1
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Sollier E, Heilmann J, Gerhauser C, Scherer M, Plass C, Lutsik P. Figeno: multi-region genomic figures with long-read support. Bioinformatics 2024; 40:btae354. [PMID: 38857451 PMCID: PMC11184262 DOI: 10.1093/bioinformatics/btae354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/17/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
SUMMARY The vast amount of publicly available genomic data requires analysis and visualization tools. Here, we present figeno, an application for generating publication-quality FIgures for GENOmics. Figeno particularly focuses on multi-region views across genomic breakpoints and on long reads with base modifications. In addition, we support epigenomic data including ATAC-seq, ChIP-seq or HiC, as well as whole genome sequencing data with copy numbers and structural variants. AVAILABILITY AND IMPLEMENTATION Figeno is available as a python package with both a command line and graphical user interface. It can be installed via PyPI and the source code is available at https://github.com/CompEpigen/figeno.
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Affiliation(s)
- Etienne Sollier
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, 69120 Heidelberg, Germany
| | - Jessica Heilmann
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Clarissa Gerhauser
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael Scherer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Oncology, KU Leuven, 3000 Leuven, Belgium
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2
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Passeri I, Vaccaro F, Mengoni A, Fagorzi C. Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges. Int J Mol Sci 2024; 25:4425. [PMID: 38674013 PMCID: PMC11050019 DOI: 10.3390/ijms25084425] [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: 02/17/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The universality of DNA methylation as an epigenetic regulatory mechanism belongs to all biological kingdoms. However, while eukaryotic systems have been the primary focus of DNA methylation studies, the molecular mechanisms in prokaryotes are less known. Nevertheless, DNA methylation in prokaryotes plays a pivotal role in many cellular processes such as defense systems against exogenous DNA, cell cycle dynamics, and gene expression, including virulence. Thanks to single-molecule DNA sequencing technologies, genome-wide identification of methylated DNA is becoming feasible on a large scale, providing the possibility to investigate more deeply the presence, variability, and roles of DNA methylation. Here, we present an overview of the multifaceted roles of DNA methylation in prokaryotes and suggest research directions and tools which can enable us to better understand the contribution of DNA methylation to prokaryotic genome evolution and adaptation. In particular, we emphasize the need to understand the presence and role of transgenerational inheritance, as well as the impact of epigenomic signatures on adaptation and genome evolution. Research directions and the importance of novel computational tools are underlined.
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Affiliation(s)
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, 50121 Firenze, Italy; (I.P.); (F.V.); (C.F.)
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3
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Wang B, Jia Y, Dang N, Yu J, Bush SJ, Gao S, He W, Wang S, Guo H, Yang X, Ma W, Ye K. Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae. BMC Genomics 2024; 25:356. [PMID: 38600443 PMCID: PMC11005252 DOI: 10.1186/s12864-024-10280-8] [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: 02/28/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Centromeres play a crucial and conserved role in cell division, although their composition and evolutionary history in green algae, the evolutionary ancestors of land plants, remains largely unknown. RESULTS We constructed near telomere-to-telomere (T2T) assemblies for two Trebouxiophyceae species, Chlorella sorokiniana NS4-2 and Chlorella pyrenoidosa DBH, with chromosome numbers of 12 and 13, and genome sizes of 58.11 Mb and 53.41 Mb, respectively. We identified and validated their centromere sequences using CENH3 ChIP-seq and found that, similar to humans and higher plants, the centromeric CENH3 signals of green algae display a pattern of hypomethylation. Interestingly, the centromeres of both species largely comprised transposable elements, although they differed significantly in their composition. Species within the Chlorella genus display a more diverse centromere composition, with major constituents including members of the LTR/Copia, LINE/L1, and LINE/RTEX families. This is in contrast to green algae including Chlamydomonas reinhardtii, Coccomyxa subellipsoidea, and Chromochloris zofingiensis, in which centromere composition instead has a pronounced single-element composition. Moreover, we observed significant differences in the composition and structure of centromeres among chromosomes with strong collinearity within the Chlorella genus, suggesting that centromeric sequence evolves more rapidly than sequence in non-centromeric regions. CONCLUSIONS This study not only provides high-quality genome data for comparative genomics of green algae but gives insight into the composition and evolutionary history of centromeres in early plants, laying an important foundation for further research on their evolution.
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Affiliation(s)
- Bo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Yanyan Jia
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Ningxin Dang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jie Yu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Stephen J Bush
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Shenghan Gao
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Wenxi He
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Sirui Wang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Hongtao Guo
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Xiaofei Yang
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Weimin Ma
- College of Life Sciences, Shanghai Normal University, Shanghai, China.
| | - Kai Ye
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China.
- Faculty of Science, Leiden University, Leiden, The Netherlands.
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4
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Kume K, Kurashige T, Muguruma K, Morino H, Tada Y, Kikumoto M, Miyamoto T, Akutsu SN, Matsuda Y, Matsuura S, Nakamori M, Nishiyama A, Izumi R, Niihori T, Ogasawara M, Eura N, Kato T, Yokomura M, Nakayama Y, Ito H, Nakamura M, Saito K, Riku Y, Iwasaki Y, Maruyama H, Aoki Y, Nishino I, Izumi Y, Aoki M, Kawakami H. CGG repeat expansion in LRP12 in amyotrophic lateral sclerosis. Am J Hum Genet 2023; 110:1086-1097. [PMID: 37339631 PMCID: PMC10357476 DOI: 10.1016/j.ajhg.2023.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/25/2023] [Accepted: 05/25/2023] [Indexed: 06/22/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the degeneration of motor neurons. Although repeat expansion in C9orf72 is its most common cause, the pathogenesis of ALS isn't fully clear. In this study, we show that repeat expansion in LRP12, a causative variant of oculopharyngodistal myopathy type 1 (OPDM1), is a cause of ALS. We identify CGG repeat expansion in LRP12 in five families and two simplex individuals. These ALS individuals (LRP12-ALS) have 61-100 repeats, which contrasts with most OPDM individuals with repeat expansion in LRP12 (LRP12-OPDM), who have 100-200 repeats. Phosphorylated TDP-43 is present in the cytoplasm of iPS cell-derived motor neurons (iPSMNs) in LRP12-ALS, a finding that reproduces the pathological hallmark of ALS. RNA foci are more prominent in muscle and iPSMNs in LRP12-ALS than in LRP12-OPDM. Muscleblind-like 1 aggregates are observed only in OPDM muscle. In conclusion, CGG repeat expansions in LRP12 cause ALS and OPDM, depending on the length of the repeat. Our findings provide insight into the repeat length-dependent switching of phenotypes.
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Affiliation(s)
- Kodai Kume
- Department of Molecular Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takashi Kurashige
- Department of Neurology, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan
| | - Keiko Muguruma
- Department of iPS Cell Applied Medicine, Graduate School of Medicine, Kansai Medical University, Osaka, Japan
| | - Hiroyuki Morino
- Department of Molecular Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yui Tada
- Department of Molecular Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Mai Kikumoto
- Department of Molecular Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan; Department of Clinical Neuroscience and Therapeutics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Tatsuo Miyamoto
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Silvia Natsuko Akutsu
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yukiko Matsuda
- Department of Molecular Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Shinya Matsuura
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Masahiro Nakamori
- Department of Clinical Neuroscience and Therapeutics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Ayumi Nishiyama
- Department of Neurology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Rumiko Izumi
- Department of Neurology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Masashi Ogasawara
- Department of Neuromuscular Research, National Institute of Neuroscience, National Centre of Neurology and Psychiatry, National Centre Hospital, Tokyo, Japan
| | - Nobuyuki Eura
- Department of Neuromuscular Research, National Institute of Neuroscience, National Centre of Neurology and Psychiatry, National Centre Hospital, Tokyo, Japan
| | - Tamaki Kato
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Mamoru Yokomura
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yoshiaki Nakayama
- Department of Neurology, Wakayama Medical University, Wakayama, Japan
| | - Hidefumi Ito
- Department of Neurology, Wakayama Medical University, Wakayama, Japan
| | | | - Kayoko Saito
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yuichi Riku
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Yasushi Iwasaki
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Hirofumi Maruyama
- Department of Clinical Neuroscience and Therapeutics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Centre of Neurology and Psychiatry, National Centre Hospital, Tokyo, Japan
| | - Yuishin Izumi
- Department of Neurology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Hideshi Kawakami
- Department of Molecular Epidemiology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan.
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5
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Smits N, Faulkner GJ. Nanopore Sequencing to Identify Transposable Element Insertions and Their Epigenetic Modifications. Methods Mol Biol 2023; 2607:151-171. [PMID: 36449163 DOI: 10.1007/978-1-0716-2883-6_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Over the past 20 years, high-throughput genomic assays have fundamentally changed how transposable elements (TEs) are studied. While short-read DNA sequencing has been at the heart of these efforts, novel technologies that generate longer reads are driving a shift in the field. Long-read sequencing now permits locus-specific approaches to locate individual TE insertions and understand their epigenetic and transcriptional regulation, while still profiling TE activity genome-wide. Here we provide detailed guidelines to implement Oxford Nanopore Technologies (ONT) sequencing to identify polymorphic TE insertions and profile TE epigenetic landscapes. Using human long interspersed element-1 (LINE-1, L1) as an example, we explain the procedures involved, including final visualization, and potential bottlenecks and pitfalls. ONT sequencing will be, in our view, a workhorse technology for the foreseeable future in the TE field.
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Affiliation(s)
- Nathan Smits
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia.
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia.
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6
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Riccardi C, Passeri I, Cangioli L, Fagorzi C, Fondi M, Mengoni A. Crossing Bacterial Genomic Features and Methylation Patterns with MeStudio: An Epigenomic Analysis Tool. Int J Mol Sci 2022; 24:ijms24010159. [PMID: 36613603 PMCID: PMC9820200 DOI: 10.3390/ijms24010159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
DNA methylation is one of the most observed epigenetic modifications. It is present in eukaryotes and prokaryotes and is related to several biological phenomena, including gene flow and adaptation to environmental conditions. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomic landscape of individuals and populations. Here, we present a pipeline named MeStudio, with the aim of analyzing and combining genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences (CDSs) and noncoding sequences, including both intergenic sequences and sequences upstream of the CDS. We apply this novel tool, showing the usage and performance of MeStudio, on a set of single-molecule real-time sequencing outputs from strains of the bacterial species Sinorhizobium meliloti.
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7
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Cheetham SW, Kindlova M, Ewing AD. Methylartist: Tools for Visualising Modified Bases from Nanopore Sequence Data. Bioinformatics 2022; 38:3109-3112. [PMID: 35482479 PMCID: PMC9154218 DOI: 10.1093/bioinformatics/btac292] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/11/2022] [Accepted: 04/21/2022] [Indexed: 11/12/2022] Open
Abstract
Summary Methylartist is a consolidated suite of tools for processing, visualizing and analysing nanopore-derived modified base calls. All detectable methylation types (e.g. 5mCpG, 5hmC, 6mA) are supported, enabling integrated study of base pairs when modified naturally or as part of an experimental protocol. Availability and implementation Methylartist is implemented in Python and is installable via PyPI and bioconda. Source code and test data are available at https://github.com/adamewing/methylartist. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Seth W Cheetham
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Michaela Kindlova
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
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8
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Pryszcz LP, Novoa EM. ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. Bioinformatics 2021; 38:257-260. [PMID: 34293115 DOI: 10.1093/bioinformatics/btab539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/07/2021] [Accepted: 07/21/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION DNA and RNA modifications can now be identified using nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data. RESULTS Here, we present ModPhred, a versatile toolkit that facilitates DNA and RNA modification analysis from nanopore sequencing reads in a user-friendly manner. ModPhred integrates probabilistic DNA and RNA modification information within the FASTQ and BAM file formats, can be used to encode multiple types of modifications simultaneously, and its output can be easily coupled to genomic track viewers, facilitating the visualization and analysis of DNA and RNA modification information in individual reads in a simple and computationally efficient manner. AVAILABILITY AND IMPLEMENTATION ModPhred is available at https://github.com/novoalab/modPhred, is implemented in Python3, and is released under an MIT license. Docker images with all dependencies preinstalled are also provided. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.,International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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9
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Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021; 39:1348-1365. [PMID: 34750572 PMCID: PMC8988251 DOI: 10.1038/s41587-021-01108-x] [Citation(s) in RCA: 427] [Impact Index Per Article: 142.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.
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10
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Su S, Gouil Q, Blewitt ME, Cook D, Hickey PF, Ritchie ME. NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data. PLoS Comput Biol 2021; 17:e1009524. [PMID: 34695109 PMCID: PMC8568149 DOI: 10.1371/journal.pcbi.1009524] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 11/04/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022] Open
Abstract
A key benefit of long-read nanopore sequencing technology is the ability to detect modified DNA bases, such as 5-methylcytosine. The lack of R/Bioconductor tools for the effective visualization of nanopore methylation profiles between samples from different experimental groups led us to develop the NanoMethViz R package. Our software can handle methylation output generated from a range of different methylation callers and manages large datasets using a compressed data format. To fully explore the methylation patterns in a dataset, NanoMethViz allows plotting of data at various resolutions. At the sample-level, we use dimensionality reduction to look at the relationships between methylation profiles in an unsupervised way. We visualize methylation profiles of classes of features such as genes or CpG islands by scaling them to relative positions and aggregating their profiles. At the finest resolution, we visualize methylation patterns across individual reads along the genome using the spaghetti plot and heatmaps, allowing users to explore particular genes or genomic regions of interest. In summary, our software makes the handling of methylation signal more convenient, expands upon the visualization options for nanopore data and works seamlessly with existing methylation analysis tools available in the Bioconductor project. Our software is available at https://bioconductor.org/packages/NanoMethViz.
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Affiliation(s)
- Shian Su
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail: (SS); (MER)
| | - Quentin Gouil
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Marnie E. Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Dianne Cook
- Econometrics & Business Statistics, Monash University, Melbourne, Australia
| | - Peter F. Hickey
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Matthew E. Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail: (SS); (MER)
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11
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Bruijnesteijn J, van der Wiel M, de Groot NG, Bontrop RE. Rapid Characterization of Complex Killer Cell Immunoglobulin-Like Receptor (KIR) Regions Using Cas9 Enrichment and Nanopore Sequencing. Front Immunol 2021; 12:722181. [PMID: 34594334 PMCID: PMC8476923 DOI: 10.3389/fimmu.2021.722181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
Long-read sequencing approaches have considerably improved the quality and contiguity of genome assemblies. Such platforms bear the potential to resolve even extremely complex regions, such as multigenic immune families and repetitive stretches of DNA. Deep sequencing coverage, however, is required to overcome low nucleotide accuracy, especially in regions with high homopolymer density, copy number variation, and sequence similarity, such as the MHC and KIR gene clusters of the immune system. Therefore, we have adapted a targeted enrichment protocol in combination with long-read sequencing to efficiently annotate complex KIR gene regions. Using Cas9 endonuclease activity, segments of the KIR gene cluster were enriched and sequenced on an Oxford Nanopore Technologies platform. This provided sufficient coverage to accurately resolve and phase highly complex KIR haplotypes. Our strategy eliminates PCR-induced amplification errors, facilitates rapid characterization of large and complex multigenic regions, including its epigenetic footprint, and is applicable in multiple species, even in the absence of a reference genome.
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Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Marit van der Wiel
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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12
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Wang B, Yang X, Jia Y, Xu Y, Jia P, Dang N, Wang S, Xu T, Zhao X, Gao S, Dong Q, Ye K. High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 20:4-13. [PMID: 34487862 PMCID: PMC9510872 DOI: 10.1016/j.gpb.2021.08.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023]
Abstract
Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, and genomics. However, the latest version of reference genome still contains significant number of missing segments. Here, we report a high-quality and almost complete Col-0 genome assembly with two gaps (Col-XJTU) using combination of Oxford Nanopore Technology ultra-long reads, PacBio high-fidelity long reads, and Hi-C data. The total genome assembly size is 133,725,193 bp, introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference genome. All five chromosomes of Col-XJTU assembly are highly accurate with consensus quality (QV) scores > 60 (ranging from 62 to 68), which are higher than those of TAIR10.1 reference (QV scores ranging from 45 to 52). We have completely resolved chromosome (Chr) 3 and Chr5 in a telomere-to-telomere manner. Chr4 has been completely resolved except the nucleolar organizing regions, which comprise long repetitive DNA fragments. The Chr1 centromere (CEN1), reportedly around 9 Mb in length, is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats. Using the cutting-edge sequencing data and novel computational approaches, we assembled about 4 Mb of sequence for CEN1 and a 3.5-Mb-long CEN2. We investigated the structure and epigenetics of centromeres. We detected four clusters of CEN180 monomers, and found that the centromere-specific histone H3-like protein (CENH3) exhibits a strong preference for CEN180 cluster 3. Moreover, we observed hypomethylation patterns in CENH3-enriched regions. We believe that this high-quality genome assembly, Col-XJTU, would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms, as well as genetic and epigenetic features in plants.
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Affiliation(s)
- Bo Wang
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiaofei Yang
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Yanyan Jia
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yu Xu
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Peng Jia
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Ningxin Dang
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Songbo Wang
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Tun Xu
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xixi Zhao
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Shenghan Gao
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Quanbin Dong
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Kai Ye
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
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Dimond JL, Nguyen N, Roberts SB. DNA METHYLATION PROFILING OF A CNIDARIAN-ALGAL SYMBIOSIS USING NANOPORE SEQUENCING. G3-GENES GENOMES GENETICS 2021; 11:6275752. [PMID: 33989381 PMCID: PMC8496274 DOI: 10.1093/g3journal/jkab148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/15/2021] [Indexed: 11/20/2022]
Abstract
Symbiosis with protists is common among cnidarians such as corals and sea anemones and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species.
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Affiliation(s)
- James L Dimond
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98195 USA.,Western Washington University, Shannon Point Marine Center, 1900 Shannon Point Rd., Anacortes, WA 98221 USA
| | - Nhung Nguyen
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY 14456 USA.,South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98195 USA
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14
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Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing. Nat Biotechnol 2021; 39:1278-1291. [PMID: 33986546 DOI: 10.1038/s41587-021-00915-6] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/06/2021] [Indexed: 01/23/2023]
Abstract
Nanopore RNA sequencing shows promise as a method for discriminating and identifying different RNA modifications in native RNA. Expanding on the ability of nanopore sequencing to detect N6-methyladenosine, we show that other modifications, in particular pseudouridine (Ψ) and 2'-O-methylation (Nm), also result in characteristic base-calling 'error' signatures in the nanopore data. Focusing on Ψ modification sites, we detected known and uncovered previously unreported Ψ sites in mRNAs, non-coding RNAs and rRNAs, including a Pus4-dependent Ψ modification in yeast mitochondrial rRNA. To explore the dynamics of pseudouridylation, we treated yeast cells with oxidative, cold and heat stresses and detected heat-sensitive Ψ-modified sites in small nuclear RNAs, small nucleolar RNAs and mRNAs. Finally, we developed a software, nanoRMS, that estimates per-site modification stoichiometries by identifying single-molecule reads with altered current intensity and trace profiles. This work demonstrates that Nm and Ψ RNA modifications can be detected in cellular RNAs and that their modification stoichiometry can be quantified by nanopore sequencing of native RNA.
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15
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Hardy A, Matelot M, Touzeau A, Klopp C, Lopez-Roques C, Duharcourt S, Defrance M. DNAModAnnot: a R toolbox for DNA modification filtering and annotation. Bioinformatics 2021; 37:2738-2740. [PMID: 33471071 PMCID: PMC8428616 DOI: 10.1093/bioinformatics/btab032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/17/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Long-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect the integration of genomic annotation and comprehensive filtering when analyzing patterns of modified bases detected using Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) data. Here, we present DNAModAnnot, a R package designed for the global analysis of DNA modification patterns using adapted filtering and visualization tools. RESULTS We tested our package using PacBio sequencing data to analyze patterns of the 6-methyladenine (6 mA) in the ciliate Paramecium tetraurelia, in which high 6 mA amounts were previously reported. We found Paramecium tetraurelia 6 mA genome-wide distribution to be similar to other ciliates. We also performed 5-methylcytosine (5mC) analysis in human lymphoblastoid cells using ONT data and confirmed previously known patterns of 5mC. DNAModAnnot provides a toolbox for the genome-wide analysis of different DNA modifications using PacBio and ONT long-read sequencing data. AVAILABILITY DNAModAnnot is distributed as a R package available via GitHub (https://github.com/AlexisHardy/DNAModAnnot). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alexis Hardy
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Mélody Matelot
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Amandine Touzeau
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Christophe Klopp
- Plateforme bioinformatique Genotoul, UR875 Mathématique et Informatique Appliquée de Toulouse, INRA, 31326, Castanet-Tolosan, France
| | | | - Sandra Duharcourt
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Matthieu Defrance
- Université Libre de Bruxelles, Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, 1050, Belgium
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