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Siebert-Kuss LM, Dietrich V, Di Persio S, Bhaskaran J, Stehling M, Cremers JF, Sandmann S, Varghese J, Kliesch S, Schlatt S, Vaquerizas JM, Neuhaus N, Laurentino S. Genome-wide DNA methylation changes in human spermatogenesis. Am J Hum Genet 2024; 111:1125-1139. [PMID: 38759652 PMCID: PMC11179423 DOI: 10.1016/j.ajhg.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024] Open
Abstract
Sperm production and function require the correct establishment of DNA methylation patterns in the germline. Here, we examined the genome-wide DNA methylation changes during human spermatogenesis and its alterations in disturbed spermatogenesis. We found that spermatogenesis is associated with remodeling of the methylome, comprising a global decline in DNA methylation in primary spermatocytes followed by selective remethylation, resulting in a spermatids/sperm-specific methylome. Hypomethylated regions in spermatids/sperm were enriched in specific transcription factor binding sites for DMRT and SOX family members and spermatid-specific genes. Intriguingly, while SINEs displayed differential methylation throughout spermatogenesis, LINEs appeared to be protected from changes in DNA methylation. In disturbed spermatogenesis, germ cells exhibited considerable DNA methylation changes, which were significantly enriched at transposable elements and genes involved in spermatogenesis. We detected hypomethylation in SVA and L1HS in disturbed spermatogenesis, suggesting an association between the abnormal programming of these regions and failure of germ cells progressing beyond meiosis.
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Affiliation(s)
- Lara M Siebert-Kuss
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Verena Dietrich
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Sara Di Persio
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Jahnavi Bhaskaran
- MRC Laboratory of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK; Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Martin Stehling
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Jann-Frederik Cremers
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital of Münster, Münster, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital of Münster, Münster, Germany
| | - Stefan Schlatt
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Juan M Vaquerizas
- MRC Laboratory of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK; Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany.
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2
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Igder S, Zamani M, Fakher S, Siri M, Ashktorab H, Azarpira N, Mokarram P. Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value. DISEASE MARKERS 2024; 2024:9943412. [PMID: 38380073 PMCID: PMC10878755 DOI: 10.1155/2024/9943412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world and the fourth leading cause of cancer-related mortality. DNA (cfDNA/ctDNA) and RNA (cfRNA/ctRNA) in the blood are promising noninvasive biomarkers for molecular profiling, screening, diagnosis, treatment management, and prognosis of CRC. Technological advancements that enable precise detection of both genetic and epigenetic abnormalities, even in minute quantities in circulation, can overcome some of these challenges. This review focuses on testing for circulating nucleic acids in the circulation as a noninvasive method for CRC detection, monitoring, detection of minimal residual disease, and patient management. In addition, the benefits and drawbacks of various diagnostic techniques and associated bioinformatics tools have been detailed.
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Affiliation(s)
- Somayeh Igder
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Fakher
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Negar Azarpira
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
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3
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Lin YH, Lehle JD, McCarrey JR. Source cell-type epigenetic memory persists in induced pluripotent cells but is lost in subsequently derived germline cells. Front Cell Dev Biol 2024; 12:1306530. [PMID: 38410371 PMCID: PMC10895008 DOI: 10.3389/fcell.2024.1306530] [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: 10/04/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction: Retention of source cell-type epigenetic memory may mitigate the potential for induced pluripotent stem cells (iPSCs) to fully achieve transitions in cell fate in vitro. While this may not preclude the use of iPSC-derived somatic cell types for therapeutic applications, it becomes a major concern impacting the potential use of iPSC-derived germline cell types for reproductive applications. The transition from a source somatic cell type to iPSCs and then on to germ-cell like cells (GCLCs) recapitulates two major epigenetic reprogramming events that normally occur during development in vivo-embryonic reprogramming in the epiblast and germline reprogramming in primordial germ cells (PGCs). We examined the extent of epigenetic and transcriptomic memory persisting first during the transition from differentiated source cell types to iPSCs, and then during the transition from iPSCs to PGC-like cells (PGCLCs). Methods: We derived iPSCs from four differentiated mouse cell types including two somatic and two germ cell types and tested the extent to which each resulting iPSC line resembled a) a validated ES cell reference line, and b) their respective source cell types, on the basis of genome-wide gene expression and DNA methylation patterns. We then induced each iPSC line to form PGCLCs, and assessed epigenomic and transcriptomic memory in each compared to endogenous PGCs/M-prospermatogonia. Results: In each iPSC line, we found residual gene expression and epigenetic programming patterns characteristic of the corresponding source differentiated cell type from which each was derived. However, upon deriving PGCLCs, we found very little evidence of lingering epigenetic or transcriptomic memory of the original source cell type. Discussion: This result indicates that derivation of iPSCs and then GCLCs from differentiated source cell types in vitro recapitulates the two-phase epigenetic reprogramming that normally occurs in vivo, and that, to a significant extent, germline cell types derived in vitro from pluripotent cells accurately recapitulate epigenetic programming and gene expression patterns corresponding to equivalent endogenous germ cell types, suggesting that they have the potential to form the basis of in vitro gametogenesis as a useful therapeutic strategy for treatment of infertility.
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Affiliation(s)
- Yu-Huey Lin
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Jake D Lehle
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
| | - John R McCarrey
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
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4
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Stuart T, Buckberry S, Nguyen TV, Lister R. Approaches for the Analysis and Interpretation of Whole-Genome Bisulfite Sequencing Data. Methods Mol Biol 2024; 2842:391-403. [PMID: 39012607 DOI: 10.1007/978-1-0716-4051-7_20] [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: 07/17/2024]
Abstract
DNA methylation is a covalent modification of DNA that plays important roles in processes such as the regulation of gene expression, transcription factor binding, and suppression of transposable elements. The use of whole-genome bisulfite sequencing (WGBS) enables the genome-wide identification and quantification of DNA methylation patterns at single-base resolution and is the gold standard for the analysis of DNA methylation. However, the computational analysis of WGBS data can be particularly challenging, as many computationally intensive steps are required. Here, we outline step-by-step an approach for the analysis and interpretation of WGBS data. First, sequencing reads must be trimmed, quality-checked, and aligned to the genome. Second, DNA methylation levels are estimated at each cytosine position using the aligned sequence reads of the bisulfite-treated DNA. Third, regions of differential cytosine methylation between samples can be identified. Finally, these data need to be visualized and interpreted in the context of the biological question at hand.
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Affiliation(s)
- Tim Stuart
- Australian Research Council Centres of Excellence in Plant Energy Biology and Plants for Space, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Sam Buckberry
- Australian Research Council Centres of Excellence in Plant Energy Biology and Plants for Space, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - Trung Viet Nguyen
- Australian Research Council Centres of Excellence in Plant Energy Biology and Plants for Space, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - Ryan Lister
- Australian Research Council Centres of Excellence in Plant Energy Biology and Plants for Space, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.
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5
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Díez-Villanueva A, Martín B, Moratalla-Navarro F, Morón-Duran FD, Galván-Femenía I, Obón-Santacana M, Carreras A, de Cid R, Peinado MA, Moreno V. Identification of intergenerational epigenetic inheritance by whole genome DNA methylation analysis in trios. Sci Rep 2023; 13:21266. [PMID: 38042866 PMCID: PMC10693549 DOI: 10.1038/s41598-023-48517-3] [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: 08/01/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
Genome-wide association studies have identified thousands of loci associated with common diseases and traits. However, a large fraction of heritability remains unexplained. Epigenetic modifications, such as the observed in DNA methylation have been proposed as a mechanism of intergenerational inheritance. To investigate the potential contribution of DNA methylation to the missing heritability, we analysed the methylomes of four healthy trios (two parents and one offspring) using whole genome bisulphite sequencing. Of the 1.5 million CpGs (19%) with over 20% variability between parents in at least one family and compatible with a Mendelian inheritance pattern, only 3488 CpGs (0.2%) lacked correlation with any SNP in the genome, marking them as potential sites for intergenerational epigenetic inheritance. These markers were distributed genome-wide, with some preference to be located in promoters. They displayed a bimodal distribution, being either fully methylated or unmethylated, and were often found at the boundaries of genomic regions with high/low GC content. This analysis provides a starting point for future investigations into the missing heritability of simple and complex traits.
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Affiliation(s)
- Anna Díez-Villanueva
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
| | - Berta Martín
- Germans Trias i Pujol Institute (IGTP), Translational Program in Cancer Research (CARE), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Ferran Moratalla-Navarro
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, 08907, Barcelona, Spain
| | - Francisco D Morón-Duran
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, 08907, Barcelona, Spain
| | - Iván Galván-Femenía
- Genomes for Life-GCAT lab., Germans Trias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Mireia Obón-Santacana
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
| | - Anna Carreras
- Genomes for Life-GCAT lab., Germans Trias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Rafael de Cid
- Genomes for Life-GCAT lab., Germans Trias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Miguel A Peinado
- Germans Trias i Pujol Institute (IGTP), Translational Program in Cancer Research (CARE), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain.
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain.
- Department of Clinical Sciences, Faculty of Medicine and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, 08907, Barcelona, Spain.
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6
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Lehle JD, McCarrey JR. Accelerating the alignment processing speed of the comprehensive end-to-end whole-genome bisulfite sequencing pipeline, wg-blimp. Biol Methods Protoc 2023; 8:bpad012. [PMID: 37431446 PMCID: PMC10329742 DOI: 10.1093/biomethods/bpad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/12/2023] Open
Abstract
Analyzing whole-genome bisulfite and related sequencing datasets is a time-intensive process due to the complexity and size of the input raw sequencing files and lengthy read alignment step requiring correction for conversion of all unmethylated Cs to Ts genome-wide. The objective of this study was to modify the read alignment algorithm associated with the whole-genome bisulfite sequencing methylation analysis pipeline (wg-blimp) to shorten the time required to complete this phase while retaining overall read alignment accuracy. Here, we report an update to the recently published pipeline wg-blimp achieved by replacing the use of the bwa-meth aligner with the faster gemBS aligner. This improvement to the wg-blimp pipeline has led to a more than ×7 acceleration in the processing speed of samples when scaled to larger publicly available FASTQ datasets containing 80-160 million reads while maintaining nearly identical accuracy of properly mapped reads when compared with data from the previous pipeline. The modifications to the wg-blimp pipeline reported here merge the speed and accuracy of the gemBS aligner with the comprehensive analysis and data visualization assets of the wg-blimp pipeline to provide a significantly accelerated workflow that can produce high-quality data much more rapidly without compromising read accuracy at the expense of increasing RAM requirements up to 48 GB.
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Affiliation(s)
- Jake D Lehle
- Correspondence address. Department of Neurosciences, Developmental and Regenerative Biology, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA. Tel: +1 (512)-992-8144; E-mail:
| | - John R McCarrey
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX 78249, USA
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7
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Kim H, Sim M, Park N, Kwon K, Kim J, Kim J. msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data. BMC Bioinformatics 2022; 23:383. [PMID: 36123620 PMCID: PMC9487059 DOI: 10.1186/s12859-022-04925-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is an important epigenetic modification that is known to regulate gene expression. Whole-genome bisulfite sequencing (WGBS) is a powerful method for studying cytosine methylation in a whole genome. However, it is difficult to obtain methylation profiles using the WGBS raw reads and is necessary to be proficient in all types of bioinformatic tools for the study of DNA methylation. In addition, recent end-to-end pipelines for DNA methylation analyses are not sufficient for addressing those difficulties. RESULTS Here we present msPIPE, a pipeline for DNA methylation analyses with WGBS data seamlessly connecting all the required tasks ranging from data pre-processing to multiple downstream DNA methylation analyses. The msPIPE can generate various methylation profiles to analyze methylation patterns in the given sample, including statistical summaries and methylation levels. Also, the methylation levels in the functional regions of a genome are computed with proper annotation. The results of methylation profiles, hypomethylation, and differential methylation analysis are plotted in publication-quality figures. The msPIPE can be easily and conveniently used with a Docker image, which includes all dependent packages and software related to DNA methylation analyses. CONCLUSION msPIPE is a new end-to-end pipeline designed for methylation calling, profiling, and various types of downstream DNA methylation analyses, leading to the creation of publication-quality figures. msPIPE allows researchers to process and analyze the WGBS data in an easy and convenient way. It is available at https://github.com/jkimlab/msPIPE and https://hub.docker.com/r/jkimlab/mspipe .
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Affiliation(s)
- Heesun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Mikang Sim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kisang Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Junyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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8
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Gong T, Borgard H, Zhang Z, Chen S, Gao Z, Deng Y. Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies. SMALL METHODS 2022; 6:e2101251. [PMID: 35064762 PMCID: PMC8963483 DOI: 10.1002/smtd.202101251] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/30/2021] [Indexed: 05/09/2023]
Abstract
DNA methylation is associated with transcriptional repression, genomic imprinting, stem cell differentiation, embryonic development, and inflammation. Aberrant DNA methylation can indicate disease states, including cancer and neurological disorders. Therefore, the prevalence and location of 5-methylcytosine in the human genome is a topic of interest. Whole-genome bisulfite sequencing (WGBS) is a high-throughput method for analyzing DNA methylation. This technique involves library preparation, alignment, and quality control. Advancements in epigenetic technology have led to an increase in DNA methylation studies. This review compares the detailed experimental methodology of WGBS using accessible and up-to-date analysis tools. Practical codes for WGBS data processing are included as a general guide to assist progress in DNA methylation studies through a comprehensive case study.
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Affiliation(s)
- Ting Gong
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu HI 96813, USA
| | - Heather Borgard
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu HI 96813, USA
| | - Zao Zhang
- Department of Medicine, The Queen’s Medical Center, Honolulu HI 96813, USA
| | - Shaoqiu Chen
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu HI 96813, USA
| | - Zitong Gao
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu HI 96813, USA
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9
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Hüther P, Hagmann J, Nunn A, Kakoulidou I, Pisupati R, Langenberger D, Weigel D, Johannes F, Schultheiss SJ, Becker C. MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data. QUANTITATIVE PLANT BIOLOGY 2022; 3:e19. [PMID: 37077980 PMCID: PMC10095865 DOI: 10.1017/qpb.2022.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 05/03/2023]
Abstract
Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Different tools have been developed to extract differentially methylated regions (DMRs), often built upon assumptions from mammalian data. Here, we present MethylScore, a pipeline to analyse WGBS data and to account for the substantially more complex and variable nature of plant DNA methylation. MethylScore uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation. It processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1,001 Genomes dataset to unveil known and unknown genotype-epigenotype associations .
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Affiliation(s)
- Patrick Hüther
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | | | - Adam Nunn
- ecSeq Bioinformatics GmbH, 04103 Leipzig, Germany
- Department of Computer Science, Leipzig University, 04107 Leipzig, Germany
| | - Ioanna Kakoulidou
- Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Rahul Pisupati
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | | | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Frank Johannes
- Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
- Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany
| | | | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
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10
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Pavlovich PV, Cauchy P. Sequences to Differences in Gene Expression: Analysis of RNA-Seq Data. Methods Mol Biol 2022; 2508:279-318. [PMID: 35737247 DOI: 10.1007/978-1-0716-2376-3_20] [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: 06/15/2023]
Abstract
RNA-Seq is now a routinely employed assay to measure gene expression. As the technique matured over the last decade, so have dedicated analytic tools. In this chapter, we first describe the mainstream as well as the most up-to-date protocols and their implications on downstream analysis. We then detail the steps entailing RNA-Seq analysis in three main stages: (i) preprocessing and data preparation, (ii) upstream processing, and (iii) high-level analyses. We review the most recent and relevant tools as one workflow following a stepwise order. The chapter further encompasses in-depth features of these tools. Details of the required code are made available throughout the chapter, as well as of the underlying statistics. We illustrate these steps with analysis of publicly available RNA-Seq data.
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Affiliation(s)
| | - Pierre Cauchy
- Universitätskilinkum Freiburg, Freiburg, Germany.
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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11
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Meng J, Wang F, Ji L, Liang Y, Nian W, Song L, Zhu A. Comprehensive methylation profile of CSF cfDNA revealed pathogenesis and diagnostic markers for early-onset Parkinson's disease. Epigenomics 2021; 13:1637-1651. [PMID: 34664993 DOI: 10.2217/epi-2021-0176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background: Early-onset Parkinson's disease (EOPD) is one uncommon Parkinson's disease subtype with characteristic clinicopathological features. The full epigenomic profile of EOPD is largely unknown. Methods: We performed the first study to investigate the EOPD full methylation profile of cerebrospinal fluid (CSF) cell-free DNA (cfDNA) from 26 EOPD patients and 10 control patients. Results: 2220 differentially methylated genes were identified in EOPD. Hypermethylation far outweighed hypomethylation in gene numbers. Clustering and enrichment analyses identified aberrant neuronal function and immune response. Weighted correlation network analysis demonstrated significant correlation between methylation signatures and clock drawing test (CDT), mini-mental state examination (MMSE), education, working status, alcohol drinking history and Hamilton anxiety scale (HAMA). Several key networking genes in EOPD aberrant methylation were also identified. Conclusions: The methylation profile and signatures of CSF cfDNA were revealed for the first time in EOPD. Aberrant methylation signatures were correlated with education, working status, alcohol drinking history, CDT, MMSE and HAMA.
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Affiliation(s)
- Jie Meng
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China.,Department of Neurology & State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, & Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Fenglin Wang
- Department of genetics and cell biology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Lei Ji
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
| | - Yuhua Liang
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
| | - Wei Nian
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
| | - Lele Song
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China.,Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, 100091, PR China
| | - Aiqin Zhu
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
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Di Persio S, Leitão E, Wöste M, Tekath T, Cremers JF, Dugas M, Li X, Meyer Zu Hörste G, Kliesch S, Laurentino S, Neuhaus N, Horsthemke B. Whole-genome methylation analysis of testicular germ cells from cryptozoospermic men points to recurrent and functionally relevant DNA methylation changes. Clin Epigenetics 2021; 13:160. [PMID: 34419158 PMCID: PMC8379757 DOI: 10.1186/s13148-021-01144-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/01/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Several studies have reported an association between male infertility and aberrant sperm DNA methylation patterns, in particular in imprinted genes. In a recent investigation based on whole methylome and deep bisulfite sequencing, we have not found any evidence for such an association, but have demonstrated that somatic DNA contamination and genetic variation confound methylation studies in sperm of severely oligozoospermic men. To find out whether testicular germ cells (TGCs) of such patients might carry aberrant DNA methylation, we compared the TGC methylomes of four men with cryptozoospermia (CZ) and four men with obstructive azoospermia, who had normal spermatogenesis and served as controls (CTR). RESULTS There was no difference in DNA methylation at the whole genome level or at imprinted regions between CZ and CTR samples. However, using stringent filters to identify group-specific methylation differences, we detected 271 differentially methylated regions (DMRs), 238 of which were hypermethylated in CZ (binominal test, p < 2.2 × 10-16). The DMRs were enriched for distal regulatory elements (p = 1.0 × 10-6) and associated with 132 genes, 61 of which are differentially expressed at various stages of spermatogenesis. Almost all of the 67 DMRs associated with the 61 genes (94%) are hypermethylated in CZ (63/67, p = 1.107 × 10-14). As judged by single-cell RNA sequencing, 13 DMR-associated genes, which are mainly expressed during meiosis and spermiogenesis, show a significantly different pattern of expression in CZ patients. In four of these genes, the promoter is hypermethylated in CZ men, which correlates with a lower expression level in these patients. In the other nine genes, eight of which downregulated in CZ, germ cell-specific enhancers may be affected. CONCLUSIONS We found that impaired spermatogenesis is associated with DNA methylation changes in testicular germ cells at functionally relevant regions of the genome. We hypothesize that the described DNA methylation changes may reflect or contribute to premature abortion of spermatogenesis and therefore not appear in the mature, motile sperm.
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Affiliation(s)
- Sara Di Persio
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University Hospital of Münster, 48149, Münster, Germany
| | - Tobias Tekath
- Institute of Medical Informatics, University Hospital of Münster, 48149, Münster, Germany
| | - Jann-Frederik Cremers
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University Hospital of Münster, 48149, Münster, Germany
| | - Xiaolin Li
- Department of Neurology, Institute of Translational Neurology, University Hospital of Münster, 48149, Münster, Germany
| | - Gerd Meyer Zu Hörste
- Department of Neurology, Institute of Translational Neurology, University Hospital of Münster, 48149, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, University Hospital of Münster, 48149, Münster, Germany.
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
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