1
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Yoshida Y, Shaikhutdinov N, Kozlova O, Itoh M, Tagami M, Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Noma S, Cherkasov A, Gazizova G, Nasibullina A, Deviatiiarov R, Shagimardanova E, Ryabova A, Yamaguchi K, Bino T, Shigenobu S, Tokumoto S, Miyata Y, Cornette R, Yamada TG, Funahashi A, Tomita M, Gusev O, Kikawada T. High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance. NAR Genom Bioinform 2022; 4:lqac029. [PMID: 35387384 PMCID: PMC8982440 DOI: 10.1093/nargab/lqac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Non-biting midges (Chironomidae) are known to inhabit a wide range of environments, and certain species can tolerate extreme conditions, where the rest of insects cannot survive. In particular, the sleeping chironomid Polypedilum vanderplanki is known for the remarkable ability of its larvae to withstand almost complete desiccation by entering a state called anhydrobiosis. Chromosome numbers in chironomids are higher than in other dipterans and this extra genomic resource might facilitate rapid adaptation to novel environments. We used improved sequencing strategies to assemble a chromosome-level genome sequence for P. vanderplanki for deep comparative analysis of genomic location of genes associated with desiccation tolerance. Using whole genome-based cross-species and intra-species analysis, we provide evidence for the unique functional specialization of Chromosome 4 through extensive acquisition of novel genes. In contrast to other insect genomes, in the sleeping chironomid a uniquely high degree of subfunctionalization in paralogous anhydrobiosis genes occurs in this chromosome, as well as pseudogenization in a highly duplicated gene family. Our findings suggest that the Chromosome 4 in Polypedilum is a site of high genetic turnover, allowing it to act as a ‘sandbox’ for evolutionary experiments, thus facilitating the rapid adaptation of midges to harsh environments.
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Affiliation(s)
- Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Nurislam Shaikhutdinov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 21205, Russian Federation
| | - Olga Kozlova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Masayoshi Itoh
- Preventive Medicine & Diagnosis Innovation Program (PMI), RIKEN, Wako, Saitama 351-0198, Japan
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Michihira Tagami
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | | | - Miki Kojima-Ishiyama
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Shohei Noma
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Alexander Cherkasov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Guzel Gazizova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Aigul Nasibullina
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Ruslan Deviatiiarov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Elena Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Alina Ryabova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Takahiro Bino
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shoko Tokumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Yugo Miyata
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| | - Richard Cornette
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa 252-0882, Japan
- Faculty of Environment and Information studies, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Oleg Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- Department of Regulatory Transcriptomics for Medical Genetic Diagnostics, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Takahiro Kikawada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
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2
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Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC, Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH. Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun 2022; 13:1200. [PMID: 35232988 PMCID: PMC8888638 DOI: 10.1038/s41467-022-28758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mathys Grapotte
- Institut de Biologie Computationnelle, Montpellier, France.,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.,SANOFI R&D, Translational Sciences, Chilly Mazarin, France
| | - Manu Saraswat
- Institut de Biologie Computationnelle, Montpellier, France.,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Chloé Bessière
- Institut de Biologie Computationnelle, Montpellier, France.,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Christophe Menichelli
- Institut de Biologie Computationnelle, Montpellier, France.,LIRMM, Univ Montpellier, CNRS, Montpellier, France
| | | | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Shohei Noma
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Martin C Frith
- Artificial Intelligence Research Center, AIST, Tokyo, Japan.,Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.,AIST-Waseda University CBBD-OIL, AIST, Tokyo, Japan
| | | | | | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Laurent Bréhélin
- Institut de Biologie Computationnelle, Montpellier, France. .,LIRMM, Univ Montpellier, CNRS, Montpellier, France.
| | - Charles-Henri Lecellier
- Institut de Biologie Computationnelle, Montpellier, France. .,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France. .,LIRMM, Univ Montpellier, CNRS, Montpellier, France.
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3
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Morioka MS, Kawaji H, Nishiyori-Sueki H, Murata M, Kojima-Ishiyama M, Carninci P, Itoh M. Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites. Methods Mol Biol 2020; 2120:277-301. [PMID: 32124327 DOI: 10.1007/978-1-0716-0327-7_20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cap analysis of gene expression (CAGE) is an approach to identify and monitor the activity (transcription initiation frequency) of transcription start sites (TSSs) at single base-pair resolution across the genome. It has been effectively used to identify active promoter and enhancer regions in cancer cells, with potential utility to identify key factors to immunotherapy. Here, we overview a series of CAGE protocols and describe detailed experimental steps of the latest protocol based on the Illumina sequencing platform; both experimental steps (see Subheadings 3.1-3.11) and computational processing steps (see Subheadings 3.12-3.20) are described.
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Affiliation(s)
- Masaki Suimye Morioka
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Hideya Kawaji
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Yokohama, Kanagawa, Japan.,Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiromi Nishiyori-Sueki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Mitsuyoshi Murata
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Miki Kojima-Ishiyama
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Yokohama, Kanagawa, Japan.
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4
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Kawaji H, Lizio M, Itoh M, Kanamori-Katayama M, Kaiho A, Nishiyori-Sueki H, Shin JW, Kojima-Ishiyama M, Kawano M, Murata M, Ninomiya-Fukuda N, Ishikawa-Kato S, Nagao-Sato S, Noma S, Hayashizaki Y, Forrest AR, Carninci P. Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing. Genome Res 2014; 24:708-17. [PMID: 24676093 PMCID: PMC3975069 DOI: 10.1101/gr.156232.113] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 12/10/2013] [Indexed: 01/11/2023]
Abstract
CAGE (cap analysis gene expression) and RNA-seq are two major technologies used to identify transcript abundances as well as structures. They measure expression by sequencing from either the 5' end of capped molecules (CAGE) or tags randomly distributed along the length of a transcript (RNA-seq). Library protocols for clonally amplified (Illumina, SOLiD, 454 Life Sciences [Roche], Ion Torrent), second-generation sequencing platforms typically employ PCR preamplification prior to clonal amplification, while third-generation, single-molecule sequencers can sequence unamplified libraries. Although these transcriptome profiling platforms have been demonstrated to be individually reproducible, no systematic comparison has been carried out between them. Here we compare CAGE, using both second- and third-generation sequencers, and RNA-seq, using a second-generation sequencer based on a panel of RNA mixtures from two human cell lines to examine power in the discrimination of biological states, detection of differentially expressed genes, linearity of measurements, and quantification reproducibility. We found that the quantified levels of gene expression are largely comparable across platforms and conclude that CAGE and RNA-seq are complementary technologies that can be used to improve incomplete gene models. We also found systematic bias in the second- and third-generation platforms, which is likely due to steps such as linker ligation, cleavage by restriction enzymes, and PCR amplification. This study provides a perspective on the performance of these platforms, which will be a baseline in the design of further experiments to tackle complex transcriptomes uncovered in a wide range of cell types.
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Affiliation(s)
- Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Marina Lizio
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | | | - Ai Kaiho
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
| | - Hiromi Nishiyori-Sueki
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Jay W. Shin
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Miki Kojima-Ishiyama
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Mitsuoki Kawano
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
| | - Mitsuyoshi Murata
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Noriko Ninomiya-Fukuda
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
| | - Sachi Ishikawa-Kato
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Sayaka Nagao-Sato
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
| | - Shohei Noma
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
| | - Alistair R.R. Forrest
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - The FANTOM Consortium
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan
- RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan;4
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
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5
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Abstract
Cap analysis of gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. By the large-scale analysis of 5' end of transcripts using CAGE method, it enables not only determination of the transcription start site but also prediction of promoter region. Here we provide a protocol for the construction of no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE). We have excluded the commonly used PCR amplification and cleavage of restriction enzyme to eliminate any potential biases. As a result, we achieved less biased simple preparation process.
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Affiliation(s)
- Mitsuyoshi Murata
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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