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Bai X, Yao HC, Wu B, Liu LR, Ding YY, Xiao CL. DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing. Brief Bioinform 2024; 25:bbae413. [PMID: 39177264 PMCID: PMC11342253 DOI: 10.1093/bib/bbae413] [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: 02/21/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 08/24/2024] Open
Abstract
Recent nanopore sequencing system (R10.4) has enhanced base calling accuracy and is being increasingly utilized for detecting CpG methylation state. However, the robustness and universality of the methylation calling model in officially supplied Dorado remains poorly tested. In this study, we obtained heterogeneous datasets from human and plant sources to carry out comprehensive evaluations, which showed that Dorado performed significantly different across datasets. We therefore developed deep neural networks and implemented several optimizations in training a new model called DeepBAM. DeepBAM achieved superior and more stable performances compared with Dorado, including higher area under the ROC curves (98.47% on average and up to 7.36% improvement) and F1 scores (94.97% on average and up to 16.24% improvement) across the datasets. DeepBAM-based whole genome methylation frequencies have achieved >0.95 correlations with BS-seq on four of five datasets, outperforming Dorado in all instances. It enables unraveling allele-specific methylation patterns, including regions of transposable elements. The enhanced performance of DeepBAM paves the way for broader applications of nanopore sequencing in CpG methylation studies.
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Affiliation(s)
- Xin Bai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China
| | - Hui-Cong Yao
- School of Artificial Intelligence, Sun Yat-Sen University, Gaoxin District, Zhuhai 519000, China
| | - Bo Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China
| | - Luo-Ran Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China
| | - Yu-Ying Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China
| | - Chuan-Le Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 7 Jinsui Road, Tianhe District, Guangzhou 510060, China
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2
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Fu Y, Aganezov S, Mahmoud M, Beaulaurier J, Juul S, Treangen TJ, Sedlazeck FJ. MethPhaser: methylation-based long-read haplotype phasing of human genomes. Nat Commun 2024; 15:5327. [PMID: 38909018 PMCID: PMC11193733 DOI: 10.1038/s41467-024-49588-0] [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: 09/12/2023] [Accepted: 06/11/2024] [Indexed: 06/24/2024] Open
Abstract
The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease. However, phasing is limited by read length and stretches of homozygosity along the genome. To overcome this limitation, we designed MethPhaser, a method that utilizes methylation signals from Oxford Nanopore Technologies to extend Single Nucleotide Variation (SNV)-based phasing. We demonstrate that haplotype-specific methylations extensively exist in Human genomes and the advent of long-read technologies enabled direct report of methylation signals. For ONT R9 and R10 cell line data, we increase the phase length N50 by 78%-151% at a phasing accuracy of 83.4-98.7% To assess the impact of tissue purity and random methylation signals due to inactivation, we also applied MethPhaser on blood samples from 4 patients, still showing improvements over SNV-only phasing. MethPhaser further improves phasing across HLA and multiple other medically relevant genes, improving our understanding of how mutations interact across multiple phenotypes. The concept of MethPhaser can also be extended to non-human diploid genomes. MethPhaser is available at https://github.com/treangenlab/methphaser .
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Affiliation(s)
- Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Sissel Juul
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Fritz J Sedlazeck
- Department of Computer Science, Rice University, Houston, TX, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
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3
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Prawitt D, Eggermann T. Molecular mechanisms of human overgrowth and use of omics in its diagnostics: chances and challenges. Front Genet 2024; 15:1382371. [PMID: 38894719 PMCID: PMC11183334 DOI: 10.3389/fgene.2024.1382371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
Overgrowth disorders comprise a group of entities with a variable phenotypic spectrum ranging from tall stature to isolated or lateralized overgrowth of body parts and or organs. Depending on the underlying physiological pathway affected by pathogenic genetic alterations, overgrowth syndromes are associated with a broad spectrum of neoplasia predisposition, (cardio) vascular and neurodevelopmental anomalies, and dysmorphisms. Pathologic overgrowth may be of prenatal or postnatal onset. It either results from an increased number of cells (intrinsic cellular hyperplasia), hypertrophy of the normal number of cells, an increase in interstitial spaces, or from a combination of all of these. The underlying molecular causes comprise a growing number of genetic alterations affecting skeletal growth and Growth-relevant signaling cascades as major effectors, and they can affect the whole body or parts of it (mosaicism). Furthermore, epigenetic modifications play a critical role in the manifestation of some overgrowth diseases. The diagnosis of overgrowth syndromes as the prerequisite of a personalized clinical management can be challenging, due to their clinical and molecular heterogeneity. Physicians should consider molecular genetic testing as a first diagnostic step in overgrowth syndromes. In particular, the urgent need for a precise diagnosis in tumor predisposition syndromes has to be taken into account as the basis for an early monitoring and therapy. With the (future) implementation of next-generation sequencing approaches and further omic technologies, clinical diagnoses can not only be verified, but they also confirm the clinical and molecular spectrum of overgrowth disorders, including unexpected findings and identification of atypical cases. However, the limitations of the applied assays have to be considered, for each of the disorders of interest, the spectrum of possible types of genomic variants has to be considered as they might require different methodological strategies. Additionally, the integration of artificial intelligence (AI) in diagnostic workflows significantly contribute to the phenotype-driven selection and interpretation of molecular and physiological data.
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Affiliation(s)
- Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Thomas Eggermann
- Institute for Human Genetics and Genome Medicine, Medical Faculty, RWTH Aachen, Aachen, Germany
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Su C, Chandradoss KR, Malachowski T, Boya R, Ryu HS, Brennand KJ, Phillips-Cremins JE. MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591790. [PMID: 38746155 PMCID: PMC11092654 DOI: 10.1101/2024.04.29.591790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
More than 60 human disorders have been linked to unstable expansion of short tandem repeat (STR) tracts. STR length and the extent of DNA methylation is linked to disease pathology and can be mosaic in a cell type-specific manner in several repeat expansion disorders. Mosaic phenomenon have been difficult to study to date due to technical bias intrinsic to repeat sequences and the need for multi-modal measurements at single-allele resolution. Nanopore long-read sequencing accurately measures STR length and DNA methylation in the same single molecule but is cost prohibitive for studies assessing a target locus across multiple experimental conditions or patient samples. Here, we describe MASTR-seq, M ultiplexed A nalysis of S hort T andem R epeats, for cost-effective, high-throughput, accurate, multi-modal measurements of DNA methylation and STR genotype at single-allele resolution. MASTR-seq couples long-read sequencing, Cas9-mediated target enrichment, and PCR-free multiplexed barcoding to achieve a >ten-fold increase in on-target read mapping for 8-12 pooled samples in a single MinION flow cell. We provide a detailed experimental protocol and computational tools and present evidence that MASTR-seq quantifies tract length and DNA methylation status for CGG and CAG STR loci in normal-length and mutation-length human cell lines. The MASTR-seq protocol takes approximately eight days for experiments and one additional day for data processing and analyses. Key points We provide a protocol for MASTR-seq: M ultiplexed A nalysis of S hort T andem R epeats using Cas9-mediated target enrichment and PCR-free, multiplexed nanopore sequencing. MASTR-seq achieves a >10-fold increase in on-target read proportion for highly repetitive, technically inaccessible regions of the genome relevant for human health and disease.MASTR-seq allows for high-throughput, efficient, accurate, and cost-effective measurement of STR length and DNA methylation in the same single allele for up to 8-12 samples in parallel in one Nanopore MinION flow cell.
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Goldsmith C, Thevin V, Fesneau O, Matias MI, Perrault J, Abid AH, Taylor N, Dardalhon V, Marie JC, Hernandez-Vargas H. Single-Molecule DNA Methylation Reveals Unique Epigenetic Identity Profiles of T Helper Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1029-1039. [PMID: 38284984 PMCID: PMC11002815 DOI: 10.4049/jimmunol.2300091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024]
Abstract
Both identity and plasticity of CD4 T helper (Th) cells are regulated in part by epigenetic mechanisms. However, a method that reliably and readily profiles DNA base modifications is still needed to finely study Th cell differentiation. Cytosine methylation in CpG context (5mCpG) and cytosine hydroxymethylation (5hmCpG) are DNA modifications that identify stable cell phenotypes, but their potential to characterize intermediate cell transitions has not yet been evaluated. To assess transition states in Th cells, we developed a method to profile Th cell identity using Cas9-targeted single-molecule nanopore sequencing. Targeting as few as 10 selected genomic loci, we were able to distinguish major in vitro polarized murine T cell subtypes, as well as intermediate phenotypes, by their native DNA 5mCpG patterns. Moreover, by using off-target sequences, we were able to infer transcription factor activities relevant to each cell subtype. Detection of 5mCpG and 5hmCpG was validated on intestinal Th17 cells escaping transforming growth factor β control, using single-molecule adaptive sampling. A total of 21 differentially methylated regions mapping to the 10-gene panel were identified in pathogenic Th17 cells relative to their nonpathogenic counterpart. Hence, our data highlight the potential to exploit native DNA methylation profiling to study physiological and pathological transition states of Th cells.
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Affiliation(s)
- Chloe Goldsmith
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
| | - Valentin Thevin
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
| | - Olivier Fesneau
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
| | - Maria I Matias
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Julie Perrault
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Ali Hani Abid
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
| | - Naomi Taylor
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Pediatric Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD
| | - Valérie Dardalhon
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Julien C Marie
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
| | - Hector Hernandez-Vargas
- Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon, The French League Against Cancer Certified Team, INSERM U1052, CNRS UMR 5286, Léon Bérard Centre and University of Lyon, Lyon, France
- Genomics Consulting, Bron, France
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Ramirez P, Sun W, Kazempour Dehkordi S, Zare H, Fongang B, Bieniek KF, Frost B. Nanopore-based DNA long-read sequencing analysis of the aged human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578450. [PMID: 38370753 PMCID: PMC10871260 DOI: 10.1101/2024.02.01.578450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Aging disrupts cellular processes such as DNA repair and epigenetic control, leading to a gradual buildup of genomic alterations that can have detrimental effects in post-mitotic cells. Genomic alterations in regions of the genome that are rich in repetitive sequences, often termed "dark loci," are difficult to resolve using traditional sequencing approaches. New long-read technologies offer promising avenues for exploration of previously inaccessible regions of the genome. Using nanopore-based long-read whole-genome sequencing of DNA extracted from aged 18 human brains, we identify previously unreported structural variants and methylation patterns within repetitive DNA, focusing on transposable elements ("jumping genes") as crucial sources of variation, particularly in dark loci. Our analyses reveal potential somatic insertion variants and provides DNA methylation frequencies for many retrotransposon families. We further demonstrate the utility of this technology for the study of these challenging genomic regions in brains affected by Alzheimer's disease and identify significant differences in DNA methylation in pathologically normal brains versus those affected by Alzheimer's disease. Highlighting the power of this approach, we discover specific polymorphic retrotransposons with altered DNA methylation patterns. These retrotransposon loci have the potential to contribute to pathology, warranting further investigation in Alzheimer's disease research. Taken together, our study provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, structural variants, and DNA methylation in the aging brain affected with Alzheimer's disease neuropathology.
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Affiliation(s)
- Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Wenyan Sun
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
- School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri
| | - Shiva Kazempour Dehkordi
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Kevin F. Bieniek
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Pathology, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
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7
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Hubert JN, Iannuccelli N, Cabau C, Jacomet E, Billon Y, Serre RF, Vandecasteele C, Donnadieu C, Demars J. Detection of DNA methylation signatures through the lens of genomic imprinting. Sci Rep 2024; 14:1694. [PMID: 38242932 PMCID: PMC10798973 DOI: 10.1038/s41598-024-52114-3] [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: 10/03/2023] [Accepted: 01/14/2024] [Indexed: 01/21/2024] Open
Abstract
Genomic imprinting represents an original model of epigenetic regulation resulting in a parent-of-origin expression. Despite the critical role of imprinted genes in mammalian growth, metabolism and neuronal function, there is no molecular tool specifically targeting them for a systematic evaluation. We show here that enzymatic methyl-seq consistently outperforms the bisulfite-based standard in capturing 165 candidate regions for genomic imprinting in the pig. This highlights the potential for a turnkey, fully customizable and reliable capture tool of genomic regions regulated by cytosine methylation in any population of interest. For the field of genomic imprinting, it opens up the possibility of detecting multilocus imprinting variations across the genome, with implications for basic research, agrigenomics and clinical practice.
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Affiliation(s)
- Jean-Noël Hubert
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | | | - Cédric Cabau
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Eva Jacomet
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
- ENVT, 31326, Castanet-Tolosan, France
| | | | - Rémy-Félix Serre
- INRAE, GeT-PlaGe, Genotoul, 31326, Castanet-Tolosan, France
- Qualyse, Le Treuil, INRAE, 19000, Tulle, France
| | | | | | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.
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8
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Bond DM, Ortega-Recalde O, Laird MK, Hayakawa T, Richardson KS, Reese FCB, Kyle B, McIsaac-Williams BE, Robertson BC, van Heezik Y, Adams AL, Chang WS, Haase B, Mountcastle J, Driller M, Collins J, Howe K, Go Y, Thibaud-Nissen F, Lister NC, Waters PD, Fedrigo O, Jarvis ED, Gemmell NJ, Alexander A, Hore TA. The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes. Nat Commun 2023; 14:6364. [PMID: 37848431 PMCID: PMC10582058 DOI: 10.1038/s41467-023-41784-8] [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: 12/12/2022] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
Combining genome assembly with population and functional genomics can provide valuable insights to development and evolution, as well as tools for species management. Here, we present a chromosome-level genome assembly of the common brushtail possum (Trichosurus vulpecula), a model marsupial threatened in parts of their native range in Australia, but also a major introduced pest in New Zealand. Functional genomics reveals post-natal activation of chemosensory and metabolic genes, reflecting unique adaptations to altricial birth and delayed weaning, a hallmark of marsupial development. Nuclear and mitochondrial analyses trace New Zealand possums to distinct Australian subspecies, which have subsequently hybridised. This admixture allowed phasing of parental alleles genome-wide, ultimately revealing at least four genes with imprinted, parent-specific expression not yet detected in other species (MLH1, EPM2AIP1, UBP1 and GPX7). We find that reprogramming of possum germline imprints, and the wider epigenome, is similar to eutherian mammals except onset occurs after birth. Together, this work is useful for genetic-based control and conservation of possums, and contributes to understanding of the evolution of novel mammalian epigenetic traits.
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Affiliation(s)
- Donna M Bond
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | - Melanie K Laird
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, 060-0808, Japan
| | - Kyle S Richardson
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Biology Department, University of Montana Western, Dillon, MT, 59725, USA
| | - Finlay C B Reese
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Bruce Kyle
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | | | | | - Amy L Adams
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Wei-Shan Chang
- School of Life and Environmental Science, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
- Health and Biosecurity, CSIRO, Canberra, ACT, Australia
| | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | | | - Joanna Collins
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Yasuhiro Go
- Graduate School of Information Science, Hyogo University, Hyogo, Japan
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Aichi, Japan
- Department of System Neuroscience, National Institute for Physiological Sciences, Aichi, Japan
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas C Lister
- School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Alana Alexander
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Timothy A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand.
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9
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Hoffmann LB, McVicar EA, Harris RV, Collar-Fernández C, Clark MB, Hannan AJ, Pang TY. Increased paternal corticosterone exposure influences offspring behaviour and expression of urinary pheromones. BMC Biol 2023; 21:186. [PMID: 37667240 PMCID: PMC10478242 DOI: 10.1186/s12915-023-01678-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 08/07/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Studies have shown that paternal stress prior to conception can influence the innate behaviours of their offspring. The evolutionary impacts of such intergenerational effects are therefore of considerable interest. Our group previously showed in a model of daily stress that glucocorticoid treatment of adult male mouse breeders prior to conception leads to increased anxiety-related behaviours in male offspring. Here, we aimed to understand the transgenerational effects of paternal stress exposure on the social behaviour of progeny and its potential influence on reproductive success. RESULTS We assessed social parameters including social reward, male attractiveness and social dominance, in the offspring (F1) and grand-offspring (F2). We report that paternal corticosterone treatment was associated with increased display of subordination towards other male mice. Those mice were unexpectedly more attractive to female mice while expressing reduced levels of the key rodent pheromone Darcin, contrary to its conventional role in driving female attraction. We investigated the epigenetic regulation of major urinary protein (Mup) expression by performing the first Oxford Nanopore direct methylation of sperm DNA in a mouse model of stress, but found no differences in Mup genes that could be attributed to corticosterone-treatment. Furthermore, no overt differences of the prefrontal cortex transcriptome were found in F1 offspring, implying that peripheral mechanisms are likely contributing to the phenotypic differences. Interestingly, no phenotypic differences were observed in the F2 grand-offspring. CONCLUSIONS Overall, our findings highlight the potential of moderate paternal stress to affect intergenerational (mal)adaptive responses, informing future studies of adaptiveness in rodents, humans and other species.
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Affiliation(s)
- Lucas B Hoffmann
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
- Florey Department of Neuroscience and Mental Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, VIC, Australia
| | - Evangeline A McVicar
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Rebekah V Harris
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Coralina Collar-Fernández
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
- Florey Department of Neuroscience and Mental Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, VIC, Australia
| | - Michael B Clark
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Anthony J Hannan
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
- Florey Department of Neuroscience and Mental Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, VIC, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Terence Y Pang
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia.
- Florey Department of Neuroscience and Mental Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, VIC, Australia.
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia.
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10
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Loftus D, Bae B, Whilden CM, Whipple AJ. Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis. Genes Dev 2023; 37:829-843. [PMID: 37821107 PMCID: PMC10620047 DOI: 10.1101/gad.350896.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brains from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we showed that imprinted chromatin structure precedes imprinted expression at the locus. Additionally, activation of a distal enhancer induced imprinted expression of Kcnk9 in an allelic chromatin structure-dependent manner. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.
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Affiliation(s)
- Daniel Loftus
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Bongmin Bae
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Courtney M Whilden
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Amanda J Whipple
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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11
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Qin H, Liu J, Fang C, Deng Y, Zhang Y. DNA methylation: The epigenetic mechanism of Alzheimer's disease. IBRAIN 2023; 9:463-472. [PMID: 38680511 PMCID: PMC11045197 DOI: 10.1002/ibra.12121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 05/01/2024]
Abstract
Nowadays, with the development of the social health care system, there is an increasing trend towards an aging society. The incidence of Alzheimer's disease (AD) is also on the rise. AD is a kind of neurodegenerative disease that can be found in any age group. For years, scientists have been committing to discovering the cause of AD. DNA methylation is one of the most common epigenetic mechanisms in mammals and plays a vital role in the pathogenesis of several diseases, including tumors. Studying chemical changes in the epigenome, or DNA methylation can help us understand the effects of our environment and life on diseases, such as smoking, depression, and menopause, which may affect people's chances of developing Alzheimer's or other diseases. Recent studies have identified some crucial genes like ANK1, RHBDF2, ABCA7, and BIN1, linking DNA methylation to AD. This review focuses on elucidating the relationship between DNA methylation and the pathogenesis of AD and provides an outlook on possible targeted therapeutic modalities.
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Affiliation(s)
- Hao‐Yue Qin
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Jiao‐Yan Liu
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Chang‐Le Fang
- Faculty of Health SciencesUniversity of AdelaideMelbourneVICAustralia
| | - Yan‐Ping Deng
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Ying Zhang
- State Key Laboratories for Quality Research in Chinese Medicines, Faculty of PharmacyMacau University of Science and TechnologyMacauChina
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12
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Wouters M, Bastiaanse H, Rombauts S, de Vries L, De Pooter T, Strazisar M, Neutelings G, Vanholme R, Boerjan W. Suppression of the Arabidopsis cinnamoyl-CoA reductase 1-6 intronic T-DNA mutation by epigenetic modification. PLANT PHYSIOLOGY 2023; 192:3001-3016. [PMID: 37139862 PMCID: PMC7614886 DOI: 10.1093/plphys/kiad261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/10/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) transfer DNA (T-DNA) insertion collections are popular resources for fundamental plant research. Cinnamoyl-CoA reductase 1 (CCR1) catalyzes an essential step in the biosynthesis of the cell wall polymer lignin. Accordingly, the intronic T-DNA insertion mutant ccr1-6 has reduced lignin levels and shows a stunted growth phenotype. Here, we report restoration of the ccr1-6 mutant phenotype and CCR1 expression levels after a genetic cross with a UDP-glucosyltransferase 72e1 (ugt72e1),-e2,-e3 T-DNA mutant. We discovered that the phenotypic recovery was not dependent on the UGT72E family loss of function but due to an epigenetic phenomenon called trans T-DNA suppression. Via trans T-DNA suppression, the gene function of an intronic T-DNA mutant was restored after the introduction of an additional T-DNA sharing identical sequences, leading to heterochromatinization and splicing out of the T-DNA-containing intron. Consequently, the suppressed ccr1-6 allele was named epiccr1-6. Long-read sequencing revealed that epiccr1-6, not ccr1-6, carries dense cytosine methylation over the full length of the T-DNA. We showed that the SAIL T-DNA in the UGT72E3 locus could trigger the trans T-DNA suppression of the GABI-Kat T-DNA in the CCR1 locus. Furthermore, we scanned the literature for other potential cases of trans T-DNA suppression in Arabidopsis and found that 22% of the publications matching our query report on double or higher-order T-DNA mutants that meet the minimal requirements for trans T-DNA suppression. These combined observations indicate that intronic T-DNA mutants need to be used with caution since methylation of intronic T-DNA might derepress gene expression and can thereby confound results.
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Affiliation(s)
- Marlies Wouters
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Héloïse Bastiaanse
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Stéphane Rombauts
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Lisanne de Vries
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Godfrey Neutelings
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), UMR 8576, CNRS, Université de Lille, Lille, France
| | - Ruben Vanholme
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wout Boerjan
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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13
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Carrion SA, Michal JJ, Jiang Z. Imprinted Genes: Genomic Conservation, Transcriptomic Dynamics and Phenomic Significance in Health and Diseases. Int J Biol Sci 2023; 19:3128-3142. [PMID: 37416777 PMCID: PMC10321285 DOI: 10.7150/ijbs.83712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/25/2023] [Indexed: 07/08/2023] Open
Abstract
Since its discovery in 1991, genomic imprinting has been the subject of numerous studies into its mechanisms of establishment and regulation, evolution and function, and presence in multiple genomes. Disturbance of imprinting has been implicated in a range of diseases, ranging from debilitating syndromes to cancers to fetal deficiencies. Despite this, studies done on the prevalence and relevance of imprinting on genes have been limited in scope, tissue types available, and focus, by both availability and resources. This has left a gap in comparative studies. To address this, we assembled a collection of imprinted genes available in current literature covering five species. Here we sought to identify trends and motifs in the imprinted gene set (IGS) in three distinct arenas: evolutionary conservation, across-tissue expression, and health phenomics. Overall, we found that imprinted genes displayed less conservation and higher proportions of non-coding RNA while maintaining synteny. Maternally expressed genes (MEGs) and paternally expressed genes (PEGs) occupied distinct roles in tissue expression and biological pathway use, while imprinted genes collectively showed a broader tissue range, notable preference for tissue specific expression and limited gene pathways than comparable sex differentiation genes. Both human and murine imprinted genes showed the same clear phenotypic trends, that were distinct from those displayed by sex differentiation genes which were less involved in mental and nervous system disease. While both sets had representation across the genome, the IGS showed clearer clustering as expected, with PEGs significantly more represented than MEGs.
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Affiliation(s)
| | | | - Zhihua Jiang
- ✉ Corresponding author: Dr. Zhihua Jiang (ORCID ID: 0000-0003-1986-088X), Professor of Genome Biology. Phone: 509-335 8761;
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14
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Loftus D, Bae B, Whilden CM, Whipple AJ. Allelic chromatin structure primes imprinted expression of Kcnk9 during neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544389. [PMID: 37333073 PMCID: PMC10274912 DOI: 10.1101/2023.06.09.544389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brain from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we show that on the maternal allele enhancer-promoter contacts formed early in development prime the brain-specific potassium leak channel Kcnk9 for maternal expression prior to neurogenesis. In contrast, these enhancer-promoter contacts are blocked by CTCF on the paternal allele, preventing paternal Kcnk9 activation. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.
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Affiliation(s)
- Daniel Loftus
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Bongmin Bae
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Courtney M. Whilden
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Amanda J. Whipple
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
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15
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Akbari V, Jones SJM. Phasing DNA Methylation. Methods Mol Biol 2023; 2590:219-235. [PMID: 36335502 DOI: 10.1007/978-1-0716-2819-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Haplotyping enables the study of allele-specific events. Heterozygous variants, primarily single nucleotide variants (SNVs), enable the assignment of the paternal and maternal origin of the chromosomes and are widely employed to phase sequencing reads to their haplotype of origin. Certain long-read technologies enable the detection of both the DNA sequence and DNA modifications. These long reads and their inherent methylation information are suitable for genome-wide haplotyping and allele-specific DNA methylation analysis. Here, we describe the workflow to phase reads and DNA methylation using nanopore sequencing.
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Affiliation(s)
- Vahid Akbari
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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16
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Catacalos C, Krohannon A, Somalraju S, Meyer KD, Janga SC, Chakrabarti K. Epitranscriptomics in parasitic protists: Role of RNA chemical modifications in posttranscriptional gene regulation. PLoS Pathog 2022; 18:e1010972. [PMID: 36548245 PMCID: PMC9778586 DOI: 10.1371/journal.ppat.1010972] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
"Epitranscriptomics" is the new RNA code that represents an ensemble of posttranscriptional RNA chemical modifications, which can precisely coordinate gene expression and biological processes. There are several RNA base modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ), etc. that play pivotal roles in fine-tuning gene expression in almost all eukaryotes and emerging evidences suggest that parasitic protists are no exception. In this review, we primarily focus on m6A, which is the most abundant epitranscriptomic mark and regulates numerous cellular processes, ranging from nuclear export, mRNA splicing, polyadenylation, stability, and translation. We highlight the universal features of spatiotemporal m6A RNA modifications in eukaryotic phylogeny, their homologs, and unique processes in 3 unicellular parasites-Plasmodium sp., Toxoplasma sp., and Trypanosoma sp. and some technological advances in this rapidly developing research area that can significantly improve our understandings of gene expression regulation in parasites.
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Affiliation(s)
- Cassandra Catacalos
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Alexander Krohannon
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, United States of America
| | - Sahiti Somalraju
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, United States of America
| | - Kate D. Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, United States of America
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- * E-mail:
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17
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Akbari V, Hanlon VC, O’Neill K, Lefebvre L, Schrader KA, Lansdorp PM, Jones SJ. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq. CELL GENOMICS 2022; 3:100233. [PMID: 36777186 PMCID: PMC9903809 DOI: 10.1016/j.xgen.2022.100233] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/08/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Hundreds of loci in human genomes have alleles that are methylated differentially according to their parent of origin. These imprinted loci generally show little variation across tissues, individuals, and populations. We show that such loci can be used to distinguish the maternal and paternal homologs for all human autosomes without the need for the parental DNA. We integrate methylation-detecting nanopore sequencing with the long-range phase information in Strand-seq data to determine the parent of origin of chromosome-length haplotypes for both DNA sequence and DNA methylation in five trios with diverse genetic backgrounds. The parent of origin was correctly inferred for all autosomes with an average mismatch error rate of 0.31% for SNVs and 1.89% for insertions or deletions (indels). Because our method can determine whether an inherited disease allele originated from the mother or the father, we predict that it will improve the diagnosis and management of many genetic diseases.
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Affiliation(s)
- Vahid Akbari
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Kieran O’Neill
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Louis Lefebvre
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kasmintan A. Schrader
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Peter M. Lansdorp
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada,Corresponding author
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Corresponding author
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18
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O’Neill H, Lee H, Gupta I, Rodger EJ, Chatterjee A. Single-Cell DNA Methylation Analysis in Cancer. Cancers (Basel) 2022; 14:cancers14246171. [PMID: 36551655 PMCID: PMC9777108 DOI: 10.3390/cancers14246171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Morphological, transcriptomic, and genomic defects are well-explored parameters of cancer biology. In more recent years, the impact of epigenetic influences, such as DNA methylation, is becoming more appreciated. Aberrant DNA methylation has been implicated in many types of cancers, influencing cell type, state, transcriptional regulation, and genomic stability to name a few. Traditionally, large populations of cells from the tissue of interest are coalesced for analysis, producing averaged methylome data. Considering the inherent heterogeneity of cancer, analysing populations of cells as a whole denies the ability to discover novel aberrant methylation patterns, identify subpopulations, and trace cell lineages. Due to recent advancements in technology, it is now possible to obtain methylome data from single cells. This has both research and clinical implications, ranging from the identification of biomarkers to improved diagnostic tools. As with all emerging technologies, distinct experimental, bioinformatic, and practical challenges present themselves. This review begins with exploring the potential impact of single-cell sequencing on understanding cancer biology and how it could eventually benefit a clinical setting. Following this, the techniques and experimental approaches which made this technology possible are explored. Finally, the present challenges currently associated with single-cell DNA methylation sequencing are described.
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Affiliation(s)
- Hannah O’Neill
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Heather Lee
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, NSW 2308, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
- School of Health Sciences and Technology, University of Petroleum and Energy Studies (UPES), Dehradun 248007, India
- Correspondence:
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19
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Glioma Stem Cells: Novel Data Obtained by Single-Cell Sequencing. Int J Mol Sci 2022; 23:ijms232214224. [PMID: 36430704 PMCID: PMC9694247 DOI: 10.3390/ijms232214224] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/04/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Glioma is the most common type of primary CNS tumor, composed of cells that resemble normal glial cells. Recent genetic studies have provided insight into the inter-tumoral heterogeneity of gliomas, resulting in the updated 2021 WHO classification of gliomas. Thorough understanding of inter-tumoral heterogeneity has already improved the prognosis and treatment outcomes of some types of gliomas. Currently, the challenge for researchers is to study the intratumoral cell heterogeneity of newly defined glioma subtypes. Cancer stem cells (CSCs) present in gliomas and many other tumors are an example of intratumoral heterogeneity of great importance. In this review, we discuss the modern concept of glioma stem cells and recent single-cell sequencing-driven progress in the research of intratumoral glioma cell heterogeneity. The particular emphasis was placed on the recently revealed variations of the cell composition of the subtypes of the adult-type diffuse gliomas, including astrocytoma, oligodendroglioma and glioblastoma. The novel data explain the inconsistencies in earlier glioma stem cell research and also provide insight into the development of more effective targeted therapy and the cell-based immunotherapy of gliomas. Separate sections are devoted to the description of single-cell sequencing approach and its role in the development of cell-based immunotherapies for glioma.
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20
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Wei W, Schon KR, Elgar G, Orioli A, Tanguy M, Giess A, Tischkowitz M, Caulfield MJ, Chinnery PF. Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes. Nature 2022; 611:105-114. [PMID: 36198798 PMCID: PMC9630118 DOI: 10.1038/s41586-022-05288-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/29/2022] [Indexed: 02/02/2023]
Abstract
DNA transfer from cytoplasmic organelles to the cell nucleus is a legacy of the endosymbiotic event-the majority of nuclear-mitochondrial segments (NUMTs) are thought to be ancient, preceding human speciation1-3. Here we analyse whole-genome sequences from 66,083 people-including 12,509 people with cancer-and demonstrate the ongoing transfer of mitochondrial DNA into the nucleus, contributing to a complex NUMT landscape. More than 99% of individuals had at least one of 1,637 different NUMTs, with 1 in 8 individuals having an ultra-rare NUMT that is present in less than 0.1% of the population. More than 90% of the extant NUMTs that we evaluated inserted into the nuclear genome after humans diverged from apes. Once embedded, the sequences were no longer under the evolutionary constraint seen within the mitochondrion, and NUMT-specific mutations had a different mutational signature to mitochondrial DNA. De novo NUMTs were observed in the germline once in every 104 births and once in every 103 cancers. NUMTs preferentially involved non-coding mitochondrial DNA, linking transcription and replication to their origin, with nuclear insertion involving multiple mechanisms including double-strand break repair associated with PR domain zinc-finger protein 9 (PRDM9) binding. The frequency of tumour-specific NUMTs differed between cancers, including a probably causal insertion in a myxoid liposarcoma. We found evidence of selection against NUMTs on the basis of size and genomic location, shaping a highly heterogenous and dynamic human NUMT landscape.
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Affiliation(s)
- Wei Wei
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Katherine R Schon
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Marc Tischkowitz
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Patrick F Chinnery
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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21
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Boza V, Peresini P, Brejova B, Vinar T. Dynamic Pooling Improves Nanopore Base Calling Accuracy. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3416-3424. [PMID: 34784283 DOI: 10.1109/tcbb.2021.3128366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In nanopore sequencing, electrical signal is measured as DNA molecules pass through the sequencing pores. Translating these signals into DNA bases (base calling) is a highly non-trivial task, and its quality has a large impact on the sequencing accuracy. The most successful nanopore base callers to date use convolutional neural networks (CNN) to accomplish the task. Convolutional layers in CNNs are typically composed of filters with constant window size, performing best in analysis of signals with uniform speed. However, the speed of nanopore sequencing varies greatly both within reads and between sequencing runs. Here, we present dynamic pooling, a novel neural network component, which addresses this problem by adaptively adjusting the pooling ratio. To demonstrate the usefulness of dynamic pooling, we developed two base callers: Heron and Osprey. Heron improves the accuracy beyond the experimental high-accuracy base caller Bonito developed by Oxford Nanopore. Osprey is a fast base caller that can compete in accuracy with Guppy high-accuracy mode, but does not require GPU acceleration and achieves a near real-time speed on common desktop CPUs. Availability: https://github.com/fmfi-compbio/osprey, https://github.com/fmfi-compbio/heron.
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22
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White LK, Hesselberth JR. Modification mapping by nanopore sequencing. Front Genet 2022; 13:1037134. [PMID: 36386798 PMCID: PMC9650216 DOI: 10.3389/fgene.2022.1037134] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 06/26/2024] Open
Abstract
Next generation sequencing (NGS) has provided biologists with an unprecedented view into biological processes and their regulation over the past 2 decades, fueling a wave of development of high throughput methods based on short read DNA and RNA sequencing. For nucleic acid modifications, NGS has been coupled with immunoprecipitation, chemical treatment, enzymatic treatment, and/or the use of reverse transcriptase enzymes with fortuitous activities to enrich for and to identify covalent modifications of RNA and DNA. However, the majority of nucleic acid modifications lack commercial monoclonal antibodies, and mapping techniques that rely on chemical or enzymatic treatments to manipulate modification signatures add additional technical complexities to library preparation. Moreover, such approaches tend to be specific to a single class of RNA or DNA modification, and generate only indirect readouts of modification status. Third generation sequencing technologies such as the commercially available "long read" platforms from Pacific Biosciences and Oxford Nanopore Technologies are an attractive alternative for high throughput detection of nucleic acid modifications. While the former can indirectly sense modified nucleotides through changes in the kinetics of reverse transcription reactions, nanopore sequencing can in principle directly detect any nucleic acid modification that produces a signal distortion as the nucleic acid passes through a nanopore sensor embedded within a charged membrane. To date, more than a dozen endogenous DNA and RNA modifications have been interrogated by nanopore sequencing, as well as a number of synthetic nucleic acid modifications used in metabolic labeling, structure probing, and other emerging applications. This review is intended to introduce the reader to nanopore sequencing and key principles underlying its use in direct detection of nucleic acid modifications in unamplified DNA or RNA samples, and outline current approaches for detecting and quantifying nucleic acid modifications by nanopore sequencing. As this technology matures, we anticipate advances in both sequencing chemistry and analysis methods will lead to rapid improvements in the identification and quantification of these epigenetic marks.
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Affiliation(s)
| | - Jay R. Hesselberth
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
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23
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Chen J, Cheng J, Chen X, Inoue M, Liu Y, Song CX. Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology. Nucleic Acids Res 2022; 50:e104. [PMID: 35849350 PMCID: PMC9561279 DOI: 10.1093/nar/gkac612] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/07/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells as a proof of concept, and an N50 read length of 3.5 kb is achieved. By sequencing wglrTAPS to 8.2× depth, we discovered a significant proportion of CpG sites that were not covered in previous 27.5× short-read TAPS. Our results demonstrate that wglrTAPS facilitates methylation profiling on problematic genomic regions with repetitive elements or structural variations, and also in an allelic manner, all of which are extremely difficult for short-read sequencing methods to resolve. This method therefore enhances applications of third-generation sequencing technologies for DNA epigenetics.
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Affiliation(s)
- Jinfeng Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Jingfei Cheng
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Xiufei Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Masato Inoue
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Yibin Liu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
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24
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Akbari V, Garant JM, O'Neill K, Pandoh P, Moore R, Marra MA, Hirst M, Jones SJM. Genome-wide detection of imprinted differentially methylated regions using nanopore sequencing. eLife 2022; 11:77898. [PMID: 35787786 PMCID: PMC9255983 DOI: 10.7554/elife.77898] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/16/2022] [Indexed: 01/02/2023] Open
Abstract
Imprinting is a critical part of normal embryonic development in mammals, controlled by defined parent-of-origin (PofO) differentially methylated regions (DMRs) known as imprinting control regions. Direct nanopore sequencing of DNA provides a means to detect allelic methylation and to overcome the drawbacks of methylation array and short-read technologies. Here, we used publicly available nanopore sequencing data for 12 standard B-lymphocyte cell lines to acquire the genome-wide mapping of imprinted intervals in humans. Using the sequencing data, we were able to phase 95% of the human methylome and detect 94% of the previously well-characterized, imprinted DMRs. In addition, we found 42 novel imprinted DMRs (16 germline and 26 somatic), which were confirmed using whole-genome bisulfite sequencing (WGBS) data. Analysis of WGBS data in mouse (Mus musculus), rhesus monkey (Macaca mulatta), and chimpanzee (Pan troglodytes) suggested that 17 of these imprinted DMRs are conserved. Some of the novel imprinted intervals are within or close to imprinted genes without a known DMR. We also detected subtle parental methylation bias, spanning several kilobases at seven known imprinted clusters. At these blocks, hypermethylation occurs at the gene body of expressed allele(s) with mutually exclusive H3K36me3 and H3K27me3 allelic histone marks. These results expand upon our current knowledge of imprinting and the potential of nanopore sequencing to identify imprinting regions using only parent-offspring trios, as opposed to the large multi-generational pedigrees that have previously been required.
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Affiliation(s)
- Vahid Akbari
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jean-Michel Garant
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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25
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Mannens MMAM, Lombardi MP, Alders M, Henneman P, Bliek J. Further Introduction of DNA Methylation (DNAm) Arrays in Regular Diagnostics. Front Genet 2022; 13:831452. [PMID: 35860466 PMCID: PMC9289263 DOI: 10.3389/fgene.2022.831452] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/08/2022] [Indexed: 12/01/2022] Open
Abstract
Methylation tests have been used for decades in regular DNA diagnostics focusing primarily on Imprinting disorders or specific loci annotated to specific disease associated gene promotors. With the introduction of DNA methylation (DNAm) arrays such as the Illumina Infinium HumanMethylation450 Beadchip array or the Illumina Infinium Methylation EPIC Beadchip array (850 k), it has become feasible to study the epigenome in a timely and cost-effective way. This has led to new insights regarding the complexity of well-studied imprinting disorders such as the Beckwith Wiedemann syndrome, but it has also led to the introduction of tests such as EpiSign, implemented as a diagnostic test in which a single array experiment can be compared to databases with known episignatures of multiple genetic disorders, especially neurodevelopmental disorders. The successful use of such DNAm tests is rapidly expanding. More and more disorders are found to be associated with discrete episignatures which enables fast and definite diagnoses, as we have shown. The first examples of environmentally induced clinical disorders characterized by discrete aberrant DNAm are discussed underlining the broad application of DNAm testing in regular diagnostics. Here we discuss exemplary findings in our laboratory covering this broad range of applications and we discuss further use of DNAm tests in the near future.
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26
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de Pontual L, Tomé S. Overview of the Complex Relationship between Epigenetics Markers, CTG Repeat Instability and Symptoms in Myotonic Dystrophy Type 1. Int J Mol Sci 2022; 23:ijms23073477. [PMID: 35408837 PMCID: PMC8998570 DOI: 10.3390/ijms23073477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 02/05/2023] Open
Abstract
Among the trinucleotide repeat disorders, myotonic dystrophy type 1 (DM1) is one of the most complex neuromuscular diseases caused by an unstable CTG repeat expansion in the DMPK gene. DM1 patients exhibit high variability in the dynamics of CTG repeat instability and in the manifestations and progression of the disease. The largest expanded alleles are generally associated with the earliest and most severe clinical form. However, CTG repeat length alone is not sufficient to predict disease severity and progression, suggesting the involvement of other factors. Several data support the role of epigenetic alterations in clinical and genetic variability. By highlighting epigenetic alterations in DM1, this review provides a new avenue on how these changes can serve as biomarkers to predict clinical features and the mutation behavior.
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Affiliation(s)
| | - Stéphanie Tomé
- Correspondence: ; Tel.: +33-1-42-16-57-16; Fax: +33-1-42-16-57-00
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27
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Hubert JN, Demars J. Genomic Imprinting in the New Omics Era: A Model for Systems-Level Approaches. Front Genet 2022; 13:838534. [PMID: 35368671 PMCID: PMC8965095 DOI: 10.3389/fgene.2022.838534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting represents a noteworthy inheritance mechanism leading to allele-specific regulations dependent of the parental origin. Imprinted loci are especially involved in essential mammalian functions related to growth, development and behavior. In this mini-review, we first offer a summary of current representations associated with genomic imprinting through key results of the three last decades. We then outline new perspectives allowed by the spread of new omics technologies tackling various interacting levels of imprinting regulations, including genomics, transcriptomics and epigenomics. We finally discuss the expected contribution of new omics data to unresolved big questions in the field.
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28
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
Rare diseases affect 30 million people in the USA and more than 300-400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25-35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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Affiliation(s)
- Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA.
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA.
| | - Joshua W Knowles
- Department of Medicine, Division of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Diabetes Research Center, Cardiovascular Institute and Prevention Research Center, Stanford, CA, USA
| | - Euan A Ashley
- Department of Medicine, Division of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA.
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA.
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA.
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29
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Rodriguez-Algarra F, Seaborne RAE, Danson AF, Yildizoglu S, Yoshikawa H, Law PP, Ahmad Z, Maudsley VA, Brew A, Holmes N, Ochôa M, Hodgkinson A, Marzi SJ, Pradeepa MM, Loose M, Holland ML, Rakyan VK. Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states. Genome Biol 2022; 23:54. [PMID: 35164830 PMCID: PMC8842540 DOI: 10.1186/s13059-022-02617-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the rDNA has thus far not been performed. RESULTS Using a combination of long- and short-read sequencing, we establish that 45S rDNA units in the C57BL/6J mouse strain exist as distinct genetic haplotypes that influence the epigenetic state and transcriptional output of any given unit. DNA methylation dynamics at these haplotypes are dichotomous and life-stage specific: at one haplotype, the DNA methylation state is sensitive to the in utero environment, but refractory to post-weaning influences, whereas other haplotypes entropically gain DNA methylation during aging only. On the other hand, individual rDNA units in human show limited evidence of genetic haplotypes, and hence little discernible correlation between genetic and epigenetic states. However, in both species, adjacent units show similar epigenetic profiles, and the overall epigenetic state at rDNA is strongly positively correlated with the total rDNA copy number. Analysis of different mouse inbred strains reveals that in some strains, such as 129S1/SvImJ, the rDNA copy number is only approximately 150 copies per diploid genome and DNA methylation levels are < 5%. CONCLUSIONS Our work demonstrates that rDNA-associated genetic variation has a considerable influence on rDNA epigenetic state and consequently rRNA expression outcomes. In the future, it will be important to consider the impact of inter-individual rDNA (epi)genetic variation on mammalian phenotypes and diseases.
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Affiliation(s)
| | - Robert A E Seaborne
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Amy F Danson
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Present Address: German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Selin Yildizoglu
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Harunori Yoshikawa
- Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Pui Pik Law
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Zakaryya Ahmad
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Victoria A Maudsley
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ama Brew
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nadine Holmes
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Mateus Ochôa
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Alan Hodgkinson
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Madapura M Pradeepa
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Matthew Loose
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Michelle L Holland
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK.
| | - Vardhman K Rakyan
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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30
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Zaletaev DV, Nemtsova MV, Strelnikov VV. Epigenetic Regulation Disturbances on Gene Expression in Imprinting Diseases. Mol Biol 2022. [DOI: 10.1134/s0026893321050149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Athanasopoulou K, Boti MA, Adamopoulos PG, Skourou PC, Scorilas A. Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics. Life (Basel) 2021; 12:life12010030. [PMID: 35054423 PMCID: PMC8780579 DOI: 10.3390/life12010030] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
Although next-generation sequencing (NGS) technology revolutionized sequencing, offering a tremendous sequencing capacity with groundbreaking depth and accuracy, it continues to demonstrate serious limitations. In the early 2010s, the introduction of a novel set of sequencing methodologies, presented by two platforms, Pacific Biosciences (PacBio) and Oxford Nanopore Sequencing (ONT), gave birth to third-generation sequencing (TGS). The innovative long-read technologies turn genome sequencing into an ease-of-handle procedure by greatly reducing the average time of library construction workflows and simplifying the process of de novo genome assembly due to the generation of long reads. Long sequencing reads produced by both TGS methodologies have already facilitated the decipherment of transcriptional profiling since they enable the identification of full-length transcripts without the need for assembly or the use of sophisticated bioinformatics tools. Long-read technologies have also provided new insights into the field of epitranscriptomics, by allowing the direct detection of RNA modifications on native RNA molecules. This review highlights the advantageous features of the newly introduced TGS technologies, discusses their limitations and provides an in-depth comparison regarding their scientific background and available protocols as well as their potential utility in research and clinical applications.
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32
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Bicci I, Calabrese C, Golder ZJ, Gomez-Duran A, Chinnery PF. Single-molecule mitochondrial DNA sequencing shows no evidence of CpG methylation in human cells and tissues. Nucleic Acids Res 2021; 49:12757-12768. [PMID: 34850165 PMCID: PMC8682748 DOI: 10.1093/nar/gkab1179] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/29/2021] [Accepted: 11/18/2021] [Indexed: 01/11/2023] Open
Abstract
Methylation on CpG residues is one of the most important epigenetic modifications of nuclear DNA, regulating gene expression. Methylation of mitochondrial DNA (mtDNA) has been studied using whole genome bisulfite sequencing (WGBS), but recent evidence has uncovered technical issues which introduce a potential bias during methylation quantification. Here, we validate the technical concerns of WGBS, and develop and assess the accuracy of a new protocol for mtDNA nucleotide variant-specific methylation using single-molecule Oxford Nanopore Sequencing (ONS). Our approach circumvents confounders by enriching for full-length molecules over nuclear DNA. Variant calling analysis against showed that 99.5% of homoplasmic mtDNA variants can be reliably identified providing there is adequate sequencing depth. We show that some of the mtDNA methylation signal detected by ONS is due to sequence-specific false positives introduced by the technique. The residual signal was observed across several human primary and cancer cell lines and multiple human tissues, but was always below the error threshold modelled using negative controls. We conclude that there is no evidence for CpG methylation in human mtDNA, thus resolving previous controversies. Additionally, we developed a reliable protocol to study epigenetic modifications of mtDNA at single-molecule and single-base resolution, with potential applications beyond CpG methylation.
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Affiliation(s)
- Iacopo Bicci
- MRC-Mitochondrial Biology Unit, The Keith Peters Building, Cambridge CB2 0XY, UK.,Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Claudia Calabrese
- MRC-Mitochondrial Biology Unit, The Keith Peters Building, Cambridge CB2 0XY, UK.,Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Zoe J Golder
- MRC-Mitochondrial Biology Unit, The Keith Peters Building, Cambridge CB2 0XY, UK.,Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Aurora Gomez-Duran
- MRC-Mitochondrial Biology Unit, The Keith Peters Building, Cambridge CB2 0XY, UK.,Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.,Centro de Investigaciones Biológicas Margarita Salas. Spanish National Research Council, Madrid, Spain
| | - Patrick F Chinnery
- MRC-Mitochondrial Biology Unit, The Keith Peters Building, Cambridge CB2 0XY, UK.,Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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33
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Bartalucci N, Romagnoli S, Vannucchi AM. A blood drop through the pore: nanopore sequencing in hematology. Trends Genet 2021; 38:572-586. [PMID: 34906378 DOI: 10.1016/j.tig.2021.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 10/19/2022]
Abstract
The development of new sequencing platforms, technologies, and bioinformatics tools in the past decade fostered key discoveries in human genomics. Among the most recent sequencing technologies, nanopore sequencing (NS) has caught the interest of researchers for its intriguing potential and flexibility. This up-to-date review highlights the recent application of NS in the hematology field, focusing on progress and challenges of the technological approaches employed for the identification of pathologic alterations. The molecular and analytic pipelines developed for the analysis of the whole-genome, target regions, and transcriptomics provide a proof of evidence of the unparalleled amount of information that could be retrieved by an innovative approach based on long-read sequencing.
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Affiliation(s)
- Niccolò Bartalucci
- CRIMM, Center of Research and Innovation of Myeloproliferative Neoplasms, Careggi University Hospital and Department of Experimental and Clinical Medicine, University of Florence, DENOTHE Excellence Center, Florence, Italy
| | - Simone Romagnoli
- CRIMM, Center of Research and Innovation of Myeloproliferative Neoplasms, Careggi University Hospital and Department of Experimental and Clinical Medicine, University of Florence, DENOTHE Excellence Center, Florence, Italy
| | - Alessandro Maria Vannucchi
- CRIMM, Center of Research and Innovation of Myeloproliferative Neoplasms, Careggi University Hospital and Department of Experimental and Clinical Medicine, University of Florence, DENOTHE Excellence Center, Florence, Italy.
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34
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Hayes BJ, Nguyen LT, Forutan M, Engle BN, Lamb HJ, Copley JP, Randhawa IAS, Ross EM. An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology. Front Genet 2021; 12:760450. [PMID: 34868240 PMCID: PMC8637324 DOI: 10.3389/fgene.2021.760450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/29/2021] [Indexed: 02/05/2023] Open
Abstract
Extensively grazed cattle are often mustered only once a year. Therefore, birthdates are typically unknown or inaccurate. Birthdates would be useful for deriving important traits (growth rate; calving interval), breed registrations, and making management decisions. Epigenetic clocks use methylation of DNA to predict an individual's age. An epigenetic clock for cattle could provide a solution to the challenges of industry birthdate recording. Here we derived the first epigenetic clock for tropically adapted cattle using portable sequencing devices from tail hair, a tissue which is widely used in industry for genotyping. Cattle (n = 66) with ages ranging from 0.35 to 15.7 years were sequenced using Oxford Nanopore Technologies MinION and methylation was called at CpG sites across the genome. Sites were then filtered and used to calculate a covariance relationship matrix based on methylation state. Best linear unbiased prediction was used with 10-fold cross validation to predict age. A second methylation relationship matrix was also calculated that contained sites associated with genes used in the dog and human epigenetic clocks. The correlation between predicted age and actual age was 0.71 for all sites and 0.60 for dog and human gene epigenetic clock sites. The mean absolute deviation was 1.4 years for animals aged less than 3 years of age, and 1.5 years for animals aged 3-10 years. This is the first reported epigenetic clock using industry relevant samples in cattle.
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Affiliation(s)
- Ben J. Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Loan T. Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Mehrnush Forutan
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Bailey N. Engle
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Harrison J. Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - James P. Copley
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | | | - Elizabeth M. Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
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35
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Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing. Sci Rep 2021; 11:22372. [PMID: 34785703 PMCID: PMC8595663 DOI: 10.1038/s41598-021-01749-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/26/2021] [Indexed: 01/31/2023] Open
Abstract
More than 900 variants have been described in the GLA gene. Some intronic variants and copy number variants in GLA can cause Fabry disease but will not be detected by classical Sanger sequence. We aimed to design and validate a method for sequencing the GLA gene using long-read Oxford Nanopore sequencing technology. Twelve Fabry patients were blindly analyzed, both by conventional Sanger sequence and by long-read sequencing of a 13 kb PCR amplicon. We used minimap2 to align the long-read data and Nanopolish and Sniffles to call variants. All the variants detected by Sanger (including a deep intronic variant) were also detected by long-read sequencing. One patient had a deletion that was not detected by Sanger sequencing but was detected by the new technology. Our long-read sequencing-based method was able to detect missense variants and an exonic deletion, with the added advantage of intronic analysis. It can be used as an efficient and cost-effective tool for screening and diagnosing Fabry disease.
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36
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Abante J, Kambhampati S, Feinberg AP, Goutsias J. Estimating DNA methylation potential energy landscapes from nanopore sequencing data. Sci Rep 2021; 11:21619. [PMID: 34732768 PMCID: PMC8566571 DOI: 10.1038/s41598-021-00781-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
High-throughput third-generation nanopore sequencing devices have enormous potential for simultaneously observing epigenetic modifications in human cells over large regions of the genome. However, signals generated by these devices are subject to considerable noise that can lead to unsatisfactory detection performance and hamper downstream analysis. Here we develop a statistical method, CpelNano, for the quantification and analysis of 5mC methylation landscapes using nanopore data. CpelNano takes into account nanopore noise by means of a hidden Markov model (HMM) in which the true but unknown (“hidden”) methylation state is modeled through an Ising probability distribution that is consistent with methylation means and pairwise correlations, whereas nanopore current signals constitute the observed state. It then estimates the associated methylation potential energy function by employing the expectation-maximization (EM) algorithm and performs differential methylation analysis via permutation-based hypothesis testing. Using simulations and analysis of published data obtained from three human cell lines (GM12878, MCF-10A, and MDA-MB-231), we show that CpelNano can faithfully estimate DNA methylation potential energy landscapes, substantially improving current methods and leading to a powerful tool for the modeling and analysis of epigenetic landscapes using nanopore sequencing data.
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Affiliation(s)
- Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Sandeep Kambhampati
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew P Feinberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.,Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
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37
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Matias MI, Yong CS, Foroushani A, Goldsmith C, Mongellaz C, Sezgin E, Levental KR, Talebi A, Perrault J, Rivière A, Dehairs J, Delos O, Bertand-Michel J, Portais JC, Wong M, Marie JC, Kelekar A, Kinet S, Zimmermann VS, Levental I, Yvan-Charvet L, Swinnen JV, Muljo SA, Hernandez-Vargas H, Tardito S, Taylor N, Dardalhon V. Regulatory T cell differentiation is controlled by αKG-induced alterations in mitochondrial metabolism and lipid homeostasis. Cell Rep 2021; 37:109911. [PMID: 34731632 PMCID: PMC10167917 DOI: 10.1016/j.celrep.2021.109911] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 08/18/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022] Open
Abstract
Suppressive regulatory T cell (Treg) differentiation is controlled by diverse immunometabolic signaling pathways and intracellular metabolites. Here we show that cell-permeable α-ketoglutarate (αKG) alters the DNA methylation profile of naive CD4 T cells activated under Treg polarizing conditions, markedly attenuating FoxP3+ Treg differentiation and increasing inflammatory cytokines. Adoptive transfer of these T cells into tumor-bearing mice results in enhanced tumor infiltration, decreased FoxP3 expression, and delayed tumor growth. Mechanistically, αKG leads to an energetic state that is reprogrammed toward a mitochondrial metabolism, with increased oxidative phosphorylation and expression of mitochondrial complex enzymes. Furthermore, carbons from ectopic αKG are directly utilized in the generation of fatty acids, associated with lipidome remodeling and increased triacylglyceride stores. Notably, inhibition of either mitochondrial complex II or DGAT2-mediated triacylglyceride synthesis restores Treg differentiation and decreases the αKG-induced inflammatory phenotype. Thus, we identify a crosstalk between αKG, mitochondrial metabolism and triacylglyceride synthesis that controls Treg fate.
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MESH Headings
- Animals
- Cell Differentiation/drug effects
- Cells, Cultured
- Cytokines/genetics
- Cytokines/metabolism
- Diacylglycerol O-Acyltransferase/metabolism
- Energy Metabolism/drug effects
- Fibrosarcoma/genetics
- Fibrosarcoma/immunology
- Fibrosarcoma/metabolism
- Fibrosarcoma/therapy
- Forkhead Transcription Factors/genetics
- Forkhead Transcription Factors/metabolism
- Homeostasis
- Humans
- Immunotherapy, Adoptive
- Ketoglutaric Acids/pharmacology
- Lipid Metabolism/drug effects
- Mice, Inbred C57BL
- Mice, Knockout
- Mitochondria/drug effects
- Mitochondria/genetics
- Mitochondria/metabolism
- Phenotype
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/metabolism
- Signal Transduction
- T-Lymphocytes, Regulatory/drug effects
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- T-Lymphocytes, Regulatory/transplantation
- Th1 Cells/drug effects
- Th1 Cells/immunology
- Th1 Cells/metabolism
- Mice
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Affiliation(s)
- Maria I Matias
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Carmen S Yong
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Amir Foroushani
- Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Chloe Goldsmith
- Cancer Research Center of Lyon, University Lyon 1, Inserm/ CNRS, Labex DEVweCAN, Lyon France
| | - Cédric Mongellaz
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institute, Solna, Sweden
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Ali Talebi
- Laboratory of Lipid Metabolism and Cancer, Leuven Cancer Institute, Leuven, Belgium
| | - Julie Perrault
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Anais Rivière
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Jonas Dehairs
- Laboratory of Lipid Metabolism and Cancer, Leuven Cancer Institute, Leuven, Belgium
| | - Océane Delos
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France; I2MC, Université de Toulouse, Inserm, Toulouse, France
| | - Justine Bertand-Michel
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France; I2MC, Université de Toulouse, Inserm, Toulouse, France
| | - Jean-Charles Portais
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Madeline Wong
- Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Julien C Marie
- Cancer Research Center of Lyon, University Lyon 1, Inserm/ CNRS, Labex DEVweCAN, Lyon France
| | - Ameeta Kelekar
- Department of Laboratory Medicine and Pathology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Sandrina Kinet
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Valérie S Zimmermann
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | | | - Johannes V Swinnen
- Laboratory of Lipid Metabolism and Cancer, Leuven Cancer Institute, Leuven, Belgium
| | - Stefan A Muljo
- Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Hector Hernandez-Vargas
- Cancer Research Center of Lyon, University Lyon 1, Inserm/ CNRS, Labex DEVweCAN, Lyon France
| | - Saverio Tardito
- Cancer Research UK, Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Naomi Taylor
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Pediatric Oncology Branch, NCI, CCR, NIH, Bethesda, MD, USA.
| | - Valérie Dardalhon
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.
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38
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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: 6] [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: 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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39
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Lu W, Lan X, Zhang T, Sun H, Ma S, Xia Q. Precise Characterization of Bombyx mori Fibroin Heavy Chain Gene Using Cpf1-Based Enrichment and Oxford Nanopore Technologies. INSECTS 2021; 12:insects12090832. [PMID: 34564273 PMCID: PMC8467315 DOI: 10.3390/insects12090832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Bombyx mori (B. mori), an important economic insect, is famous for its silk. B. mori silk is mainly composed of silk fibroin coated with sericin. Among them, the silk fibroin heavy chain protein has the highest content and the largest molecular weight, which is encoded by the silk fibroin heavy chain (FibH) gene. At present, apart from the complete sequence of the FibH of the B. mori strain p50T, there are no other reports regarding this protein. This is mainly because the special structure formed by the GC-rich repetitive sequence in FibH hinders the amplification of polymerase and the application of Sanger sequencing. Here, the FibH sequence of Dazao, which has 99.98% similarity to that of p50T, was obtained by means of CEO. As far as we know, this is the first complete FibH sequence of the Chinese B. mori strain. Additionally, the methylated CG sites in the FibH repeat unit were identified. Abstract To study the evolution of gene function and a species, it is essential to characterize the tandem repetitive sequences distributed across the genome. Cas9-based enrichment combined with nanopore sequencing is an important technique for targeting repetitive sequences. Cpf1 has low molecular weight, low off-target efficiency, and the same editing efficiency as Cas9. There are numerous studies on enrichment sequencing using Cas9 combined with nanopore, while there are only a few studies on the enrichment sequencing of long and highly repetitive genes using Cpf1. We developed Cpf1-based enrichment combined with ONT sequencing (CEO) to characterize the B. mori FibH gene, which is composed of many repeat units with a long and GC-rich sequence up to 17 kb and is not easily amplified by means of a polymerase chain reaction (PCR). CEO has four steps: the dephosphorylation of genomic DNA, the Cpf1 targeted cleavage of FibH, adapter ligation, and ONT sequencing. Using CEO, we determined the fine structure of B. moriFibH, which is 16,845 bp long and includes 12 repetitive domains separated by amorphous regions. Except for the difference of three bases in the intron from the reference gene, the other sequences are identical. Surprisingly, many methylated CG sites were found and distributed unevenly on the FibH repeat unit. The CEO we established is an available means to depict highly repetitive genes, but also a supplement to the enrichment method based on Cas9.
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Affiliation(s)
- Wei Lu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
| | - Xinhui Lan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
| | - Tong Zhang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
| | - Hao Sun
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
- Correspondence: (S.M.); (Q.X.)
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
- Correspondence: (S.M.); (Q.X.)
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40
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Alfonzo JD, Brown JA, Byers PH, Cheung VG, Maraia RJ, Ross RL. A call for direct sequencing of full-length RNAs to identify all modifications. Nat Genet 2021; 53:1113-1116. [PMID: 34267373 DOI: 10.1038/s41588-021-00903-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Juan D Alfonzo
- Department of Microbiology; Center for RNA Biology and Ohio State Biochemistry Program, Ohio State University, Columbus, OH, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Peter H Byers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA, USA
| | - Vivian G Cheung
- Department of Pediatrics, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
| | - Richard J Maraia
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert L Ross
- Department of Cancer and Cell Biology, Metabolomics Mass Spectrometry Laboratory, University of Cincinnati, Cincinnati, OH, USA
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41
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Raas MWD, Zijlmans DW, Vermeulen M, Marks H. There is another: H3K27me3-mediated genomic imprinting. Trends Genet 2021; 38:82-96. [PMID: 34304914 DOI: 10.1016/j.tig.2021.06.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022]
Abstract
DNA methylation has long been considered the primary epigenetic mediator of genomic imprinting in mammals. Recent epigenetic profiling during early mouse development revealed the presence of domains of trimethylation of lysine 27 on histone H3 (H3K27me3) and chromatin compaction specifically at the maternally derived allele, independent of DNA methylation. Within these domains, genes are exclusively expressed from the paternally derived allele. This novel mechanism of noncanonical imprinting plays a key role in the development of mouse extraembryonic tissues and in the regulation of imprinted X-chromosome inactivation, highlighting the importance of parentally inherited epigenetic histone modifications. Here, we discuss the mechanisms underlying H3K27me3-mediated noncanonical imprinting in perspective of the dynamic chromatin landscape during early mouse development and explore evolutionary origins of noncanonical imprinting.
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Affiliation(s)
- Maximilian W D Raas
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525GA Nijmegen, The Netherlands
| | - Dick W Zijlmans
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525GA Nijmegen, The Netherlands.
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42
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Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nat Commun 2021; 12:3804. [PMID: 34155196 PMCID: PMC8217501 DOI: 10.1038/s41467-021-23510-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 04/30/2021] [Indexed: 02/06/2023] Open
Abstract
In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation. In most mammals, imprinted genes contain epigenetic marks that differ in each parental genome and control their parent-of-origin-specific expression. Here, the authors map imprinted genes in mouse preimplantation embryos and find that imprinted gene expression in blastocysts is mainly dependent on Polycomb-mediated H3K27me3-associated gene silencing.
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Affiliation(s)
- Laura Santini
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Florian Halbritter
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabian Titz-Teixeira
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Toru Suzuki
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Maki Asami
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Xiaoyan Ma
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Julia Ramesmayer
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Andreas Lackner
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Nick Warr
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell, UK
| | - Florian Pauler
- Institute for Science and Technology Austria, Klosterneuburg, Austria
| | - Simon Hippenmeyer
- Institute for Science and Technology Austria, Klosterneuburg, Austria
| | - Ernest Laue
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Andreas Beyer
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Anthony C F Perry
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath, UK.
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria.
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43
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Zhang J, Xie S, Xu J, Liu H, Wan S. Cancer Biomarkers Discovery of Methylation Modification With Direct High-Throughput Nanopore Sequencing. Front Genet 2021; 12:672804. [PMID: 34122526 PMCID: PMC8188482 DOI: 10.3389/fgene.2021.672804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/07/2021] [Indexed: 01/12/2023] Open
Abstract
Cancer is a complex disease, driven by a combination of genetic and epigenetic alterations. DNA and RNA methylation modifications are the most common epigenetic events that play critical roles in cancer development and progression. Bisulfite converted sequencing is a widely used technique to detect base modifications in DNA methylation, but its main drawbacks lie in DNA degradation, lack of specificity, or short reads with low sequence diversity. The nanopore sequencing technology can directly detect base modifications in native DNA as well as RNA without harsh chemical treatment, compared to bisulfite sequencing. Furthermore, CRISPR/Cas9-targeted enrichment nanopore sequencing techniques are straightforward and cost-effective when targeting genomic regions are of interest. In this review, we mainly focus on DNA and RNA methylation modification detection in cancer with the current nanopore sequencing approaches. We also present the respective strengths, weaknesses of nanopore sequencing techniques, and their future translational applications in identification of epigenetic biomarkers for cancer detection and prognosis.
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Affiliation(s)
- Junjie Zhang
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Shuilian Xie
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Jingxiang Xu
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Hui Liu
- Institute of Hepatology, The Affiliated Fifth People’s Hospital of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Shaogui Wan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
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44
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Zhao X, Collins RL, Lee WP, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, Walker M, Lowther C, Fu J, Gerstein MB, Devine SE, Marschall T, Korbel JO, Eichler EE, Chaisson MJP, Lee C, Mills RE, Brand H, Talkowski ME. Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. Am J Hum Genet 2021; 108:919-928. [PMID: 33789087 PMCID: PMC8206509 DOI: 10.1016/j.ajhg.2021.03.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/12/2021] [Indexed: 12/13/2022] Open
Abstract
Virtually all genome sequencing efforts in national biobanks, complex and Mendelian disease programs, and medical genetic initiatives are reliant upon short-read whole-genome sequencing (srWGS), which presents challenges for the detection of structural variants (SVs) relative to emerging long-read WGS (lrWGS) technologies. Given this ubiquity of srWGS in large-scale genomics initiatives, we sought to establish expectations for routine SV detection from this data type by comparison with lrWGS assembly, as well as to quantify the genomic properties and added value of SVs uniquely accessible to each technology. Analyses from the Human Genome Structural Variation Consortium (HGSVC) of three families captured ~11,000 SVs per genome from srWGS and ~25,000 SVs per genome from lrWGS assembly. Detection power and precision for SV discovery varied dramatically by genomic context and variant class: 9.7% of the current GRCh38 reference is defined by segmental duplication (SD) and simple repeat (SR), yet 91.4% of deletions that were specifically discovered by lrWGS localized to these regions. Across the remaining 90.3% of reference sequence, we observed extremely high (93.8%) concordance between technologies for deletions in these datasets. In contrast, lrWGS was superior for detection of insertions across all genomic contexts. Given that non-SD/SR sequences encompass 95.9% of currently annotated disease-associated exons, improved sensitivity from lrWGS to discover novel pathogenic deletions in these currently interpretable genomic regions is likely to be incremental. However, these analyses highlight the considerable added value of assembly-based lrWGS to create new catalogs of insertions and transposable elements, as well as disease-associated repeat expansions in genomic sequences that were previously recalcitrant to routine assessment.
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Affiliation(s)
- Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Wan-Ping Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alexandra M Weber
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Yukyung Jun
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ben Weisburd
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Yongqing Huang
- Data Sciences Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Harold Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mark Walker
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Mark B Gerstein
- Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, CT 06520, USA
| | - Scott E Devine
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Mark J P Chaisson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Graduate Studies - Life Sciences, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, South Korea; Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an 710061, Shaanxi, People's Republic of China
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Disorders, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA.
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45
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Graw S, Chappell K, Washam CL, Gies A, Bird J, Robeson MS, Byrum SD. Multi-omics data integration considerations and study design for biological systems and disease. Mol Omics 2021; 17:170-185. [PMID: 33347526 PMCID: PMC8058243 DOI: 10.1039/d0mo00041h] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With the advancement of next-generation sequencing and mass spectrometry, there is a growing need for the ability to merge biological features in order to study a system as a whole. Features such as the transcriptome, methylome, proteome, histone post-translational modifications and the microbiome all influence the host response to various diseases and cancers. Each of these platforms have technological limitations due to sample preparation steps, amount of material needed for sequencing, and sequencing depth requirements. These features provide a snapshot of one level of regulation in a system. The obvious next step is to integrate this information and learn how genes, proteins, and/or epigenetic factors influence the phenotype of a disease in context of the system. In recent years, there has been a push for the development of data integration methods. Each method specifically integrates a subset of omics data using approaches such as conceptual integration, statistical integration, model-based integration, networks, and pathway data integration. In this review, we discuss considerations of the study design for each data feature, the limitations in gene and protein abundance and their rate of expression, the current data integration methods, and microbiome influences on gene and protein expression. The considerations discussed in this review should be regarded when developing new algorithms for integrating multi-omics data.
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Affiliation(s)
- Stefan Graw
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Kevin Chappell
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Charity L Washam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
| | - Allen Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Jordan Bird
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Michael S Robeson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
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46
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Goldsmith C, Rodríguez-Aguilera JR, El-Rifai I, Jarretier-Yuste A, Hervieu V, Raineteau O, Saintigny P, Chagoya de Sánchez V, Dante R, Ichim G, Hernandez-Vargas H. Low biological fluctuation of mitochondrial CpG and non-CpG methylation at the single-molecule level. Sci Rep 2021; 11:8032. [PMID: 33850190 PMCID: PMC8044111 DOI: 10.1038/s41598-021-87457-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/30/2021] [Indexed: 12/16/2022] Open
Abstract
Mammalian cytosine DNA methylation (5mC) is associated with the integrity of the genome and the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mC has a regulatory role in this context. Here, we used bisulfite-independent single-molecule sequencing of native human and mouse DNA to study mitochondrial 5mC across different biological conditions. We first validated the ability of long-read nanopore sequencing to detect 5mC in CpG (5mCpG) and non-CpG (5mCpH) context in nuclear DNA at expected genomic locations (i.e. promoters, gene bodies, enhancers, and cell type-specific transcription factor binding sites). Next, using high coverage nanopore sequencing we found low levels of mtDNA CpG and CpH methylation (with several exceptions) and little variation across biological processes: differentiation, oxidative stress, and cancer. 5mCpG and 5mCpH were overall higher in tissues compared to cell lines, with small additional variation between cell lines of different origin. Despite general low levels, global and single-base differences were found in cancer tissues compared to their adjacent counterparts, in particular for 5mCpG. In conclusion, nanopore sequencing is a useful tool for the detection of modified DNA bases on mitochondria that avoid the biases introduced by bisulfite and PCR amplification. Enhanced nanopore basecalling models will provide further resolution on the small size effects detected here, as well as rule out the presence of other DNA modifications such as oxidized forms of 5mC.
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Affiliation(s)
- Chloe Goldsmith
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France.
| | - Jesús Rafael Rodríguez-Aguilera
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Ines El-Rifai
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Adrien Jarretier-Yuste
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Valérie Hervieu
- Department of Surgical Pathology, Hospices Civils de Lyon, Groupement Hospitalier Est, Lyon, France
| | - Olivier Raineteau
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, Bron, France
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France
| | - Victoria Chagoya de Sánchez
- Department of Cellular Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Robert Dante
- Dependence Receptors Cancer and Development Laboratory, Department of Signaling of Tumoral Escape. Cancer Research. Center of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Gabriel Ichim
- Cancer Cell Death Laboratory, Part of LabEx DEVweCAN, Université de Lyon, Lyon, France
- Cancer Research Centre of Lyon (CRCL), Inserm U 1052, CNRS UMR 5286, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France
| | - Hector Hernandez-Vargas
- Department of Tumor Escape, Resistance and Immunity, TGF-Beta and Immuno-Regulation Team, Cancer Research Centre of Lyon (CRCL), INSERM U 1052, CNRS UMR 5286, UCBL1, Université de Lyon, Centre Léon Bérard, 28 rue Laennec, 69373, Lyon Cedex 08, France.
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France.
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47
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Galan C, Serra RW, Sun F, Rinaldi VD, Conine CC, Rando OJ. Stability of the cytosine methylome during post-testicular sperm maturation in mouse. PLoS Genet 2021; 17:e1009416. [PMID: 33661909 PMCID: PMC7963034 DOI: 10.1371/journal.pgen.1009416] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/16/2021] [Accepted: 02/14/2021] [Indexed: 12/28/2022] Open
Abstract
Beyond the haploid genome, mammalian sperm carry a payload of epigenetic information with the potential to modulate offspring phenotypes. Recent studies show that the small RNA repertoire of sperm is remodeled during post-testicular maturation in the epididymis. Epididymal maturation has also been linked to changes in the sperm methylome, suggesting that the epididymis might play a broader role in shaping the sperm epigenome. Here, we characterize the genome-wide methylation landscape in seven germ cell populations from throughout the male reproductive tract. We find very few changes in the cytosine methylation landscape between testicular germ cell populations and cauda epididymal sperm, demonstrating that the sperm methylome is stable throughout post-testicular maturation. Although our sequencing data suggested that caput epididymal sperm exhibit a highly unusual methylome, follow-up studies revealed that this resulted from contamination of caput sperm by extracellular DNA. Extracellular DNA formed web-like structures that ensnared sperm, and was present only in sperm samples obtained from the caput epididymis and vas deferens of virgin males. Curiously, contaminating extracellular DNA was associated with citrullinated histone H3, potentially resulting from a PAD-driven genome decondensation process. Taken together, our data emphasize the stability of cytosine methylation in mammalian sperm, and identify a surprising, albeit transient, period during which sperm are associated with extracellular DNA.
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Affiliation(s)
- Carolina Galan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Ryan W. Serra
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Fengyun Sun
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Vera D. Rinaldi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Colin C. Conine
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Oliver J. Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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48
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van Haasteren J, Munis AM, Gill DR, Hyde SC. Genome-wide integration site detection using Cas9 enriched amplification-free long-range sequencing. Nucleic Acids Res 2021; 49:e16. [PMID: 33290561 PMCID: PMC7897500 DOI: 10.1093/nar/gkaa1152] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/13/2020] [Accepted: 11/10/2020] [Indexed: 12/31/2022] Open
Abstract
The gene and cell therapy fields are advancing rapidly, with a potential to treat and cure a wide range of diseases, and lentivirus-based gene transfer agents are the vector of choice for many investigators. Early cases of insertional mutagenesis caused by gammaretroviral vectors highlighted that integration site (IS) analysis was a major safety and quality control checkpoint for lentiviral applications. The methods established to detect lentiviral integrations using next-generation sequencing (NGS) are limited by short read length, inadvertent PCR bias, low yield, or lengthy protocols. Here, we describe a new method to sequence IS using Amplification-free Integration Site sequencing (AFIS-Seq). AFIS-Seq is based on amplification-free, Cas9-mediated enrichment of high-molecular-weight chromosomal DNA suitable for long-range Nanopore MinION sequencing. This accessible and low-cost approach generates long reads enabling IS mapping with high certainty within a single day. We demonstrate proof-of-concept by mapping IS of lentiviral vectors in a variety of cell models and report up to 1600-fold enrichment of the signal. This method can be further extended to sequencing of Cas9-mediated integration of genes and to in vivo analysis of IS. AFIS-Seq uses long-read sequencing to facilitate safety evaluation of preclinical lentiviral vector gene therapies by providing IS analysis with improved confidence.
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Affiliation(s)
- Joost van Haasteren
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Altar M Munis
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Deborah R Gill
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen C Hyde
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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49
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Akbari V, Garant JM, O'Neill K, Pandoh P, Moore R, Marra MA, Hirst M, Jones SJM. Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase. Genome Biol 2021; 22:68. [PMID: 33618748 PMCID: PMC7898412 DOI: 10.1186/s13059-021-02283-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/29/2021] [Indexed: 02/08/2023] Open
Abstract
The ability of nanopore sequencing to simultaneously detect modified nucleotides while producing long reads makes it ideal for detecting and phasing allele-specific methylation. However, there is currently no complete software for detecting SNPs, phasing haplotypes, and mapping methylation to these from nanopore sequence data. Here, we present NanoMethPhase, a software tool to phase 5-methylcytosine from nanopore sequencing. We also present SNVoter, which can post-process nanopore SNV calls to improve accuracy in low coverage regions. Together, these tools can accurately detect allele-specific methylation genome-wide using nanopore sequence data with low coverage of about ten-fold redundancy.
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Affiliation(s)
- Vahid Akbari
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jean-Michel Garant
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
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50
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Anreiter I, Mir Q, Simpson JT, Janga SC, Soller M. New Twists in Detecting mRNA Modification Dynamics. Trends Biotechnol 2021; 39:72-89. [PMID: 32620324 PMCID: PMC7326690 DOI: 10.1016/j.tibtech.2020.06.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022]
Abstract
Modified nucleotides in mRNA are an essential addition to the standard genetic code of four nucleotides in animals, plants, and their viruses. The emerging field of epitranscriptomics examines nucleotide modifications in mRNA and their impact on gene expression. The low abundance of nucleotide modifications and technical limitations, however, have hampered systematic analysis of their occurrence and functions. Selective chemical and immunological identification of modified nucleotides has revealed global candidate topology maps for many modifications in mRNA, but further technical advances to increase confidence will be necessary. Single-molecule sequencing introduced by Oxford Nanopore now promises to overcome such limitations, and we summarize current progress with a particular focus on the bioinformatic challenges of this novel sequencing technology.
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Affiliation(s)
- Ina Anreiter
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Quoseena Mir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Sarath C Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Computational Biology and Bioinformatics, 5021 Health Information and Translational Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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