylation may play a key role in regulating TMEM100 expression.
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Affiliation(s)
- Yue-Feng Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui Province, China
| | - Yan Dang
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui Province, China
| | - Wei-Bo Kong
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui Province, China
| | - Han-Lin Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui Province, China
| | - Xiu Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui Province, China
| | - Long Yao
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui Province, China
| | - Yuan Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui Province, China
| | - Ren-Quan Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui Province, China
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2
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Adams M, Vollmers C. Generation and analysis of a mouse multi-tissue genome annotation atlas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578267. [PMID: 38352519 PMCID: PMC10862843 DOI: 10.1101/2024.01.31.578267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Generating an accurate and complete genome annotation for an organism is complex because the cells within each tissue can express a unique set of transcript isoforms from a unique set of genes. A comprehensive genome annotation should contain information on what tissues express what transcript isoforms at what level. This tissue-level isoform information can then inform a wide range of research questions as well as experiment designs. Long-read sequencing technology combined with advanced full-length cDNA library preparation methods has now achieved throughput and accuracy where generating these types of annotations is achievable. Here, we show this by generating a genome annotation of the mouse (Mus musculus). We used the nanopore-based R2C2 long-read sequencing method to generate 64 million highly accurate full length cDNA consensus reads - averaging 5.4 million reads per tissue for a dozen tissues. Using the Mandalorion tool we processed these reads to generate the Tissue-level Atlas of Mouse Isoforms (TAMI - available at https://genome.ucsc.edu/s/vollmers/TAMI) which we believe will be a valuable complement to conventional, manually curated reference genome annotations.
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Affiliation(s)
- Matthew Adams
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz
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3
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Zhang M, Feng J, Li Y, Qin PZ, Chai Y. Generation of tamoxifen-inducible Tfap2b-CreER T2 mice using CRISPR-Cas9. Genesis 2024; 62:e23582. [PMID: 38069547 PMCID: PMC11021159 DOI: 10.1002/dvg.23582] [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: 09/13/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 01/11/2024]
Abstract
Tfap2b, a pivotal transcription factor, plays critical roles within neural crest cells and their derived lineage. To unravel the intricate lineage dynamics and contribution of these Tfap2b+ cells during craniofacial development, we established a Tfap2b-CreERT2 knock-in transgenic mouse line using the CRISPR-Cas9-mediated homologous direct repair. By breeding with tdTomato reporter mice and initiating Cre activity through tamoxifen induction at distinct developmental time points, we show the Tfap2b lineage within the key neural crest-derived domains, such as the facial mesenchyme, midbrain, cerebellum, spinal cord, and limbs. Notably, the migratory neurons stemming from the dorsal root ganglia are visible subsequent to Cre activity initiated at E8.5. Intriguingly, Tfap2b+ cells, serving as the progenitors for limb development, show activity predominantly commencing at E10.5. Across the mouse craniofacial landscape, Tfap2b exhibits a widespread presence throughout the facial organs. Here we validate its role as a marker of progenitors in tooth development and have confirmed that this process initiates from E12.5. Our study not only validates the Tfap2b-CreERT2 transgenic line, but also provides a powerful tool for lineage tracing and genetic targeting of Tfap2b-expressing cells and their progenitor in a temporally and spatially regulated manner during the intricate process of development and organogenesis.
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Affiliation(s)
- Mingyi Zhang
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Yue Li
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
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4
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Yue T, Wang Y, Zhang L, Gu C, Xue H, Wang W, Lyu Q, Dun Y. Deep Learning for Genomics: From Early Neural Nets to Modern Large Language Models. Int J Mol Sci 2023; 24:15858. [PMID: 37958843 PMCID: PMC10649223 DOI: 10.3390/ijms242115858] [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: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
The data explosion driven by advancements in genomic research, such as high-throughput sequencing techniques, is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in various fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning, since we expect a superhuman intelligence that explores beyond our knowledge to interpret the genome from deep learning. A powerful deep learning model should rely on the insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with proper deep learning-based architecture, and we remark on practical considerations of developing deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research and point out current challenges and potential research directions for future genomics applications. We believe the collaborative use of ever-growing diverse data and the fast iteration of deep learning models will continue to contribute to the future of genomics.
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Affiliation(s)
- Tianwei Yue
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Yuanxin Wang
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Longxiang Zhang
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Chunming Gu
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Haoru Xue
- The Robotics Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA;
| | - Wenping Wang
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (Y.W.); (L.Z.); (W.W.)
| | - Qi Lyu
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI 48824, USA;
| | - Yujie Dun
- School of Information and Communications Engineering, Xi’an Jiaotong University, Xi’an 710049, China;
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Tao S, Hou Y, Diao L, Hu Y, Xu W, Xie S, Xiao Z. Long noncoding RNA study: Genome-wide approaches. Genes Dis 2023; 10:2491-2510. [PMID: 37554208 PMCID: PMC10404890 DOI: 10.1016/j.gendis.2022.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/09/2022] [Accepted: 10/23/2022] [Indexed: 11/30/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been confirmed to play a crucial role in various biological processes across several species. Though many efforts have been devoted to the expansion of the lncRNAs landscape, much about lncRNAs is still unknown due to their great complexity. The development of high-throughput technologies and the constantly improved bioinformatic methods have resulted in a rapid expansion of lncRNA research and relevant databases. In this review, we introduced genome-wide research of lncRNAs in three parts: (i) novel lncRNA identification by high-throughput sequencing and computational pipelines; (ii) functional characterization of lncRNAs by expression atlas profiling, genome-scale screening, and the research of cancer-related lncRNAs; (iii) mechanism research by large-scale experimental technologies and computational analysis. Besides, primary experimental methods and bioinformatic pipelines related to these three parts are summarized. This review aimed to provide a comprehensive and systemic overview of lncRNA genome-wide research strategies and indicate a genome-wide lncRNA research system.
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Affiliation(s)
- Shuang Tao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yarui Hou
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Liting Diao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yanxia Hu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Wanyi Xu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Shujuan Xie
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
- Institute of Vaccine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Zhendong Xiao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
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6
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Kratz A, Ranganathan S. Christian Schönbach 1965-2023. BIOINFORMATICS ADVANCES 2023; 3:vbad147. [PMID: 37886713 PMCID: PMC10599964 DOI: 10.1093/bioadv/vbad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023]
Affiliation(s)
- Anton Kratz
- The Systems Biology Institute, Tokyo 141-0022, Japan
| | - Shoba Ranganathan
- Applied Biosciences, Macquarie University, Sydney, NSW 2109, Australia
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Polina I, Mishra J, Cypress MW, Landherr M, Valkov N, Chaput I, Nieto B, Mende U, Zhang P, Jhun BS, O-Uchi J. Mitochondrial Ca 2+ uniporter (MCU) variants form plasma-membrane channels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551242. [PMID: 37577584 PMCID: PMC10418069 DOI: 10.1101/2023.07.31.551242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
MCU is widely recognized as a responsible gene for encoding a pore-forming subunit of highly mitochondrial-specific and Ca 2+ -selective channel, mitochondrial Ca 2+ uniporter complex (mtCUC). Here, we report a novel short variant derived from the MCU gene (termed MCU-S) which lacks mitochondria-targeted sequence and forms a Ca 2+ - permeable channel outside of mitochondria. MCU-S was ubiquitously expressed in all cell-types/tissues, with particularly high expression in human platelets. MCU-S formed Ca 2+ channels at the plasma membrane, which exhibited similar channel properties to those observed in mtCUC. MCU-S channels at the plasma membrane served as an additional Ca 2+ influx pathway for platelet activation. Our finding is completely distinct from the originally reported MCU gene function and provides novel insights into the molecular basis of MCU variant-dependent cellular Ca 2+ handling.
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8
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Guo LT, Pyle AM. End-to-end RT-PCR of long RNA and highly structured RNA. Methods Enzymol 2023; 691:3-15. [PMID: 37914451 DOI: 10.1016/bs.mie.2023.07.002] [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] [Indexed: 11/03/2023]
Abstract
RNA molecules play important roles in numerous normal cellular processes and disease states, from protein coding to gene regulation. RT-PCR, applying the power of polymerase chain reaction (PCR) to RNA by coupling reverse transcription with PCR, is one of the most important techniques to characterize RNA transcripts and monitor gene expression. The ability to analyze full-length RNA transcripts and detect their expression is critical to decipher their biological functions. However, due to the low processivity of retroviral reverse transcriptases (RTs), we can only monitor a small fraction of long RNA transcripts, especially those containing stable secondary and tertiary structures. The full-length sequences can only be deduced by computational analysis, which is often misleading. Group II intron-encoded RTs are a new type of RT enzymes. They have evolved specialized structural elements that unwind template structures and maintain close contact with the RNA template. Therefore, group II intron-encoded RTs are more processive than the retroviral RTs. The discovery, optimization and deployment of processive group II intron RTs provide us the opportunity to analyze RNA transcripts with single molecule resolution. MarathonRT, the most processive group II intron RT, has been extensively optimized for processive reverse transcription. In this chapter, we use MarathonRT to deliver a general protocol for long amplicon generation by RT-PCR, and also provide guidance for troubleshooting and further optimization.
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Affiliation(s)
- Li-Tao Guo
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States; Department of Chemistry, Yale University, New Haven, CT, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States.
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9
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Son KH, Aldonza MBD, Nam AR, Lee KH, Lee JW, Shin KJ, Kang K, Cho JY. Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies. SCIENCE ADVANCES 2023; 9:eade3399. [PMID: 37406108 DOI: 10.1126/sciadv.ade3399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023]
Abstract
Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. We addressed this through integrative next-generation sequencing of transcriptomes paired with five histone marks and DNA methylome profiling across 11 tissue types, deciphering the dog's epigenetic code by defining distinct chromatin states, super-enhancer, and methylome landscapes, and thus showed that these regions are associated with a wide range of biological functions and cell/tissue identity. In addition, we confirmed that the phenotype-associated variants are enriched in tissue-specific regulatory regions and, therefore, the tissue of origin of the variants can be traced. Ultimately, we delineated conserved and dynamic epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog that can be used for comparative biology and medical research.
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Affiliation(s)
- Keun Hong Son
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Mark Borris D Aldonza
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - A-Reum Nam
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Kang-Hoon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Jeong-Woon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Kyung-Ju Shin
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, Korea
| | - Je-Yoel Cho
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
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Fukunishi Y, Higo J, Kasahara K. Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles. Biophys Rev 2022; 14:1423-1447. [PMID: 36465086 PMCID: PMC9703445 DOI: 10.1007/s12551-022-01015-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/06/2022] [Indexed: 11/29/2022] Open
Abstract
Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various computation molecular docking methods: fundamental in silico (virtual) screening, ensemble docking, enhanced sampling (generalized ensemble) methods, and other methods to improve the accuracy of the complex structure. We explain not only the merits of these methods but also their limits of application and discuss some interaction terms which are not considered in the in silico methods. In silico screening and ensemble docking are useful when one focuses on obtaining the native complex structure (the most thermodynamically stable complex). Generalized ensemble method provides a free-energy landscape, which shows the distribution of the most stable complex structure and semi-stable ones in a conformational space. Also, barriers separating those stable structures are identified. A researcher should select one of the methods according to the research aim and depending on complexity of the molecular system to be studied.
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Affiliation(s)
- Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-Ku, Tokyo, 135-0064 Japan
| | - Junichi Higo
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima Minamimachi, Chuo-Ku, Kobe, Hyogo 650-0047 Japan ,Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
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Dindhoria K, Monga I, Thind AS. Computational approaches and challenges for identification and annotation of non-coding RNAs using RNA-Seq. Funct Integr Genomics 2022; 22:1105-1112. [DOI: 10.1007/s10142-022-00915-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022]
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12
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Wang C, Yu H, Lu S, Ke S, Xu Y, Feng Z, Qian B, Bai M, Yin B, Li X, Hua Y, Dong L, Li Y, Zhang B, Li Z, Chen D, Chen B, Zhou Y, Pan S, Fu Y, Jiang H, Wang D, Ma Y. LncRNA Hnf4αos exacerbates liver ischemia/reperfusion injury in mice via Hnf4αos/Hnf4α duplex-mediated PGC1α suppression. Redox Biol 2022; 57:102498. [PMID: 36242914 PMCID: PMC9576992 DOI: 10.1016/j.redox.2022.102498] [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: 09/22/2022] [Revised: 10/02/2022] [Accepted: 10/05/2022] [Indexed: 11/27/2022] Open
Abstract
LncRNAs are involved in the pathophysiologic processes of multiple diseases, but little is known about their functions in hepatic ischemia/reperfusion injury (HIRI). As a novel lncRNA, the pathogenetic significance of hepatic nuclear factor 4 alpha, opposite strand (Hnf4αos) in hepatic I/R injury remains unclear. Here, differentially expressed Hnf4αos and Hnf4α antisense RNA 1 (Hnf4α-as1) were identified in liver tissues from mouse ischemia/reperfusion models and patients who underwent liver resection surgery. Hnf4αos deficiency in Hnf4αos-KO mice led to improved liver function, alleviated the inflammatory response and reduced cell death. Mechanistically, we found a regulatory role of Hnf4αos-KO in ROS metabolism through PGC1α upregulation. Hnf4αos also promoted the stability of Hnf4α mRNA through an RNA/RNA duplex, leading to the transcriptional activation of miR-23a and miR-23a depletion was required for PGC1α function in hepatoprotective effects on HIRI. Together, our findings reveal that Hnf4αos elevation in HIRI leads to severe liver damage via Hnf4αos/Hnf4α/miR-23a axis-mediated PGC1α inhibition.
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Affiliation(s)
- Chaoqun Wang
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Hongjun Yu
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Shounan Lu
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Shanjia Ke
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Yanan Xu
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China; Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhigang Feng
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China; The First Department of General Surgery, The Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Baolin Qian
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Miaoyu Bai
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Bing Yin
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Xinglong Li
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Yongliang Hua
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China; Department of Pediatric Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Liqian Dong
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Yao Li
- Department of Intensive Care Unit, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bao Zhang
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Zhongyu Li
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dong Chen
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bangliang Chen
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yongzhi Zhou
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shangha Pan
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China
| | - Yao Fu
- Department of Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hongchi Jiang
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China; Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dawei Wang
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China; Department of Anorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Yong Ma
- Department of Minimal Invasive Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, China.
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Innovative Hybrid-Alignment Annotation Method for Bioinformatics Identification and Functional Verification of a Novel Nitric Oxide Synthase in Trichomonas vaginalis. BIOLOGY 2022; 11:biology11081210. [PMID: 36009837 PMCID: PMC9404748 DOI: 10.3390/biology11081210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/06/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Both the annotation and identification of genes in pathogenic parasites remain challenging. As a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV). However, nitric oxide synthase (NOS) has not yet been annotated in the TV genome. By aligning whole coding sequences of TV against a thousand sequences of known proteins from other organisms via the Smith–Waterman and Needleman–Wunsch algorithms, we developed a witness-to-suspect strategy to identify incorrectly annotated genes in TV. A novel NOS of TV (TV NOS) with a high witness-to-suspect ratio, which was originally annotated as a hydrogenase in the NCBI database, was successfully identified. We then performed in silico modeling of the protein structure and the molecular docking of all cofactors (NADPH, tetrahydrobiopterin (BH4), heme and flavin adenine dinucleotide (FAD)), cloned the gene, expressed and purified the protein, and ultimately performed mass spectrometry analysis and enzymatic activity assays. We clearly showed that although the predicted structure of TV NOS is not similar to that of NOS proteins of other species, all cofactor-binding motifs can interact with their ligands with high affinities. Most importantly, the purified protein is a functional NOS, as it has a high enzymatic activity for generating NO in vitro. This study provides an innovative approach to identify incorrectly annotated genes. Abstract Both the annotation and identification of genes in pathogenic parasites are still challenging. Although, as a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV), nitric oxide synthase (NOS) has not yet been annotated in the TV genome. We developed a witness-to-suspect strategy to identify incorrectly annotated genes in TV via the Smith–Waterman and Needleman–Wunsch algorithms through in-depth and repeated alignment of whole coding sequences of TV against thousands of sequences of known proteins from other organisms. A novel NOS of TV (TV NOS), which was annotated as hydrogenase in the NCBI database, was successfully identified; this TV NOS had a high witness-to-suspect ratio and contained all the NOS cofactor-binding motifs (NADPH, tetrahydrobiopterin (BH4), heme and flavin adenine dinucleotide (FAD) motifs). To confirm this identification, we performed in silico modeling of the protein structure and cofactor docking, cloned the gene, expressed and purified the protein, performed mass spectrometry analysis, and ultimately performed an assay to measure enzymatic activity. Our data showed that although the predicted structure of the TV NOS protein was not similar to the structure of NOSs of other species, all cofactor-binding motifs could interact with their ligands with high affinities. We clearly showed that the purified protein had high enzymatic activity for generating NO in vitro. This study provides an innovative approach to identify incorrectly annotated genes in TV and highlights a novel NOS that might serve as a virulence factor of TV.
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Harikrishnan NB, Pranay SY, Nagaraj N. Classification of SARS-CoV-2 viral genome sequences using Neurochaos Learning. Med Biol Eng Comput 2022; 60:2245-2255. [PMID: 35668230 PMCID: PMC9170350 DOI: 10.1007/s11517-022-02591-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/28/2022] [Indexed: 12/01/2022]
Abstract
Abstract The high spread rate of SARS-CoV-2 virus has put the researchers all over the world in a demanding situation. The need of the hour is to develop novel learning algorithms that can effectively learn a general pattern by training with fewer genome sequences of coronavirus. Learning from very few training samples is necessary and important during the beginning of a disease outbreak when sequencing data is limited. This is because a successful detection and isolation of patients can curb the spread of the virus. However, this poses a huge challenge for machine learning and deep learning algorithms as they require huge amounts of training data to learn the pattern and distinguish from other closely related viruses. In this paper, we propose a new paradigm – Neurochaos Learning (NL) for classification of coronavirus genome sequence that addresses this specific problem. NL is inspired from the empirical evidence of chaos and non-linearity at the level of neurons in biological neural networks. The average sensitivity, specificity and accuracy for NL are 0.998, 0.999 and 0.998 respectively for the multiclass classification problem (SARS-CoV-2, Coronaviridae, Metapneumovirus, Rhinovirus and Influenza) using leave one out crossvalidation. With just one training sample per class for 1000 independent random trials of training, we report an average macro F1-score \documentclass[12pt]{minimal}
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\begin{document}$$> 0.99$$\end{document}>0.99 for the classification of SARS-CoV-2 from SARS-CoV-1 genome sequences. We compare the performance of NL with K-nearest neighbours (KNN), logistic regression, random forest, SVM, and naïve Bayes classifiers. We foresee promising future applications in genome classification using NL with novel combinations of chaotic feature engineering and other machine learning algorithms. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s11517-022-02591-3.
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Affiliation(s)
- N. B. Harikrishnan
- The University of Trans-Disciplinary Health Sciences and Technology, Bengaluru, 560064 Karnataka India
- Consciousness Studies Programme, National Institute of Advanced Studies, Indian Institute of Science Campus, Bengaluru, 560012 Karnataka India
| | - S. Y. Pranay
- Consciousness Studies Programme, National Institute of Advanced Studies, Indian Institute of Science Campus, Bengaluru, 560012 Karnataka India
| | - Nithin Nagaraj
- Consciousness Studies Programme, National Institute of Advanced Studies, Indian Institute of Science Campus, Bengaluru, 560012 Karnataka India
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15
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Bono H, Sakamoto T, Kasukawa T, Tabunoki H. Systematic Functional Annotation Workflow for Insects. INSECTS 2022; 13:insects13070586. [PMID: 35886762 PMCID: PMC9319598 DOI: 10.3390/insects13070586] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/12/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing has revolutionized entomological study, rendering it possible to analyze the genomes and transcriptomes of non-model insects. However, use of this technology is often limited to obtaining the nucleotide sequences of target or related genes, with many of the acquired sequences remaining unused because other available sequences are not sufficiently annotated. To address this issue, we have developed a functional annotation workflow for transcriptome-sequenced insects to determine transcript descriptions, which represents a significant improvement over the previous method (functional annotation pipeline for insects). The developed workflow attempts to annotate not only the protein sequences obtained from transcriptome analysis but also the ncRNA sequences obtained simultaneously. In addition, the workflow integrates the expression-level information obtained from transcriptome sequencing for application as functional annotation information. Using the workflow, functional annotation was performed on the sequences obtained from transcriptome sequencing of the stick insect (Entoria okinawaensis) and silkworm (Bombyx mori), yielding richer functional annotation information than that obtained in our previous study. The improved workflow allows the more comprehensive exploitation of transcriptome data and is applicable to other insects because the workflow has been openly developed on GitHub.
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Affiliation(s)
- Hidemasa Bono
- Laboratory of Bio-DX, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Japan
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Japan
- Correspondence: ; Tel.: +81-82-424-4013
| | - Takuma Sakamoto
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan; (T.S.); (H.T.)
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan;
| | - Hiroko Tabunoki
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan; (T.S.); (H.T.)
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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16
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Nguyen H, Wu H, Ung A, Yamazaki Y, Fogelgren B, Ward WS. Deletion of Orc4 during oogenesis severely reduces polar body extrusion and blocks zygotic DNA replication†. Biol Reprod 2022; 106:730-740. [PMID: 34977916 PMCID: PMC9040667 DOI: 10.1093/biolre/ioab237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/21/2021] [Accepted: 12/15/2021] [Indexed: 11/14/2022] Open
Abstract
Origin recognition complex subunit 4 (ORC4) is a DNA-binding protein required for DNA replication. During oocyte maturation, after the last oocyte DNA replication step and before zygotic DNA replication, the oocyte undergoes two meiotic cell divisions in which half the DNA is ejected in much smaller polar bodies. We previously demonstrated that ORC4 forms a cytoplasmic cage around the DNA that is ejected in both polar body extrusion (PBE) events. Here, we used ZP3 activated Cre to delete exon 7 of Orc4 during oogenesis to test how it affected both predicted functions of ORC4: its recently discovered role in PBE and its well-known role in DNA synthesis. Orc4 deletion severely reduced PBE. Almost half of Orc4-depleted germinal vesicle (GV) oocytes cultured in vitro were arrested before anaphase I (48%), and only 25% produced normal first polar bodies. This supports the role of ORC4 in PBE and suggests that transcription of the full-length Orc4 during oogenesis is required for efficient PBE. Orc4 deletion also abolished zygotic DNA synthesis. Fewer Orc4-depleted oocytes developed to the metaphase II (MII) stage, and after activation these oocytes were arrested at the two-cell stage without undergoing DNA synthesis. This confirms that transcription of full-length Orc4 after the primary follicle stage is required for zygotic DNA replication. The data also suggest that MII oocytes do not have a replication licensing checkpoint as cytokinesis progressed without DNA synthesis. Together, the data confirm that oocyte ORC4 is important for both PBE and zygotic DNA synthesis.
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Affiliation(s)
- Hieu Nguyen
- Department of Anatomy, Biochemistry & Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Hongwen Wu
- Department of Anatomy, Biochemistry & Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Anna Ung
- Department of Anatomy, Biochemistry & Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Yukiko Yamazaki
- Department of Anatomy, Biochemistry & Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Ben Fogelgren
- Department of Anatomy, Biochemistry & Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - W Steven Ward
- Department of Anatomy, Biochemistry & Physiology, Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
- Department of Obstetrics, Gynecology & Women’s Health, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
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17
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Micheel J, Safrastyan A, Wollny D. Advances in Non-Coding RNA Sequencing. Noncoding RNA 2021; 7:70. [PMID: 34842804 PMCID: PMC8628893 DOI: 10.3390/ncrna7040070] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.
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Affiliation(s)
| | | | - Damian Wollny
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, 07743 Jena, Germany; (J.M.); (A.S.)
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18
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Abstract
Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is frequently observed in human diseases including cancer. In this review, we discuss the breadth of techniques that have been used to globally profile TSSs and the resulting insights into gene regulation, as well as future prospects in this area of inquiry.
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Affiliation(s)
| | - Gabriel E. Zentner
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
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19
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Guerrini MM, Oguchi A, Suzuki A, Murakawa Y. Cap analysis of gene expression (CAGE) and noncoding regulatory elements. Semin Immunopathol 2021; 44:127-136. [PMID: 34468849 DOI: 10.1007/s00281-021-00886-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/13/2021] [Indexed: 01/06/2023]
Abstract
Cap analysis of gene expression (CAGE) was developed to detect the 5' end of RNA. Trapping of the RNA 5'-cap structure enables the enrichment and selective sequencing of complete transcripts. Upscaled high-throughput versions of CAGE have enabled the genome-wide identification of transcription start sites, including transcriptionally active promoters and enhancers. CAGE sequencing can be exploited to draw comprehensive maps of active genomic regulatory elements in a cell type- and activation-specific manner. The cells of the immune system are among the best candidates to be analyzed in humans, since they are easily accessible. In this review, we discuss how CAGE data are instrumental for integrative analyses with quantitative trait loci and omics data, and their usefulness in the mechanistic interpretation of the effects of genetic variations over the entire human genome. Integrating CAGE data with the currently available omics information will contribute to better understanding of the genome-wide association study variants that lie outside of annotated genes, deepening our knowledge on human diseases, and enabling the targeted design of more specific therapeutic interventions.
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Affiliation(s)
- Matteo Maurizio Guerrini
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
| | - Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- IFOM-the FIRC Institute of Molecular Oncology, Milan, Italy
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20
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Zhuang J, Huang Y, Zheng W, Yang S, Zhu G, Wang J, Lin X, Ye J. TMEM100 expression suppresses metastasis and enhances sensitivity to chemotherapy in gastric cancer. Biol Chem 2021; 401:285-296. [PMID: 31188741 DOI: 10.1515/hsz-2019-0161] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/01/2019] [Indexed: 12/11/2022]
Abstract
The gene encoding transmembrane protein 100 (TMEM100) was first discovered to be transcribed by the murine genome. It has been recently proven that TMEM100 contributes to hepatocellular carcinoma and non-small-cell lung carcinoma (NSCLC). This study investigates the impact of TMEM100 expression on gastric cancer (GC). TMEM100 expression was remarkably downregulated in GC samples compared to the surrounding non-malignant tissues (p < 0.01). Excessive TMEM100 expression prohibited the migration and invasion of GC cells without influencing their growth. However, TMEM100 knockdown restored their migration and invasion potential. Additionally, TMEM100 expression restored the sensitivity of GC cells to chemotherapeutic drugs such as 5-fluouracil (5-FU) and cisplatin. In terms of TMEM100 modulation, it was revealed that BMP9 rather than BMP10, is the upstream modulator of TM3M100. HIF1α downregulation modulated the impact of TMEM100 on cell migration, chemotherapy sensitivity and invasion in GC cells. Eventually, the in vivo examination of TMEM100 activity revealed that its upregulation prohibits the pulmonary metastasis of GC cells and increases the sensitivity of xenograft tumors to 5-FU treatment. In conclusion, TMEM100 serves as a tumor suppressor in GC and could be used as a promising target for the treatment of GC and as a predictor of GC clinical outcome.
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Affiliation(s)
- Jinfu Zhuang
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou 350004, Fujian, China
| | - Yongjian Huang
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou 350004, Fujian, China
| | - Wei Zheng
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou 350004, Fujian, China
| | - Shugang Yang
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou 350004, Fujian, China
| | - Guangwei Zhu
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou 350004, Fujian, China
| | - Jinzhou Wang
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou 350004, Fujian, China
| | - Xiaohan Lin
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou 350004, Fujian, China
| | - Jianxin Ye
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou 350004, Fujian, China
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21
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Bertozzi TM, Takahashi N, Hanin G, Kazachenka A, Ferguson-Smith AC. A spontaneous genetically induced epiallele at a retrotransposon shapes host genome function. eLife 2021; 10:e65233. [PMID: 33755012 PMCID: PMC8084528 DOI: 10.7554/elife.65233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Intracisternal A-particles (IAPs) are endogenous retroviruses (ERVs) responsible for most insertional mutations in the mouse. Full-length IAPs harbour genes flanked by long terminal repeats (LTRs). Here, we identify a solo LTR IAP variant (Iap5-1solo) recently formed in the inbred C57BL/6J mouse strain. In contrast to the C57BL/6J full-length IAP at this locus (Iap5-1full), Iap5-1solo lacks DNA methylation and H3K9 trimethylation. The distinct DNA methylation levels between the two alleles are established during preimplantation development, likely due to loss of KRAB zinc finger protein binding at the Iap5-1solo variant. Iap5-1solo methylation increases and becomes more variable in a hybrid genetic background yet is unresponsive to maternal dietary methyl supplementation. Differential epigenetic modification of the two variants is associated with metabolic differences and tissue-specific changes in adjacent gene expression. Our characterisation of Iap5-1 as a genetically induced epiallele with functional consequences establishes a new model to study transposable element repression and host-element co-evolution.
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Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Nozomi Takahashi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Geula Hanin
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
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22
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Zhu Y, Lin Y, He Y, Wang H, Chen S, Li Z, Song N, Sun F. Deletion of lncRNA5512 has no effect on spermatogenesis and reproduction in mice. Reprod Fertil Dev 2021; 32:706-713. [PMID: 32317095 DOI: 10.1071/rd19246] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/21/2019] [Indexed: 01/13/2023] Open
Abstract
Long non-coding (lnc) RNAs are a series of RNAs longer than 200 nucleotides that do not code for protein products. Whole-genome expression profiles of lncRNAs suggest that they play important roles in spermatogenesis because they are particularly abundant in testes. However, most of their characteristics and functions remain unclear. The aim of this study was to define the function of lncRNA5512, which is abundant in spermatocytes and round spermatids, in mouse fertility invivo. To investigate this we generated lncRNA5512-knockout mice by clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) 9 technology. Knockout mice showed normal spermatogenesis and fertility, and had no detectable abnormalities. This indicates that lncRNA5512 does not affect mouse fertility despite its high expression in the testes. Its specific localisation in spermatocytes and round spermatids suggests that it could be a useful marker for the identification of spermatocytes and round spermatids in mouse testes.
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Affiliation(s)
- Yu Zhu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Yu Lin
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Yue He
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Hanshu Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Shitao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Zhenhua Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Ning Song
- Shanghai Key Laboratory of Reproductive Medicine, School of Medicine, Shanghai Jiao Tong University, 280 South Chongqing Road, Huangpu District, Shanghai 200025, China; and Corresponding authors. ;
| | - Fei Sun
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China; and Corresponding authors. ;
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23
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Abugessaisa I, Ramilowski JA, Lizio M, Severin J, Hasegawa A, Harshbarger J, Kondo A, Noguchi S, Yip CW, Ooi J, Tagami M, Hori F, Agrawal S, Hon C, Cardon M, Ikeda S, Ono H, Bono H, Kato M, Hashimoto K, Bonetti A, Kato M, Kobayashi N, Shin J, de Hoon M, Hayashizaki Y, Carninci P, Kawaji H, Kasukawa T. FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. Nucleic Acids Res 2021; 49:D892-D898. [PMID: 33211864 PMCID: PMC7779024 DOI: 10.1093/nar/gkaa1054] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 11/15/2022] Open
Abstract
The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.
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Affiliation(s)
- Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jesicca Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jayson Harshbarger
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Atsushi Kondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Fumi Hori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Melissa Cardon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shuya Ikeda
- Database Center for Life Science, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Hiromasa Ono
- Database Center for Life Science, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Hidemasa Bono
- Database Center for Life Science, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University
| | - Masaki Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Alessandro Bonetti
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Karolinska Institutet, Stockholm, Sweden
| | - Masaki Kato
- RIKEN Head Office for Information Systems and Cybersecurity, Wako, Saitama, Japan
| | - Norio Kobayashi
- RIKEN Head Office for Information Systems and Cybersecurity, Wako, Saitama, Japan
| | - Jay Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hideya Kawaji
- Correspondence may also be addressed to Hideya Kawaji.
| | - Takeya Kasukawa
- To whom correspondence should be addressed. Tel: +81 45 503 9222; Fax: +81 45 503 9219;
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Liau WS, Samaddar S, Banerjee S, Bredy TW. On the functional relevance of spatiotemporally-specific patterns of experience-dependent long noncoding RNA expression in the brain. RNA Biol 2021; 18:1025-1036. [PMID: 33397182 DOI: 10.1080/15476286.2020.1868165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The majority of transcriptionally active RNA derived from the mammalian genome does not code for protein. Long noncoding RNA (lncRNA) is the most abundant form of noncoding RNA found in the brain and is involved in many aspects of cellular metabolism. Beyond their fundamental role in the nucleus as decoys for RNA-binding proteins associated with alternative splicing or as guides for the epigenetic regulation of protein-coding gene expression, recent findings indicate that activity-induced lncRNAs also regulate neural plasticity. In this review, we discuss how lncRNAs may exert molecular control over brain function beyond their known roles in the nucleus. We propose that subcellular localization is a critical feature of experience-dependent lncRNA activity in the brain, and that lncRNA-mediated control over RNA metabolism at the synapse serves to regulate local mRNA stability and translation, thereby influencing neuronal function, learning and memory.
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Affiliation(s)
- Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | | | | | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
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25
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Eggert S, Gruebl T, Rajender R, Rupp C, Sander B, Heesch A, Zimmermann M, Hoepfner S, Zentgraf H, Kins S. The Rab5 activator RME-6 is required for amyloid precursor protein endocytosis depending on the YTSI motif. Cell Mol Life Sci 2020; 77:5223-5242. [PMID: 32065241 PMCID: PMC7671991 DOI: 10.1007/s00018-020-03467-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 12/20/2019] [Accepted: 01/14/2020] [Indexed: 12/13/2022]
Abstract
Endocytosis of the amyloid precursor protein (APP) is critical for generation of β-amyloid, aggregating in Alzheimer's disease. APP endocytosis depending on the intracellular NPTY motif is well investigated, whereas involvement of the YTSI (also termed BaSS) motif remains controversial. Here, we show that APP lacking the YTSI motif (ΔYTSI) displays reduced localization to early endosomes and decreased internalization rates, similar to APP ΔNPTY. Additionally, we show that the YTSI-binding protein, PAT1a interacts with the Rab5 activator RME-6, as shown by several independent assays. Interestingly, knockdown of RME-6 decreased APP endocytosis, whereas overexpression increased the same. Similarly, APP ΔNPTY endocytosis was affected by PAT1a and RME-6 overexpression, whereas APP ΔYTSI internalization remained unchanged. Moreover, we could show that RME-6 mediated increase of APP endocytosis can be diminished upon knocking down PAT1a. Together, our data identify RME-6 as a novel player in APP endocytosis, involving the YTSI-binding protein PAT1a.
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Affiliation(s)
- Simone Eggert
- Department of Human Biology and Human Genetics, Technical University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Tomas Gruebl
- Department of Human Biology and Human Genetics, Technical University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Ritu Rajender
- Department of Human Biology and Human Genetics, Technical University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Carsten Rupp
- Department of Human Biology and Human Genetics, Technical University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Bianca Sander
- Department of Human Biology and Human Genetics, Technical University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Amelie Heesch
- Department of Human Biology and Human Genetics, Technical University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Marius Zimmermann
- Department of Human Biology and Human Genetics, Technical University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany
| | - Sebastian Hoepfner
- MPI of Molecular Cell Biology and Genetics, Dresden, Germany
- Bird & Bird LLM, Munich, Germany
| | | | - Stefan Kins
- Department of Human Biology and Human Genetics, Technical University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663, Kaiserslautern, Germany.
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26
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Mao J, Zigo M, Zuidema D, Sutovsky M, Sutovsky P. NEDD4-like ubiquitin ligase 2 protein (NEDL2) in porcine spermatozoa, oocytes, and preimplantation embryos and its role in oocyte fertilization†. Biol Reprod 2020; 104:117-129. [PMID: 33030211 DOI: 10.1093/biolre/ioaa186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/25/2020] [Accepted: 10/06/2020] [Indexed: 02/03/2023] Open
Abstract
The ubiquitin-proteasome system plays diverse regulatory and homeostatic roles in mammalian reproduction. Ubiquitin ligases are the substrate-specific mediators of ubiquitin-binding to its substrate proteins. The NEDD4-like ubiquitin ligase 2 (aliases NEDL2, HECW2) is a HECT-type ubiquitin ligase that contains one N-terminal HECW ubiquitin ligase domain, one C-terminal HECT ubiquitin ligase domain, one C2 domain, and two WW protein-protein interaction modules. Beyond its predicted ubiquitin-ligase activity, its cellular functions are largely unknown. Current studies were designed to investigate the content and distribution of NEDL2 in porcine spermatozoa, oocytes, zygotes, and early preimplantation embryos, and in cumulus cells before and after in vitro maturation with oocytes, and fibroblast cells as positive control by western blot and immunocytochemistry, and to examine its roles during oocyte fertilization. Multiple isoforms of NEDL2 were identified by WB. One at approximately 52 kDa was detected only in the germinal vesicle (GV) stage and metaphase II oocytes, and in early preimplantation embryos. Other isoforms were high mass bands at 91, 136, and 155 kDa, which were only detected in somatic cells. Interestingly, ejaculated spermatozoa prominently displayed the same 52 kDa band as oocytes; they also had two minor bands of 74 and 129 kDa, which were not detected in somatic cells or oocytes. By immunofluorescence, NEDL2 showed a diffused cytoplasmic localization in all cell types and accumulated in distinct foci in the germinal vesicles (GVs) of immature oocytes, in maternal and paternal pronuclei of zygotes and nuclei of embryo blastomeres and somatic cells. In blastocysts, the labeling intensity of NEDL2 was stronger in the inner cell mass than in trophoblast, indicating higher NEDL2 content in the ICM cells than in trophectoderm. NEDL2 abundance was 10 times higher in post-maturation oocyte-surrounding cumulus cells than that of cumulus cells before in vitro maturation with hormones, indicating that NEDL2 may have a unique role in cumulus cells after ovulation. Microinjection of anti-NEDL2 antibody into oocyte before IVF did not affect the percentage of oocytes fertilized, percentage of oocytes cleaved, or blastocyst formation. However, the anti-NEDL2 antibody decreased the number of pronuclei, accelerated the formation of nuclear precursor bodies at 6 h postfertilization, inhibited sperm DNA decondensation, and resulted in more fertilized oocytes without male pronuclear formation. In summary, NEDL2 may play a key role during fertilization, especially during sperm DNA decondensation.
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Affiliation(s)
- Jiude Mao
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Michal Zigo
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Dalen Zuidema
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Miriam Sutovsky
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Peter Sutovsky
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA.,Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO, USA
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Azazi D, Mudge JM, Odom DT, Flicek P. Functional signatures of evolutionarily young CTCF binding sites. BMC Biol 2020; 18:132. [PMID: 32988407 PMCID: PMC7520972 DOI: 10.1186/s12915-020-00863-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 09/03/2020] [Indexed: 01/01/2023] Open
Abstract
Background The introduction of novel CTCF binding sites in gene regulatory regions in the rodent lineage is partly the effect of transposable element expansion, particularly in the murine lineage. The exact mechanism and functional impact of evolutionarily novel CTCF binding sites are not yet fully understood. We investigated the impact of novel subspecies-specific CTCF binding sites in two Mus genus subspecies, Mus musculus domesticus and Mus musculus castaneus, that diverged 0.5 million years ago. Results CTCF binding site evolution is influenced by the action of the B2-B4 family of transposable elements independently in both lineages, leading to the proliferation of novel CTCF binding sites. A subset of evolutionarily young sites may harbour transcriptional functionality as evidenced by the stability of their binding across multiple tissues in M. musculus domesticus (BL6), while overall the distance of subspecies-specific CTCF binding to the nearest transcription start sites and/or topologically associated domains (TADs) is largely similar to musculus-common CTCF sites. Remarkably, we discovered a recurrent regulatory architecture consisting of a CTCF binding site and an interferon gene that appears to have been tandemly duplicated to create a 15-gene cluster on chromosome 4, thus forming a novel BL6 specific immune locus in which CTCF may play a regulatory role. Conclusions Our results demonstrate that thousands of CTCF binding sites show multiple functional signatures rapidly after incorporation into the genome.
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Affiliation(s)
- Dhoyazan Azazi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.,German Cancer Research Center (DKFZ), Division Regulatory Genomics and Cancer Evolution, 69120, Heidelberg, Germany
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. .,University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK. .,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Ejigu GF, Jung J. Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. BIOLOGY 2020; 9:E295. [PMID: 32962098 PMCID: PMC7565776 DOI: 10.3390/biology9090295] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022]
Abstract
Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to decode the information contained in nucleotide sequences. This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders. Here, we present a summary of both structural and functional annotations, as well as the associated comparative annotation tools and pipelines. We highlight visualization tools that immensely aid the annotation process and the contributions of the scientific community to the annotation. Further, we discuss quality-control practices and the need for re-annotation, and highlight the future of annotation.
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Affiliation(s)
| | - Jaehee Jung
- Department of Information and Communication Engineering, Myongji University, Yongin-si 17058, Gyeonggi-do, Korea;
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29
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Hughes DC, Baehr LM, Driscoll JR, Lynch SA, Waddell DS, Bodine SC. Identification and characterization of Fbxl22, a novel skeletal muscle atrophy-promoting E3 ubiquitin ligase. Am J Physiol Cell Physiol 2020; 319:C700-C719. [PMID: 32783651 DOI: 10.1152/ajpcell.00253.2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Muscle-specific E3 ubiquitin ligases have been identified in muscle atrophy-inducing conditions. The purpose of the current study was to explore the functional role of F-box and leucine-rich protein 22 (Fbxl22), and a newly identified splice variant (Fbxl22-193), in skeletal muscle homeostasis and neurogenic muscle atrophy. In mouse C2C12 muscle cells, promoter fragments of the Fbxl22 gene were cloned and fused with the secreted alkaline phosphatase reporter gene to assess the transcriptional regulation of Fbxl22. The tibialis anterior muscles of male C57/BL6 mice (12-16 wk old) were electroporated with expression plasmids containing the cDNA of two Fbxl22 splice variants and tissues collected after 7, 14, and 28 days. Gastrocnemius muscles of wild-type and muscle-specific RING finger 1 knockout (MuRF1 KO) mice were electroporated with an Fbxl22 RNAi or empty plasmid and denervated 3 days posttransfection, and tissues were collected 7 days postdenervation. The full-length gene and novel splice variant are transcriptionally induced early (after 3 days) during neurogenic muscle atrophy. In vivo overexpression of Fbxl22 isoforms in mouse skeletal muscle leads to evidence of myopathy/atrophy, suggesting that both are involved in the process of neurogenic muscle atrophy. Knockdown of Fbxl22 in the muscles of MuRF1 KO mice resulted in significant additive muscle sparing 7 days after denervation. Targeting two E3 ubiquitin ligases appears to have a strong additive effect on protecting muscle mass loss with denervation, and these findings have important implications in the development of therapeutic strategies to treat muscle atrophy.
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Affiliation(s)
- David C Hughes
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Leslie M Baehr
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Julia R Driscoll
- Department of Biology, University of North Florida, Jacksonville, Florida
| | - Sarah A Lynch
- Department of Biology, University of North Florida, Jacksonville, Florida
| | - David S Waddell
- Department of Biology, University of North Florida, Jacksonville, Florida
| | - Sue C Bodine
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
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Laptev I, Shvetsova E, Levitskii S, Serebryakova M, Rubtsova M, Bogdanov A, Kamenski P, Sergiev P, Dontsova O. Mouse Trmt2B protein is a dual specific mitochondrial metyltransferase responsible for m 5U formation in both tRNA and rRNA. RNA Biol 2020; 17:441-450. [PMID: 31736397 PMCID: PMC7237156 DOI: 10.1080/15476286.2019.1694733] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/27/2019] [Accepted: 11/14/2019] [Indexed: 10/25/2022] Open
Abstract
RNA molecules of all species contain modified nucleotides and particularly m5U residues. The vertebrate mitochondrial small subunit rRNA contains m5U nucleotide in a unique site. In this work we found an enzyme, TRMT2B, responsible for the formation of this nucleotide and m5U residues in a number of mitochondrial tRNA species. Inactivation of the Trmt2B gene leads to a reduction of the activity of respiratory chain complexes I, III and IV, containing the subunits synthesized by the mitochondrial protein synthesis apparatus. Comparative sequence analysis of m5U-specific RNA methyltransferases revealed an unusual evolutionary pathway of TRMT2B formation which includes consecutive substrate specificity switches from the large subunit rRNA to tRNA and then to the small subunit rRNA.
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Affiliation(s)
- Ivan Laptev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Shvetsova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey Levitskii
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Marina Serebryakova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow Region, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Rubtsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Bogdanov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Piotr Kamenski
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, Russia
| | - Olga Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow Region, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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31
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Determinants of enhancer and promoter activities of regulatory elements. Nat Rev Genet 2019; 21:71-87. [DOI: 10.1038/s41576-019-0173-8] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2019] [Indexed: 12/13/2022]
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Kasuga Y, Fudge AD, Zhang Y, Li H. Characterization of a long noncoding RNA Pcdh17it as a novel marker for immature premyelinating oligodendrocytes. Glia 2019; 67:2166-2177. [PMID: 31328332 DOI: 10.1002/glia.23684] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 01/12/2023]
Abstract
Oligodendrocyte precursors (OPs) proliferate and differentiate into oligodendrocytes (OLs) during postnatal development and into adulthood in the central nervous system (CNS). Following the initiation of differentiation, OPs give rise to immature, premyelinating OLs, which undergo further differentiation and mature into myelin-forming OLs. We identified an immature OL-specific long noncoding RNA, named Pcdh17it. Through co-localization analysis and morphological characterization of OLs, we found that Pcdh17it is a specific marker for newly born immature OLs in the developing and adult forebrain of mice, and we used this new marker to analyze OL generation over the lifespan of mice. Pcdh17it is an effective tool for monitoring newly born OLs in adult brain, allowing detailed study of the dynamics of OP differentiation into OLs in the normal and pathological CNS.
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Affiliation(s)
- Yusuke Kasuga
- Wolfson Institute for Biomedical Research, University College London, London, UK
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Alexander D Fudge
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Yumeng Zhang
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Huiliang Li
- Wolfson Institute for Biomedical Research, University College London, London, UK
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Abstract
Genetic, transcriptional, and post-transcriptional variations shape the transcriptome of individual cells, rendering establishing an exhaustive set of reference RNAs a complicated matter. Current reference transcriptomes, which are based on carefully curated transcripts, are lagging behind the extensive RNA variation revealed by massively parallel sequencing. Much may be missed by ignoring this unreferenced RNA diversity. There is plentiful evidence for non-reference transcripts with important phenotypic effects. Although reference transcriptomes are inestimable for gene expression analysis, they may turn limiting in important medical applications. We discuss computational strategies for retrieving hidden transcript diversity.
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Affiliation(s)
- Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248, Paris, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.
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Cao F, Li X, Yang Y, Fang H, Qu H, Chang N, Ma Q, Cao W, Zhou J, Wang W. Toward Candidate Proteomic Biomarkers in Clinical Monitoring of Acute Promyelocytic Leukemia Treatment with Arsenic Trioxide. ACTA ACUST UNITED AC 2019; 23:119-130. [PMID: 30767729 DOI: 10.1089/omi.2018.0178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Fenglin Cao
- Department of Central Laboratory, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xingang Li
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Yiju Yang
- The Third People's Hospital of Hainan Province, Sanya, China
| | - Honghong Fang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Haixia Qu
- Bioyong (Beijing) Technology Co., Ltd., Beijing, China
| | - Naibai Chang
- Department of Hematology, Beijing Hospital, Beijing, China
| | - Qingwei Ma
- Bioyong (Beijing) Technology Co., Ltd., Beijing, China
| | - Weifan Cao
- College of Life Science, Northeast Forest University, Harbin, China
| | - Jin Zhou
- Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
- School of Public Health, Taishan Medical University, Taishan, China
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35
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Pan LX, Li LY, Zhou H, Cheng SQ, Liu YM, Lian PP, Li L, Wang LL, Rong SJ, Shen CP, Li J, Xu T. TMEM100 mediates inflammatory cytokines secretion in hepatic stellate cells and its mechanism research. Toxicol Lett 2019; 317:82-91. [PMID: 30639579 DOI: 10.1016/j.toxlet.2018.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/31/2018] [Accepted: 12/21/2018] [Indexed: 12/12/2022]
Abstract
Recent studies have shown that Transmembrane protein 100 (TMEM100) is a gene at locus 17q32 encoding a 134-amino acid protein with two hypothetical transmembrane domainsa, and first identified as a transcript from the mouse genome. As a downstream target gene of bone morphogenetic protein (BMP)-activin receptor-like kinase 1 (ALK1) signaling, it was activated to participate in inducing arterial endothelium differentiation, maintaining vascular integrity, promoting cell apoptosis, inhibiting metastasis and proliferation of cancer cells. However, evidence for the function of TMEM100 in inflammation is still limited. In this study, we explore the role of TMEM100 in inflammatory cytokine secretion and the role of MAPK signaling pathways in tumor necrosis factor-alpha (TNF-α)-induced TMEM100 expression in LX-2 cells. We found that the expression of TMEM100 was decreased markedly in human liver fibrosis tissues, and its expression was also inhibited in LX-2 cells induced by TNF-α, suggesting that it might be associated with the development of inflammation. Therefore, we demonstrated that overexpression of TMEM100 by transfecting pEGFP-C2-TMEM100 could lead to the down-regulation of IL-1β and IL-6 secretion. Moreover, we found that expression changes of TMEM100 could be involved in inhibition or activation of MAPK signaling pathways accompanied with regulating phosphorylation levels of ERK and JNK protein in response to TNF-α. These results suggested that TMEM100 might play an important role in the secretion of inflammatory cytokines (IL-1β and IL-6) of LX-2 cells induced by TNF-α, and MAPK (ERK and JNK) signaling pathways might participate in its induction of expression.
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Affiliation(s)
- Lin-Xin Pan
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Liang-Yun Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Hong Zhou
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China; Anhui Provincial Cancer Hospital, West Branch of The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230031, China
| | - Shu-Qi Cheng
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Yu-Min Liu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Pan-Pan Lian
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Li Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China; Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Le-le Wang
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Shan-Jie Rong
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Chuan-Pu Shen
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China
| | - Jun Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China.
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, 230032, China.
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SAKAKI Y. A Japanese history of the Human Genome Project. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2019; 95:441-458. [PMID: 31611500 PMCID: PMC6819149 DOI: 10.2183/pjab.95.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/04/2019] [Indexed: 06/10/2023]
Abstract
The Human Genome Project (HGP) is one of the most important international achievements in life sciences, to which Japanese scientists made remarkable contributions. In the early 1980s, Akiyoshi Wada pioneered the first project for the automation of DNA sequencing technology. Ken-ichi Matsubara exhibited exceptional leadership to launch the comprehensive human genome program in Japan. Hideki Kambara made a major contribution by developing a key device for high-speed DNA sequencers, which enabled scientists to construct human genome draft sequences. The RIKEN team led by Yoshiyuki Sakaki (the author) played remarkable roles in the draft sequencing and completion of chromosomes 21, 18, and 11. Additionally, the Keio University team led by Nobuyoshi Shimizu made noteworthy contributions to the completion of chromosomes 22, 21, and 8. In April 2003, the Japanese team joined the international consortium in declaring the completion of the human genome sequence. Consistent with the HGP mandate, Japan has successfully developed a wide range of ambitious genomic sciences.
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Affiliation(s)
- Yoshiyuki SAKAKI
- Emeritus Professor, The University of Tokyo, Tokyo, Japan
- Emeritus Professor, Kyushu University, Fukuoka, Japan
- Emeritus Researcher, RIKEN, Wako, Saitama, Japan
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Porf-2 = Arhgap39 = Vilse: A Pivotal Role in Neurodevelopment, Learning and Memory. eNeuro 2018; 5:eN-REV-0082-18. [PMID: 30406180 PMCID: PMC6220574 DOI: 10.1523/eneuro.0082-18.2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 01/06/2023] Open
Abstract
Small GTP-converting enzymes, GTPases, are essential for the efficient completion of many physiological and developmental processes. They are regulated by GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs). Arhgap39, also known as preoptic regulatory factor-2 (Porf-2) or Vilse, a member of the Rho GAP group, was first identified in 1990 in the rat CNS. It has since been shown to regulate apoptosis, cell migration, neurogenesis, and cerebral and hippocampal dendritic spine morphology. It plays a pivotal role in neurodevelopment and learning and memory. Homologous or orthologous genes are found in more than 280 vertebrate and invertebrate species, suggesting preservation through evolution. Not surprisingly, loss of the Arhgap39/Porf-2 gene in mice manifests as an embryonic lethal condition. Although Arhgap39/Porf-2 is highly expressed in the brain, it is also widely distributed throughout the body, with potential additional roles in oncogenesis and morphogenesis. This review summarizes, for the first time, the known information about this gene under its various names, in addition to considering its transcripts and proteins. The majority of findings described have been made in rats, mice, humans, and fruit flies. This work surveys the known functions, functional mediators, variables modifying expression and upstream regulators of expression, and potential physiological and pathological roles of Arhgap39/Porf-2 in health and disease.
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38
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Realizing the significance of noncoding functionality in clinical genomics. Exp Mol Med 2018; 50:1-8. [PMID: 30089779 PMCID: PMC6082831 DOI: 10.1038/s12276-018-0087-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 03/04/2018] [Accepted: 03/09/2018] [Indexed: 12/14/2022] Open
Abstract
Clinical genomics promises unprecedented precision in understanding the genetic basis of disease. Understanding the impact of variation across the genome is required to realize this potential. Currently, clinical genomics analyses focus on protein-coding genes. However, the noncoding genome is substantially larger than the protein-coding counterpart, and contains structural, regulatory, and transcribed information that needs to be incorporated into genome annotations if the full extent of the opportunity to use genomic information in healthcare is to be realized. This article reviews the challenges and opportunities in unlocking the clinical significance of coding and noncoding genomic information and translating its utility in practice. Most of the DNA in the genome does not consist of genes that code for proteins, and understanding the function of these less examined parts of our genetic material is essential to fully understand human development and disease. Brian Gloss and Marcel Dinger at the Garvan Institute of Medical Research in Sydney, Australia, review the challenges and opportunities in unraveling the clinical significance of all parts of our DNA. Many regions of DNA that do not encode protein molecules perform crucial functions in regulating the activity and interactions of the protein-coding genes. Variations in these regions may significantly influence the risks and causes of disease. Studying all parts of the genome will be critical for ensuring that the powerful modern techniques of genetic analysis have maximal impact on healthcare.
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39
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Chowdhury S, Zhang J, Kurgan L. In Silico Prediction and Validation of Novel RNA Binding Proteins and Residues in the Human Proteome. Proteomics 2018; 18:e1800064. [PMID: 29806170 DOI: 10.1002/pmic.201800064] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/05/2018] [Indexed: 12/22/2022]
Abstract
Deciphering a complete landscape of protein-RNA interactions in the human proteome remains an elusive challenge. We computationally elucidate RNA binding proteins (RBPs) using an approach that complements previous efforts. We employ two modern complementary sequence-based methods that provide accurate predictions from the structured and the intrinsically disordered sequences, even in the absence of sequence similarity to the known RBPs. We generate and analyze putative RNA binding residues on the whole proteome scale. Using a conservative setting that ensures low, 5% false positive rate, we identify 1511 putative RBPs that include 281 known RBPs and 166 RBPs that were previously predicted. We empirically demonstrate that these overlaps are statistically significant. We also validate the putative RBPs based on two major hallmarks of their RNA binding residues: high levels of evolutionary conservation and enrichment in charged amino acids. Moreover, we show that the novel RBPs are significantly under-annotated functionally which coincides with the fact that they were not yet found to interact with RNAs. We provide two examples of our novel putative RBPs for which there is recent evidence of their interactions with RNAs. The dataset of novel putative RBPs and RNA binding residues for the future hypothesis generation is provided in the Supporting Information.
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Affiliation(s)
- Shomeek Chowdhury
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, Maharaja Sayajirao University of Baroda, Gujarat, 390005, India.,Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Jian Zhang
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA.,School of Computer and Information Technology, Xinyang Normal University, Xinyang, 464000, P. R. China
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
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40
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Trejo-Reveles V, McTeir L, Summers K, Rainger J. An analysis of anterior segment development in the chicken eye. Mech Dev 2018. [PMID: 29526791 DOI: 10.1016/j.mod.2018.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Precise anterior segment (AS) development in the vertebrate eye is essential for maintaining ocular health throughout life. Disruptions to genetic programs can lead to severe structural AS disorders at birth, while more subtle AS defects may disrupt the drainage of ocular fluids and cause dysregulation of intraocular pressure homeostasis, leading to progressive vision loss. To date, the mouse has served as the major model to study AS development and pathogenesis. Here we present an accurate histological atlas of chick AS formation throughout eye development, with a focus on the formation of drainage structures. We performed expression analyses for a panel of known AS disorder genes, and showed that chick PAX6 was localized to cells of neural retina and surface ectoderm derived structures, displaying remarkable similarity to the mouse. We provide a comparison to mouse and humans for chick AS developmental sequences and structures and confirm that AS development shares common features in all three species, although the main AS structures in the chick are developed prior to hatching. These features enable the unique experimental advantages inherent to chick embryos, and we therefore propose the chick as an appropriate additional model for AS development and disease.
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Affiliation(s)
- Violeta Trejo-Reveles
- The Roslin Institute Chicken Embryology (RICE) group, The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Lynn McTeir
- The Roslin Institute Chicken Embryology (RICE) group, The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Kim Summers
- Mater Research Institute-UQ, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia.
| | - Joe Rainger
- The Roslin Institute Chicken Embryology (RICE) group, The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
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41
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Cipriano A, Ballarino M. The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions. Front Mol Biosci 2018; 5:20. [PMID: 29560353 PMCID: PMC5845540 DOI: 10.3389/fmolb.2018.00020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/20/2018] [Indexed: 12/12/2022] Open
Abstract
The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as “junk” DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs), which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins) endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.
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Affiliation(s)
- Andrea Cipriano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
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42
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Zheng Q, Yang HJ, Yuan YA. Autoantigen La Regulates MicroRNA Processing from Stem–Loop Precursors by Association with DGCR8. Biochemistry 2017; 56:6098-6110. [DOI: 10.1021/acs.biochem.7b00693] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Quan Zheng
- Department
of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Hai-Jie Yang
- Department
of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Y. Adam Yuan
- Department
of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
- National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Suzhou, Jiangsu 215123, China
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43
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The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types. Sci Data 2017; 4:170113. [PMID: 28850107 PMCID: PMC5574373 DOI: 10.1038/sdata.2017.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 07/14/2017] [Indexed: 11/11/2022] Open
Abstract
The latest project from the FANTOM consortium, an international collaborative effort initiated by RIKEN, generated atlases of transcriptomes, in particular promoters, transcribed enhancers, and long-noncoding RNAs, across a diverse set of mammalian cell types. Here, we introduce the FANTOM5 collection, bringing together data descriptors, articles and analyses of FANTOM5 data published across the Nature Research journals. Associated data are openly available for reuse by all.
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44
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Noguchi S, Arakawa T, Fukuda S, Furuno M, Hasegawa A, Hori F, Ishikawa-Kato S, Kaida K, Kaiho A, Kanamori-Katayama M, Kawashima T, Kojima M, Kubosaki A, Manabe RI, Murata M, Nagao-Sato S, Nakazato K, Ninomiya N, Nishiyori-Sueki H, Noma S, Saijyo E, Saka A, Sakai M, Simon C, Suzuki N, Tagami M, Watanabe S, Yoshida S, Arner P, Axton RA, Babina M, Baillie JK, Barnett TC, Beckhouse AG, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Carlisle AJ, Clevers HC, Davis CA, Detmar M, Dohi T, Edge AS, Edinger M, Ehrlund A, Ekwall K, Endoh M, Enomoto H, Eslami A, Fagiolini M, Fairbairn L, Farach-Carson MC, Faulkner GJ, Ferrai C, Fisher ME, Forrester LM, Fujita R, Furusawa JI, Geijtenbeek TB, Gingeras T, Goldowitz D, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Hasegawa Y, Herlyn M, Heutink P, Hitchens KJ, Hume DA, Ikawa T, Ishizu Y, Kai C, Kawamoto H, Kawamura YI, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klein S, Klinken SP, Knox AJ, Kojima S, Koseki H, Koyasu S, Lee W, Lennartsson A, Mackay-sim A, Mejhert N, Mizuno Y, Morikawa H, Morimoto M, Moro K, Morris KJ, Motohashi H, Mummery CL, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nozaki T, Ogishima S, Ohkura N, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Passier R, Patrikakis M, Pombo A, Pradhan-Bhatt S, Qin XY, Rehli M, Rizzu P, Roy S, Sajantila A, Sakaguchi S, Sato H, Satoh H, Savvi S, Saxena A, Schmidl C, Schneider C, Schulze-Tanzil GG, Schwegmann A, Sheng G, Shin JW, Sugiyama D, Sugiyama T, Summers KM, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tomoiu A, Toyoda H, van de Wetering M, van den Berg LM, Verardo R, Vijayan D, Wells CA, Winteringham LN, Wolvetang E, Yamaguchi Y, Yamamoto M, Yanagi-Mizuochi C, Yoneda M, Yonekura Y, Zhang PG, Zucchelli S, Abugessaisa I, Arner E, Harshbarger J, Kondo A, Lassmann T, Lizio M, Sahin S, Sengstag T, Severin J, Shimoji H, Suzuki M, Suzuki H, Kawai J, Kondo N, Itoh M, Daub CO, Kasukawa T, Kawaji H, Carninci P, Forrest AR, Hayashizaki Y. FANTOM5 CAGE profiles of human and mouse samples. Sci Data 2017; 4:170112. [PMID: 28850106 PMCID: PMC5574368 DOI: 10.1038/sdata.2017.112] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/25/2017] [Indexed: 01/22/2023] Open
Abstract
In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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Affiliation(s)
- Shuhei Noguchi
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Arakawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Shiro Fukuda
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Masaaki Furuno
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Fumi Hori
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Sachi Ishikawa-Kato
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Kaoru Kaida
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Ai Kaiho
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | | | - Tsugumi Kawashima
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Miki Kojima
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | | | - Ri-ichiroh Manabe
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Sayaka Nagao-Sato
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | | | - Noriko Ninomiya
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori-Sueki
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Shohei Noma
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Eri Saijyo
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Saka
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Mizuho Sakai
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | | | - Naoko Suzuki
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Michihira Tagami
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Shoko Watanabe
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | | | - Peter Arner
- Department of Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
- Karolinska University Hospital, Center for Metabolism and Endocrinology, 141 86, Stockholm, Sweden
| | - Richard A. Axton
- Scottish Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Magda Babina
- Department of Dermatology and Allergy, Charite University Medicine Berlin, Charitéplatz 1, 10117 Berlin, German
| | - J. Kenneth Baillie
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK
| | - Timothy C. Barnett
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | | | - Antje Blumenthal
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102 Australia
| | - Beatrice Bodega
- IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143 Rome, Italy
| | - Alessandro Bonetti
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - James Briggs
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, St Lucia, QLD 4072, Australia
| | - Frank Brombacher
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
- Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Anzio Road, Observatory 7925, Cape Town, South Africa
| | - Ailsa J. Carlisle
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK
| | - Hans C. Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- University Medical Centre Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands
| | - Carrie A. Davis
- Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11797, USA
| | - Michael Detmar
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 3, HCI H 303, 8093 Zurich, Switzerland
| | - Taeko Dohi
- Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan
| | - Albert S.B. Edge
- Department of Otology and Laryngology, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Matthias Edinger
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93053 Regensburg, Germany
- RCI Regensburg Centre for Interventional Immunology, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93053 Regensburg, Germany
| | - Anna Ehrlund
- Department of Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
- Karolinska University Hospital, Center for Metabolism and Endocrinology, 141 86, Stockholm, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Halsovagen 7-9, SE-141 83 Huddinge, Sweden
| | - Mitsuhiro Endoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hideki Enomoto
- Laboratory for Neuronal Differentiation and Regeneration, RIKEN Center for Developmental Biology, Chuou-ku, Kobe 650-0047, Japan
| | - Afsaneh Eslami
- Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Michela Fagiolini
- F.M. Kirby Neurobiology Center, Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Lynsey Fairbairn
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK
| | - Mary C. Farach-Carson
- The University of Texas Health Science Center at Houston, Houston, TX 77251-1892, USA
| | - Geoffrey J. Faulkner
- Cancer Biology Program, Mater Medical Research Institute, South Brisbane, Queensland 4101, Australia
| | - Carmelo Ferrai
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center, Robert Roessle Str.10, 13125 Berlin, Germany
| | - Malcolm E. Fisher
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK
| | - Lesley M. Forrester
- Scottish Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Rie Fujita
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Jun-ichi Furusawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Teunis B. Geijtenbeek
- Experimental Immunology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Thomas Gingeras
- Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11797, USA
| | - Daniel Goldowitz
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Sven Guhl
- Department of Dermatology and Allergy, Charite University Medicine Berlin, Charitéplatz 1, 10117 Berlin, German
| | - Reto Guler
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
- Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Anzio Road, Observatory 7925, Cape Town, South Africa
| | - Stefano Gustincich
- Neuroscience, SISSA, Via Bonomea 265, 34136 Trieste, Italy
- Department of Neuroscience and Brian Technologies, Italian Istitute of Technology, Via Morego 30, Genova, Italy
| | - Thomas J. Ha
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Masahide Hamaguchi
- Department of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mitsuko Hara
- RIKEN Center for Life Science Technologies, Wako, Saitama 351-0198, Japan
| | - Yuki Hasegawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Meenhard Herlyn
- Melanoma Research Center, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE)-Tübingen, Otfried Müller Straße 23, 72076 Tübingen, Germany
| | - Kelly J. Hitchens
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, St Lucia, QLD 4072, Australia
| | - David A. Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK
| | - Tomokatsu Ikawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yuri Ishizu
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Chieko Kai
- Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Hiroshi Kawamoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki I. Kawamura
- Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan
| | - Judith S. Kempfle
- Department of Otology and Laryngology, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Tony J. Kenna
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, QLD 4102, Australia
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Halsovagen 7-9, SE-141 83 Huddinge, Sweden
- Department of Genetics and Molecular Medicine, King's College London, Guy’s St Thomas Street, London, UK
| | - Levon M. Khachigian
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia
- Vascular Biology and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Toshio Kitamura
- Division of Cellular Therapy and Division of Stem Cell Signaling, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Sarah Klein
- Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 3, HCI H 303, 8093 Zurich, Switzerland
| | - S. Peter Klinken
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Alan J. Knox
- Respiratory Medicine, University of Nottingham, Hucknall Road, Nottingham NG5 1PB, UK
| | - Soichi Kojima
- RIKEN Center for Life Science Technologies, Wako, Saitama 351-0198, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Shigeo Koyasu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Weonju Lee
- Dermatology, School of Medicine Kyungpook National University, Jung-gu, Daegu 41944, Korea
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Halsovagen 7-9, SE-141 83 Huddinge, Sweden
| | | | - Niklas Mejhert
- Department of Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
- Karolinska University Hospital, Center for Metabolism and Endocrinology, 141 86, Stockholm, Sweden
| | - Yosuke Mizuno
- Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan
| | - Hiromasa Morikawa
- Department of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mitsuru Morimoto
- Laboratory for Neuronal Differentiation and Regeneration, RIKEN Center for Developmental Biology, Chuou-ku, Kobe 650-0047, Japan
| | - Kazuyo Moro
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Kelly J. Morris
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center, Robert Roessle Str.10, 13125 Berlin, Germany
| | - Hozumi Motohashi
- Center for Radioisotope Sciences, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Christine L. Mummery
- Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Yutaka Nakachi
- Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan
| | - Fumio Nakahara
- Division of Cellular Therapy and Division of Stem Cell Signaling, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Toshiyuki Nakamura
- Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Tadasuke Nozaki
- Department of Clinical Molecular Genetics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Soichi Ogishima
- Department of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Naganari Ohkura
- Department of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuhiro Ohshima
- Department of Biochemistry, Ohu University School of Pharmaceutical Sciences, Koriyama, Fukushima 963-8611 Japan
| | - Mariko Okada-Hatakeyama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Insitute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasushi Okazaki
- Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan
| | - Valerio Orlando
- IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, 00143 Rome, Italy
- Environmental Epigenetics Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Dmitry A. Ovchinnikov
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, St Lucia, QLD 4072, Australia
| | - Robert Passier
- Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Margaret Patrikakis
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Ana Pombo
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center, Robert Roessle Str.10, 13125 Berlin, Germany
| | | | - Xian-Yang Qin
- RIKEN Center for Life Science Technologies, Wako, Saitama 351-0198, Japan
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93053 Regensburg, Germany
- RCI Regensburg Centre for Interventional Immunology, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93053 Regensburg, Germany
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE)-Tübingen, Otfried Müller Straße 23, 72076 Tübingen, Germany
| | - Sugata Roy
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Antti Sajantila
- Hjelt Institute, Department of Forensic Medicine, University of Helsinki, Kytosuontie 11, 003000 Helsinki, Finland
| | - Shimon Sakaguchi
- Department of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroki Sato
- Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Hironori Satoh
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Suzana Savvi
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
- Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Anzio Road, Observatory 7925, Cape Town, South Africa
| | - Alka Saxena
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Christian Schmidl
- Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93053 Regensburg, Germany
| | | | - Gundula G. Schulze-Tanzil
- Department of Orthopedic, Trauma and Reconstructive Surgery, Charite Universitatsmedizin Berlin, Charitéplatz 1, 10117 Berlin, German
| | - Anita Schwegmann
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
- Immunology of Infectious Diseases, Faculty of Health Sciences, South African Medical Research Council (SAMRC), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town Component, Anzio Road, Observatory 7925, Cape Town, South Africa
| | - Guojun Sheng
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Chuo-ku, Kumamoto 860-0811, Japan
| | - Jay W. Shin
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Daisuke Sugiyama
- Department of Clinical Study, Center for Advanced Medical Innovation, Kyushu University, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Takaaki Sugiyama
- Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Kim M. Summers
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK
| | - Naoko Takahashi
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Takai
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Hiroshi Tanaka
- Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hideki Tatsukawa
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Andru Tomoiu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK
| | - Hiroo Toyoda
- Center for Radioisotope Sciences, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Marc van de Wetering
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Linda M. van den Berg
- Experimental Immunology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Roberto Verardo
- Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie (LNCIB), Padriciano 99, 34149 Trieste, Italy
| | - Dipti Vijayan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Christine A. Wells
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, MDHS, University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, St Lucia, QLD 4072, Australia
| | - Yoko Yamaguchi
- Department of Biochemistry, Nihon University School of Dentistry, Chiyoda-ku, Tokyo 101-8310, Japan
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Chiyo Yanagi-Mizuochi
- Center for Clinical and Translational Reseach, Kyushu University Hospital, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Misako Yoneda
- Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Yohei Yonekura
- Laboratory for Neuronal Differentiation and Regeneration, RIKEN Center for Developmental Biology, Chuou-ku, Kobe 650-0047, Japan
| | - Peter G. Zhang
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | | | - Imad Abugessaisa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Erik Arner
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Kondo
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Timo Lassmann
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
- Telethon Kids Institute, the University of Western Australia, Perth, WA, Australia
| | - Marina Lizio
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Serkan Sahin
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | | | - Jessica Severin
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Hisashi Shimoji
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
- Preventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Kanagawa 230-0045, Japan
| | - Masanori Suzuki
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Harukazu Suzuki
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kawai
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Naoto Kondo
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Carsten O. Daub
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
- Department of Biosciences and Nutrition, Karolinska Institutet, Halsovagen 7-9, SE-141 83 Huddinge, Sweden
| | - Takeya Kasukawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
- Preventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Alistair R.R. Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
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Li B, Qing T, Zhu J, Wen Z, Yu Y, Fukumura R, Zheng Y, Gondo Y, Shi L. A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq. Sci Rep 2017; 7:4200. [PMID: 28646208 PMCID: PMC5482823 DOI: 10.1038/s41598-017-04520-z] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/16/2017] [Indexed: 02/07/2023] Open
Abstract
The mouse has been widely used as a model organism for studying human diseases and for evaluating drug safety and efficacy. Many diseases and drug effects exhibit tissue specificity that may be reflected by tissue-specific gene-expression profiles. Here we construct a comprehensive mouse transcriptomic BodyMap across 17 tissues of six-weeks old C57BL/6JJcl mice using RNA-seq. We find different expression patterns between protein-coding and non-coding genes. Liver expressed the least complex transcriptomes, that is, the smallest number of genes detected in liver across all 17 tissues, whereas testis and ovary harbor more complex transcriptomes than other tissues. We report a comprehensive list of tissue-specific genes across 17 tissues, along with a list of 4,781 housekeeping genes in mouse. In addition, we propose a list of 27 consistently and highly expressed genes that can be used as reference controls in expression-profiling analysis. Our study provides a unique resource of mouse gene-expression profiles, which is helpful for further biomedical research.
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Affiliation(s)
- Bin Li
- Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Tao Qing
- Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Jinhang Zhu
- Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
| | - Zhuo Wen
- Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Ying Yu
- Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438, China
| | - Ryutaro Fukumura
- Mutagenesis and Genomics Team, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yuanting Zheng
- Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438, China.
| | - Yoichi Gondo
- Mutagenesis and Genomics Team, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan.
| | - Leming Shi
- Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438, China.
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46
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Huynh NPT, Anderson BA, Guilak F, McAlinden A. Emerging roles for long noncoding RNAs in skeletal biology and disease. Connect Tissue Res 2017; 58:116-141. [PMID: 27254479 PMCID: PMC5301950 DOI: 10.1080/03008207.2016.1194406] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Normal skeletal development requires tight coordination of transcriptional networks, signaling pathways, and biomechanical cues, and many of these pathways are dysregulated in pathological conditions affecting cartilage and bone. Recently, a significant role has been identified for long noncoding RNAs (lncRNAs) in developing and maintaining cellular phenotypes, and improvements in sequencing technologies have led to the identification of thousands of lncRNAs across diverse cell types, including the cells within cartilage and bone. It is clear that lncRNAs play critical roles in regulating gene expression. For example, they can function as epigenetic regulators in the nucleus via chromatin modulation to control gene transcription, or in the cytoplasm, where they can function as scaffolds for protein-binding partners or modulate the activity of other coding and noncoding RNAs. In this review, we discuss the growing list of lncRNAs involved in normal development and/or homeostasis of the skeletal system, the potential mechanisms by which these lncRNAs might function, and recent improvements in the methodologies available to study lncRNA functions in vitro and in vivo. Finally, we address the likely utility of lncRNAs as biomarkers and therapeutic targets for diseases of the skeletal system, including osteoarthritis, osteoporosis, and in cancers of the skeletal system.
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Affiliation(s)
- Nguyen P. T. Huynh
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Shriners Hospitals for Children – St. Louis, St. Louis, MO, USA,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Britta A. Anderson
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Shriners Hospitals for Children – St. Louis, St. Louis, MO, USA,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, USA,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA,Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA
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47
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Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest ARR, Kasukawa T, Kawaji H. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res 2016; 45:D737-D743. [PMID: 27794045 PMCID: PMC5210666 DOI: 10.1093/nar/gkw995] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/17/2016] [Indexed: 12/26/2022] Open
Abstract
Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.
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Affiliation(s)
- Marina Lizio
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shuei Noguchi
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Kondo
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jessica Severin
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chris Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, 84R01, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - David Arenillas
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital Research, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, 0372 Oslo, Norway
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Leninsky prospect, 33, build. 2, 119071 Moscow, Russia.,Vavilov Institute of General Genetics, Russian Academy of Science, Gubkina str. 3, Moscow 119991, Russia
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7-9, 14183 Huddinge, Sweden
| | - Finn Drabløs
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), P.O. Box 8905, NO-7491 Trondheim, Norway
| | - Jordan A Ramilowski
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Owen Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke's National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore
| | - Julian Gough
- Department of Computer Science, University of Bristol, Merchant Venturers Building, Woodland Road, Bristol BS8 1UB UK
| | - Robin Andersson
- The Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Albin Sandelin
- Section for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Hans Ienasescu
- Section for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Hiromasa Ono
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), 1111 Yata, Mishima 411-8540, Japan
| | - Hidemasa Bono
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), 1111 Yata, Mishima 411-8540, Japan
| | - Yoshihide Hayashizaki
- Preventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Systems biology and Genomics, Harry Perkins Institute of MedicalResearch, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6008, Australia
| | - Piero Carninci
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takeya Kasukawa
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan .,RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Preventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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48
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Abstract
The discovery of an ever-expanding plethora of coding and non-coding RNAs with nodal and causal roles in the regulation of lung physiology and disease is reinvigorating interest in the clinical utility of the oligonucleotide therapeutic class. This is strongly supported through recent advances in nucleic acids chemistry, synthetic oligonucleotide delivery and viral gene therapy that have succeeded in bringing to market at least three nucleic acid-based drugs. As a consequence, multiple new candidates such as RNA interference modulators, antisense, and splice switching compounds are now progressing through clinical evaluation. Here, manipulation of RNA for the treatment of lung disease is explored, with emphasis on robust pharmacological evidence aligned to the five pillars of drug development: exposure to the appropriate tissue, binding to the desired molecular target, evidence of the expected mode of action, activity in the relevant patient population and commercially viable value proposition.
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49
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Zhou S, Treloar AE, Lupien M. Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations. Cancer Discov 2016; 6:1215-1229. [PMID: 27807102 DOI: 10.1158/2159-8290.cd-16-0745] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/17/2016] [Indexed: 12/14/2022]
Abstract
The emergence of whole-genome annotation approaches is paving the way for the comprehensive annotation of the human genome across diverse cell and tissue types exposed to various environmental conditions. This has already unmasked the positions of thousands of functional cis-regulatory elements integral to transcriptional regulation, such as enhancers, promoters, and anchors of chromatin interactions that populate the noncoding genome. Recent studies have shown that cis-regulatory elements are commonly the targets of genetic and epigenetic alterations associated with aberrant gene expression in cancer. Here, we review these findings to showcase the contribution of the noncoding genome and its alteration in the development and progression of cancer. We also highlight the opportunities to translate the biological characterization of genetic and epigenetic alterations in the noncoding cancer genome into novel approaches to treat or monitor disease. SIGNIFICANCE The majority of genetic and epigenetic alterations accumulate in the noncoding genome throughout oncogenesis. Discriminating driver from passenger events is a challenge that holds great promise to improve our understanding of the etiology of different cancer types. Advancing our understanding of the noncoding cancer genome may thus identify new therapeutic opportunities and accelerate our capacity to find improved biomarkers to monitor various stages of cancer development. Cancer Discov; 6(11); 1215-29. ©2016 AACR.
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Affiliation(s)
- Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aislinn E Treloar
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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50
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Wu T, Ren MX, Chen GP, Jin ZM, Wang G. Rrp15 affects cell cycle, proliferation, and apoptosis in NIH3T3 cells. FEBS Open Bio 2016; 6:1085-1092. [PMID: 27833849 PMCID: PMC5095146 DOI: 10.1002/2211-5463.12128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 07/27/2016] [Accepted: 09/08/2016] [Indexed: 11/06/2022] Open
Abstract
Riken 2810430M08 (hereinafter referred to as Rrp15) is a newly identified and reported gene from the mouse genome. In our previous work, we found that the gene had a relationship with the proliferation and activation of T cells. Rrp15 protein is highly homologous with RRP15 (budding yeast), which has an important role in ribosomal RNA processing. We explored the potential function of Rrp15 in apoptosis, cell proliferation, and its involvement with RNA in the nucleus. We constructed a knockdown of the Rrp15 gene in NIH3T3 cells and then performed real-time PCR, western blotting, flow cytometry, and immunofluorescence to determine the function of the Rrp15 gene. Knockdown of the Rrp15 gene suppresses proliferation and induces apoptosis. We also found that the Rrp15 protein was normally distributed in the nucleus and bound to RNA or pre-RNA in the nucleus. Additionally, Rrp15 altered the activity of the 20S proteasome. Rrp15 promotes proliferation and inhibits apoptosis in NIH3T3 cells and may have a relationship with RNA in the nucleus.
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Affiliation(s)
- Tao Wu
- Department of Cardiology The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Mei-Xia Ren
- Department of Cardiology The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Guo-Ping Chen
- Department of Endocrinology The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Zheng-Ming Jin
- Department of Cardiology The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Gang Wang
- Cancer Institute of Integrative Medicine Tongde Hospital of Zhejiang Province Zhejiang Provincial Academy of Traditional Chinese Medicine Hangzhou China
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