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Flynn R, Washer S, Jeffries AR, Andrayas A, Shireby G, Kumari M, Schalkwyk LC, Mill J, Hannon E. Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays. Hum Mol Genet 2022; 31:3181-3190. [PMID: 35567415 PMCID: PMC9476619 DOI: 10.1093/hmg/ddac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/25/2022] [Accepted: 05/05/2022] [Indexed: 11/14/2022] Open
Abstract
Most epigenetic epidemiology to date has utilized microarrays to identify positions in the genome where variation in DNA methylation is associated with environmental exposures or disease. However, these profile less than 3% of DNA methylation sites in the human genome, potentially missing affected loci and preventing the discovery of disrupted biological pathways. Third generation sequencing technologies, including Nanopore sequencing, have the potential to revolutionise the generation of epigenetic data, not only by providing genuine genome-wide coverage but profiling epigenetic modifications direct from native DNA. Here we assess the viability of using Nanopore sequencing for epidemiology by performing a comparison with DNA methylation quantified using the most comprehensive microarray available, the Illumina EPIC array. We implemented a CRISPR-Cas9 targeted sequencing approach in concert with Nanopore sequencing to profile DNA methylation in three genomic regions to attempt to rediscover genomic positions that existing technologies have shown are differentially methylated in tobacco smokers. Using Nanopore sequencing reads, DNA methylation was quantified at 1779 CpGs across three regions, providing a finer resolution of DNA methylation patterns compared to the EPIC array. The correlation of estimated levels of DNA methylation between platforms was high. Furthermore, we identified 12 CpGs where hypomethylation was significantly associated with smoking status, including 10 within the AHRR gene. In summary, Nanopore sequencing is a valid option for identifying genomic loci where large differences in DNAm are associated with a phenotype and has the potential to advance our understanding of the role differential methylation plays in the aetiology of complex disease.
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Affiliation(s)
- Robert Flynn
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Sam Washer
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Aaron R Jeffries
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Alexandria Andrayas
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Gemma Shireby
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Leonard C Schalkwyk
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
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Schrauben M, Smith AR, Washer S, Dempster E, Lunnon K. Investigating epigenetic loci implicated in Alzheimer's disease via the CRISPR-Cas9 system. Alzheimers Dement 2022. [PMID: 34971175 DOI: 10.1002/alz.058573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Differentially methylated positions (DMPs) identified by Epigenome-wide association studies (EWAS) of Alzheimer's disease (AD) were modified by the CRISPR-Cas9 system to investigate the role of epigenetic alterations in AD pathogenesis. METHOD Cell lines of neuronal phenotype (SH-SY5Y) and microglial phenotype (IHM-SV40) were used to explore the functional consequence of loci demethylation, where removal of the methyl groups was achieved by the modified CRISPR-dCas9 system. Lentiviral delivery of the dCas9-TET1CD demethylase tool and guide RNA (gRNA) constructs targeting the CpG sites associated with differential expression of ANK1 and BIN1 in AD was validated by fluorescence-activated cell sorting (FACS). Bisulphite pyrosequencing was applied to confirm the DNA methylation edit. RESULT High transduction efficiencies were observed during FACS of SH-SY5Y cells transduced with CRISPR-dCas9 constructs targeting the BIN1 locus and IHM-SV40 cells with constructs against the ANK1 locus. Methylation analysis of these target regions in the modified cell lines demonstrated a reduction in methylation when compared to the untreated control cells. This modification was maintained over a three-week period. CONCLUSION Delivery and activity of our CRISPR-dCas9 fusion constructs was demonstrated in cell line models of AD. In the future, we intend to profile the epigenome and transcriptome of these modified cell lines to identify any off-target effects of the CRISPR-dCas9 system and determine differences in mRNA transcript variant levels of our target genes.
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Affiliation(s)
| | | | - Sam Washer
- University of Oxford, Oxford, United Kingdom
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Santos-Ledo A, Washer S, Dhanaseelan T, Eley L, Alqatani A, Chrystal PW, Papoutsi T, Henderson DJ, Chaudhry B. Alternative splicing of jnk1a in zebrafish determines first heart field ventricular cardiomyocyte numbers through modulation of hand2 expression. PLoS Genet 2020; 16:e1008782. [PMID: 32421721 PMCID: PMC7259801 DOI: 10.1371/journal.pgen.1008782] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/29/2020] [Accepted: 04/18/2020] [Indexed: 02/07/2023] Open
Abstract
The planar cell polarity pathway is required for heart development and whilst the functions of most pathway members are known, the roles of the jnk genes in cardiac morphogenesis remain unknown as mouse mutants exhibit functional redundancy, with early embryonic lethality of compound mutants. In this study zebrafish were used to overcome early embryonic lethality in mouse models and establish the requirement for Jnk in heart development. Whole mount in-situ hybridisation and RT-PCR demonstrated that evolutionarily conserved alternative spliced jnk1a and jnk1b transcripts were expressed in the early developing heart. Maternal zygotic null mutant zebrafish lines for jnk1a and jnk1b, generated using CRISPR-Cas9, revealed a requirement for jnk1a in formation of the proximal, first heart field (FHF)-derived portion of the cardiac ventricular chamber. Rescue of the jnk1a mutant cardiac phenotype was only possible by injection of the jnk1a EX7 Lg alternatively spliced transcript. Analysis of mutants indicated that there was a reduction in the size of the hand2 expression field in jnk1a mutants which led to a specific reduction in FHF ventricular cardiomyocytes within the anterior lateral plate mesoderm. Moreover, the jnk1a mutant ventricular defect could be rescued by injection of hand2 mRNA. This study reveals a novel and critical requirement for Jnk1 in heart development and highlights the importance of alternative splicing in vertebrate cardiac morphogenesis. Genetic pathways functioning through jnk1 may be important in human heart malformations with left ventricular hypoplasia.
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Affiliation(s)
- Adrian Santos-Ledo
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Sam Washer
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Tamil Dhanaseelan
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Lorraine Eley
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Ahlam Alqatani
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Paul W. Chrystal
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Tania Papoutsi
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Deborah J. Henderson
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Bill Chaudhry
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
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Policicchio S, Washer S, Viana J, Iatrou A, Burrage J, Hannon E, Turecki G, Kaminsky Z, Mill J, Dempster EL, Murphy TM. Genome-wide DNA methylation meta-analysis in the brains of suicide completers. Transl Psychiatry 2020; 10:69. [PMID: 32075955 PMCID: PMC7031296 DOI: 10.1038/s41398-020-0752-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
Suicide is the second leading cause of death globally among young people representing a significant global health burden. Although the molecular correlates of suicide remains poorly understood, it has been hypothesised that epigenomic processes may play a role. The objective of this study was to identify suicide-associated DNA methylation changes in the human brain by utilising previously published and unpublished methylomic datasets. We analysed prefrontal cortex (PFC, n = 211) and cerebellum (CER, n = 114) DNA methylation profiles from suicide completers and non-psychiatric, sudden-death controls, meta-analysing data from independent cohorts for each brain region separately. We report evidence for altered DNA methylation at several genetic loci in suicide cases compared to controls in both brain regions with suicide-associated differentially methylated positions enriched among functional pathways relevant to psychiatric phenotypes and suicidality, including nervous system development (PFC) and regulation of long-term synaptic depression (CER). In addition, we examined the functional consequences of variable DNA methylation within a PFC suicide-associated differentially methylated region (PSORS1C3 DMR) using a dual luciferase assay and examined expression of nearby genes. DNA methylation within this region was associated with decreased expression of firefly luciferase but was not associated with expression of nearby genes, PSORS1C3 and POU5F1. Our data suggest that suicide is associated with DNA methylation, offering novel insights into the molecular pathology associated with suicidality.
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Affiliation(s)
- Stefania Policicchio
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Sam Washer
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joana Viana
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Artemis Iatrou
- grid.240684.c0000 0001 0705 3621Rush Alzheimer’s Neurodisease Center, Rush University Medical Center, 600 South Paulina Street, Chicago, IL 60612 USA
| | - Joe Burrage
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Gustavo Turecki
- grid.14709.3b0000 0004 1936 8649Douglas Institute, Department of Psychiatry, McGill University, Verdun, QC H4H 1R3 Canada
| | - Zachary Kaminsky
- grid.21107.350000 0001 2171 9311Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Jonathan Mill
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma L. Dempster
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Therese M. Murphy
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK ,grid.497880.aSchool of Biological and Health Sciences, Technological University Dublin, City Campus, Dublin, 2 Ireland
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Abstract
A subtractive hybridization method is described that allows the generation of a subtractive gene library from small amounts of plant or other eukaryotic tissues. The method uses paramagnetic oligo-dT beads to capture poly-adenylated mRNA and to synthesize the complementary cDNA on a solid support. The use of magnetic beads facilitates the change of reaction buffers and the removal of primers and minimizes yield losses. Subtracted material obtained from this method can either be cloned directly or used to screen a specific library.
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Affiliation(s)
- T Heinrich
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, Australia.
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