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Weng J, Wang H, Cheng D, Liu T, Zeng D, Dai C, Luo C. The Effects of DNA Methylation on Cytoplasmic Male Sterility in Sugar Beet. Int J Mol Sci 2024; 25:1118. [PMID: 38256191 PMCID: PMC10817047 DOI: 10.3390/ijms25021118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
DNA methylation is widely found in higher plants and can control gene expression by regulation without changing the DNA sequence. In this study, the whole-genome methylation map of sugar beet was constructed by WGBS (whole-genome bisulfite sequencing) technology, and the results of WGBS were verified by bisulfite transformation, indicating that the results of WGBS technology were reliable. In addition, 12 differential methylation genes (DMGs) were identified, which were related to carbohydrate and energy metabolism, pollen wall development, and endogenous hormone regulation. Quantitative real-time PCR (qRT-PCR) showed that 75% of DMG expression levels showed negative feedback with methylation level, indicating that DNA methylation can affect gene expression to a certain extent. In addition, we found hypermethylation inhibited gene expression, which laid a foundation for further study on the molecular mechanism of DNA methylation at the epigenetic level in sugar beet male sterility.
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Affiliation(s)
- Jiamin Weng
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China; (J.W.); (H.W.); (T.L.); (C.L.)
| | - Hui Wang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China; (J.W.); (H.W.); (T.L.); (C.L.)
| | - Dayou Cheng
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China; (J.W.); (H.W.); (T.L.); (C.L.)
| | - Tianjiao Liu
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China; (J.W.); (H.W.); (T.L.); (C.L.)
| | - Deyong Zeng
- School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, China; (D.Z.); (C.D.)
| | - Cuihong Dai
- School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, China; (D.Z.); (C.D.)
| | - Chengfei Luo
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China; (J.W.); (H.W.); (T.L.); (C.L.)
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Yu T, Zhang C, Song W, Zhao X, Cheng Y, Liu J, Su J. Single-cell RNA-seq and single-cell bisulfite-sequencing reveal insights into yak preimplantation embryogenesis. J Biol Chem 2024; 300:105562. [PMID: 38097189 PMCID: PMC10821408 DOI: 10.1016/j.jbc.2023.105562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/17/2023] [Accepted: 12/03/2023] [Indexed: 01/13/2024] Open
Abstract
Extensive epigenetic reprogramming occurs during preimplantation embryonic development. However, the impact of DNA methylation in plateau yak preimplantation embryos and how epigenetic reprogramming contributes to transcriptional regulatory networks are unclear. In this study, we quantified gene expression and DNA methylation in oocytes and a series of yak embryos at different developmental stages and at single-cell resolution using single-cell bisulfite-sequencing and RNA-seq. We characterized embryonic genome activation and maternal transcript degradation and mapped epigenetic reprogramming events critical for embryonic development. Through cross-species transcriptome analysis, we identified 31 conserved maternal hub genes and 39 conserved zygotic hub genes, including SIN3A, PRC1, HDAC1/2, and HSPD1. Notably, by combining single-cell DNA methylation and transcriptome analysis, we identified 43 candidate methylation driver genes, such as AURKA, NUSAP1, CENPF, and PLK1, that may be associated with embryonic development. Finally, using functional approaches, we further determined that the epigenetic modifications associated with the histone deacetylases HDAC1/2 are essential for embryonic development and that the deubiquitinating enzyme USP7 may affect embryonic development by regulating DNA methylation. Our data represent an extensive resource on the transcriptional dynamics of yak embryonic development and DNA methylation remodeling, and provide new insights into strategies for the conservation of germplasm resources, as well as a better understanding of mammalian early embryonic development that can be applied to investigate the causes of early developmental disorders.
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Affiliation(s)
- Tong Yu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Chengtu Zhang
- Academician Zhang Yong Innovation Center, Xining Animal Disease Control Center, Xining, Qinghai, China
| | - Weijia Song
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyi Zhao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuyao Cheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jianmin Su
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
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Morselli M, Bennett R, Shaidani NI, Horb M, Peshkin L, Pellegrini M. Age-associated DNA methylation changes in Xenopus frogs. Epigenetics 2023; 18:2201517. [PMID: 37092296 PMCID: PMC10128463 DOI: 10.1080/15592294.2023.2201517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 04/06/2023] [Indexed: 04/25/2023] Open
Abstract
Age-associated changes in DNA methylation have been characterized across various animals, but not yet in amphibians, which are of particular interest because they include widely studied model organisms. In this study, we present clear evidence that the aquatic vertebrate species Xenopus tropicalis displays patterns of age-associated changes in DNA methylation. We have generated whole-genome bisulfite sequencing (WGBS) profiles from skin samples of nine frogs representing young, mature, and old adults and characterized the gene- and chromosome-scale DNA methylation changes with age. Many of the methylation features and changes we observe are consistent with what is known in mammalian species, suggesting that the mechanism of age-related changes is conserved. Moreover, we selected a few thousand age-associated CpG sites to build an assay based on targeted DNA methylation analysis (TBSseq) to expand our findings in future studies involving larger cohorts of individuals. Preliminary results of a pilot TBSeq experiment recapitulate the findings obtained with WGBS setting the basis for the development of an epigenetic clock assay. The results of this study will allow us to leverage the unique resources available for Xenopus to study how DNA methylation relates to other hallmarks of ageing.
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Affiliation(s)
- Marco Morselli
- Molecular, Cell & Developmental Biology, UCLA, Los Angeles, CA, USA
| | - Ronan Bennett
- Molecular, Cell & Developmental Biology, UCLA, Los Angeles, CA, USA
| | - Nikko-Ideen Shaidani
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Marko Horb
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Leonid Peshkin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, USA
- Systems Biology, Harvard Medical School, Boston, MA, USA
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Lu DQ, Yao XY, Ren YT, Zhang KY, Zhu XC, Hong T, Yu X, Xie ZM, Chen LY, Wang XC. Genome-wide DNA methylation sequencing reveals epigenetic features and potential biomarkers of Sjögren syndrome. Int J Rheum Dis 2023; 26:2223-2232. [PMID: 37740638 DOI: 10.1111/1756-185x.14918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/08/2023] [Accepted: 09/03/2023] [Indexed: 09/24/2023]
Abstract
AIM Sjögren syndrome (SS) is a slowly progressive, inflammatory, autoimmune disease. The aim of this study was to construct the DNA methylation profiles of whole blood of SS patients and healthy controls (HC), and to explore the role of differentially methylated genes in the pathogenesis of the disease. METHODS Whole-genome bisulfite sequencing was performed on three SS patients and four HC. The biological function of genes associated with differentially methylated regions (DMRs) was investigated using Gene Ontology functional analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis, using network-based key driver analysis (KDA) to find KDA genes. In clinical samples of SS patients and controls, the expression levels of KDA genes were validated by quantitative real-time polymerase chain reaction and immunohistochemical analysis. Moreover, the diagnostic value of KDA genes for SS was confirmed using receiver operating characteristic curves. RESULTS We identified 322 DMRs, annotated as 162 associated genes. Six genes were selected via the number of networks of KDA genes. Differential expression of genes such as human leukocyte antigen (HLA) class I, ADAR, and OAS2 was observed in patients' peripheral blood mononuclear cells and the minor salivary glands, which can be used as potential diagnostic biomarkers for SS. CONCLUSION Clinical sample validation suggested that HLA class I, ADAR, and OAS2 might play a role in the development of SS. Our study shows epigenetic regulatory mechanisms and potential disease markers associated with SS, which in turn will enable us to identify new therapeutic targets.
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Affiliation(s)
- Ding-Qi Lu
- Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xin-Yi Yao
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Ya-Ting Ren
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Kai-Yuan Zhang
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xin-Chao Zhu
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Tao Hong
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xue Yu
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Zhi-Min Xie
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Li-Ying Chen
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xin-Chang Wang
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
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Ho TC, Wan HT, Lee WK, Lam TKY, Lin X, Chan TF, Lai KP, Wong CKC. Effects of In Utero PFOS Exposure on Epigenetics and Metabolism in Mouse Fetal Livers. Environ Sci Technol 2023; 57:14892-14903. [PMID: 37759171 PMCID: PMC10569047 DOI: 10.1021/acs.est.3c05207] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/16/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023]
Abstract
Prenatal exposure to perfluorooctanesulfonate (PFOS) increases fetus' metabolic risk; however, the investigation of the underlying mechanism is limited. In this study, pregnant mice in the gestational days (GD, 4.5-17.5) were exposed to PFOS (0.3 and 3 μg/g of body weight). At GD 17.5, PFOS perturbed maternal lipid metabolism and upregulated metabolism-regulating hepatokines (Angptl4, Angptl8, and Selenop). Mass-spectrometry imaging and whole-genome bisulfite sequencing revealed, respectively, selective PFOS localization and deregulation of gene methylation in fetal livers, involved in inflammation, glucose, and fatty acid metabolism. PCR and Western blot analysis of lipid-laden fetal livers showed activation of AMPK signaling, accompanied by significant increases in the expression of glucose transporters (Glut2/4), hexose-phosphate sensors (Retsat and ChREBP), and the key glycolytic enzyme, pyruvate kinase (Pk) for glucose catabolism. Additionally, PFOS modulated the expression levels of PPARα and PPARγ downstream target genes, which simultaneously stimulated fatty acid oxidation (Cyp4a14, Acot, and Acox) and lipogenesis (Srebp1c, Acaca, and Fasn). Using human normal hepatocyte (MIHA) cells, the underlying mechanism of PFOS-elicited nuclear translocation of ChREBP, associated with a fatty acid synthesizing pathway, was revealed. Our finding implies that in utero PFOS exposure altered the epigenetic landscape associated with dysregulation of fetal liver metabolism, predisposing postnatal susceptibility to metabolic challenges.
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Affiliation(s)
- Tsz Chun Ho
- Croucher
Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
- State
Key Laboratory in Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Hin Ting Wan
- Croucher
Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Wang Ka Lee
- Croucher
Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Thomas Ka Yam Lam
- State
Key Laboratory in Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Xiao Lin
- Department
of Psychiatry, Icahn School of Medicine
at Mount Sinai, New York, New York 10029, United States
| | - Ting Fung Chan
- School
of Life Sciences, State Key Laboratory of Agrobiotechnology, Bioinformatics
Centre, The Chinese University of Hong Kong, New Territories 999077, Hong Kong SAR, China
| | - Keng Po Lai
- Key
Laboratory of Environmental Pollution and Integrative Omics, Education
Department of Guangxi Zhuang Autonomous Region, Guilin Medical University, Guilin 541100, China
| | - Chris Kong Chu Wong
- Croucher
Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
- State
Key Laboratory in Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
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Simko I. Differentially methylated genomic regions of lettuce seeds relate to divergence across morphologically distinct horticultural types. AoB Plants 2023; 15:plad060. [PMID: 37680204 PMCID: PMC10482144 DOI: 10.1093/aobpla/plad060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 08/22/2023] [Indexed: 09/09/2023]
Abstract
Heritable cytosine methylation plays a role in shaping plant phenotypes; however, no information is available about DNA methylation in cultivated lettuce (Lactuca sativa), one of the most important leafy vegetables. Whole-genome bisulfite sequencing (WGBS) performed on seeds of 95 accessions from eight morphologically distinct horticultural types (Batavia, butterhead, iceberg, Latin, leaf, oilseed, romaine and stem) revealed a high level of methylation in lettuce genome with an average methylation of 90.6 % in the CG context, 72.9 % in the CHG context and 7.5 % in the CHH context. Although WGBS did not show substantial differences in overall methylation levels across eight horticultural types, 350 differentially methylated regions (DMR) were identified. Majority of the 41 pivotal DMR overlapped with genomic features predicted or confirmed to be involved in plant growth and development. These results provide the first insight into lettuce DNA methylation and indicate a potential role for heritable variation in cytosine methylation in lettuce morphology. The results reveal that differences in methylation profiles of morphologically distinct horticultural types are already detectable in seeds. Identified DMR can be a focus of the future functional studies.
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Affiliation(s)
- Ivan Simko
- Crop Improvement and Protection Research Unit, US Department of Agriculture, Agricultural Research Service, Salinas, CA 93905, USA
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Sindi S, Hamdi N, Hassan S, Ganash M, Alharbi M, Alburae N, Azhari S, Alkhayyat S, Linjawi A, Alkhatabi H, Elaimi A, Alrefaei G, Alsubhi N, Alrafiah A, Alhazmi S. Promoter Methylation-Regulated Differentially Expressed Genes in Breast Cancer. Breast Cancer (Dove Med Press) 2023; 15:435-450. [PMID: 37434588 PMCID: PMC10332364 DOI: 10.2147/bctt.s408711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/21/2023] [Indexed: 07/13/2023]
Abstract
Background Breast cancer is one of the most common malignancies among women. Recent studies revealed that differentially methylated regions (DMRs) are implicated in regulating gene expression. The goal of this research was to determine which genes and pathways are dysregulated in breast cancer when their promoters are methylated in an abnormal way, leading to differential expression. Whole-genome bisulfite sequencing was applied to analyze DMRs for eight peripheral blood samples collected from five Saudi females diagnosed with stages I and II of breast cancer aligned with three normal females. Three of those patients and three normal samples were used to determine differentially expressed genes (DEG) using Illumina platform NovaSeq PE150. Results Based on ontology (GO) and KEGG pathways, the analysis indicated that DMGs and DEG are closely related to associated processes, such as ubiquitin-protein transferase activity, ubiquitin-mediated proteolysis, and oxidative phosphorylation. The findings indicated a potentially significant association between global hypomethylation and breast cancer in Saudi patients. Our results revealed 81 differentially promoter-methylated and expressed genes. The most significant differentially methylated and expressed genes found in gene ontology (GO) are pumilio RNA binding family member 1 (PUM1) and zinc finger AN1-type containing 2B (ZFAND2B) also known as (AIRAPL). Conclusion The essential outcomes of this study suggested that aberrant hypermethylation at crucial genes that have significant parts in the molecular pathways of breast cancer could be used as a potential prognostic biomarker for breast cancer.
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Affiliation(s)
- Samar Sindi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Norah Hamdi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biology, King Khalid University, Abha, Saudi Arabia
| | - Sabah Hassan
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Magdah Ganash
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najla Alburae
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sheren Azhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shadi Alkhayyat
- Department of Internal Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Heba Alkhatabi
- Hematology Research Unit (HRU), King Fahad Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Elaimi
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ghadeer Alrefaei
- Department of Biology, University of Jeddah, Jeddah, Saudi Arabia
| | - Nouf Alsubhi
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Aziza Alrafiah
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Safiah Alhazmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Yue C, Wang J, Shen Y, Zhang J, Liu J, Xiao A, Liu Y, Eer H, Zhang QE. Whole-genome DNA methylation profiling reveals epigenetic signatures in developing muscle in Tan and Hu sheep and their offspring. Front Vet Sci 2023; 10:1186040. [PMID: 37388464 PMCID: PMC10301830 DOI: 10.3389/fvets.2023.1186040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction The Tan sheep is a popular local breed in China because of its tenderness and flavor. The Hu sheep breed is also famous for its high litter size, and its muscle growth rate is faster than that of Tan sheep. However, the epigenetic mechanism behind these muscle-related phenotypes is unknown. Methods In this study, the longissimus dorsi tissue from 18 6 month-old Tan sheep, Hu sheep, and Tan-Hu F2 generation (6 sheep per population) were collected. After genomic DNA extraction, whole-genome bisulfite sequencing (WGBS) and bioinformatics analysis were performed to construct genome-wide DNA methylome maps for the Tan sheep, Hu sheep and their Tan-Hu F2 generation. Results Distinct genome-wide DNA methylation patterns were observed between Tan sheep and Hu sheep. Moreover, DNA methylated regions were significantly increased in the skeletal muscle from Tan sheep vs. the F2 generation compared to the Hu sheep vs. F2 generation and the Tan sheep vs. Hu sheep. Compared with Hu sheep, the methylation levels of actin alpha 1 (ACTA1), myosin heavy chain 11 (MYH11), Wiskott-Aldrich syndrome protein (WAS), vav guanine nucleotide exchange factor 1 (VAV1), fibronectin 1 (FN1) and Rho-associated protein kinase 2 (ROCK2) genes were markedly distinct in the Tan sheep. Furthermore, Gene Ontology analysis indicated that these genes were involved in myotube differentiation, myotube cell development, smooth muscle cell differentiation and striated muscle cell differentiation. Conclusion The findings from this study, in addition to data from previous research, demonstrated that the ACTA1, MYH11, WAS, VAV1, FN1, and ROCK2 genes may exert regulatory effects on muscle development.
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Affiliation(s)
- Caijuan Yue
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Jiakang Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yifei Shen
- Institute of Marxism, China University of Geosciences, Wuhan, Hubei, China
| | - Junli Zhang
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Jian Liu
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Aiping Xiao
- Animal Husbandry Extension Station, Yinchuan, Ningxia, China
| | - Yisha Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
| | - Hehua Eer
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Qiao-e Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
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10
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Zhang Y, Wei Y, Meng J, Wang Y, Nie S, Zhang Z, Wang H, Yang Y, Gao Y, Wu J, Li T, Liu X, Zhang H, Gu L. Chromosome-scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana. Plant J 2023; 114:1490-1505. [PMID: 36971060 DOI: 10.1111/tpj.16201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 02/15/2023] [Accepted: 03/13/2023] [Indexed: 06/17/2023]
Abstract
Australian pine (Casuarina spp.) is extensively planted in tropical and subtropical regions for wood production, shelterbelts, environmental protection, and ecological restoration due to their superior biological characteristics, such as rapid growth, wind and salt tolerance, and nitrogen fixation. To analyze the genomic diversity of Casuarina, we sequenced the genomes and constructed de novo genome assemblies of the three most widely planted Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana. We generated chromosome-scale genome sequences using both Pacific Biosciences (PacBio) Sequel sequencing and chromosome conformation capture technology (Hi-C). The total genome sizes for C. equisetifolia, C. glauca, and C. cunninghamiana are 268 942 579 bp, 296 631 783 bp, and 293 483 606 bp, respectively, of which 25.91, 27.15, and 27.74% were annotated as repetitive sequences. We annotated 23 162, 24 673, and 24 674 protein-coding genes in C. equisetifolia, C. glauca, and C. cunninghamiana, respectively. We then collected branchlets from male and female individuals for whole-genome bisulfite sequencing (BS-seq) to explore the epigenetic regulation of sex determination in these three species. Transcriptome sequencing (RNA-seq) revealed differential expression of phytohormone-related genes between male and female plants. In summary, we generated three chromosome-level genome assemblies and comprehensive DNA methylation and transcriptome datasets from both male and female material for three Casuarina species, providing a basis for the comprehensive investigation of genomic diversity and functional gene discovery of Casuarina in the future.
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Affiliation(s)
- Yong Zhang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Yongcheng Wei
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Jingxiang Meng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Yujiao Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Sen Nie
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, 350012, China
| | - Zeyu Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiyuan Wang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongkang Yang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ji Wu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tuhe Li
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xuqing Liu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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11
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Mouat JS, Li S, Myint SS, Laufer BI, Lupo PJ, Schraw JM, Woodhouse JP, de Smith AJ, LaSalle JM. Epigenomic signature of major congenital heart defects in newborns with Down syndrome. medRxiv 2023:2023.05.02.23289417. [PMID: 37205408 PMCID: PMC10187438 DOI: 10.1101/2023.05.02.23289417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Background Congenital heart defects (CHDs) affect approximately half of individuals with Down syndrome (DS) but the molecular reasons for incomplete penetrance are unknown. Previous studies have largely focused on identifying genetic risk factors associated with CHDs in individuals with DS, but comprehensive studies of the contribution of epigenetic marks are lacking. We aimed to identify and characterize DNA methylation differences from newborn dried blood spots (NDBS) of DS individuals with major CHDs compared to DS individuals without CHDs. Methods We used the Illumina EPIC array and whole-genome bisulfite sequencing (WGBS) to quantitate DNA methylation for 86 NDBS samples from the California Biobank Program: 1) 45 DS-CHD (27 female, 18 male) and 2) 41 DS non-CHD (27 female, 14 male). We analyzed global CpG methylation and identified differentially methylated regions (DMRs) in DS-CHD vs DS non-CHD comparisons (both sex-combined and sex-stratified) corrected for sex, age of blood collection, and cell type proportions. CHD DMRs were analyzed for enrichment in CpG and genic contexts, chromatin states, and histone modifications by genomic coordinates and for gene ontology enrichment by gene mapping. DMRs were also tested in a replication dataset and compared to methylation levels in DS vs typical development (TD) WGBS NDBS samples. Results We found global CpG hypomethylation in DS-CHD males compared to DS non-CHD males, which was attributable to elevated levels of nucleated red blood cells and not seen in females. At a regional level, we identified 58, 341, and 3,938 CHD-associated DMRs in the Sex Combined, Females Only, and Males Only groups, respectively, and used machine learning algorithms to select 19 Males Only loci that could distinguish CHD from non-CHD. DMRs in all comparisons were enriched for gene exons, CpG islands, and bivalent chromatin and mapped to genes enriched for terms related to cardiac and immune functions. Lastly, a greater percentage of CHD-associated DMRs than background regions were differentially methylated in DS vs TD samples. Conclusions A sex-specific signature of DNA methylation was detected in NDBS of DS-CHD compared to DS non-CHD individuals. This supports the hypothesis that epigenetics can reflect the variability of phenotypes in DS, particularly CHDs.
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Affiliation(s)
- Julia S Mouat
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, CA USA
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, CA USA
| | - Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
| | - Philip J Lupo
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Jeremy M Schraw
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - John P Woodhouse
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, CA USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA USA
- Genome Center, University of California, Davis, CA USA
- MIND Institute, University of California, Davis, CA USA
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12
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Martin EM, Grimm SA, Xu Z, Taylor JA, Wade PA. Beadchip technology to detect DNA methylation in mouse faithfully recapitulates whole-genome bisulfite sequencing. Epigenomics 2023; 15:115-129. [PMID: 37020391 PMCID: PMC10131490 DOI: 10.2217/epi-2023-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Aim: To facilitate wide-scale implementation of Illumina Mouse Methylation BeadChip (MMB) technology, array-based measurement of cytosine methylation was compared with the gold-standard assessment of DNA methylation by whole-genome bisulfite sequencing (WGBS). Methods: DNA methylation across two mouse strains (C57B6 and C3H) and both sexes was assessed using the MMB and compared with previously existing deep-coverage WGBS of mice of the same strain and sex. Results & conclusion: The findings demonstrated that 93.3-99.2% of sites had similar measurements of methylation across technologies and that differentially methylated cytosines and regions identified by each technology overlap and enrich for similar biological functions, suggesting that the MMB faithfully recapitulates the findings of WGBS.
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Affiliation(s)
- Elizabeth M Martin
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Sara A Grimm
- Integrative Bioinformatics, Biostatistics & Computational Biology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Jack A Taylor
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
- Epidemiology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Paul A Wade
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
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13
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Liu F, Zhang P, Liang Z, Yuan Y, Liu Y, Wu Y. The global dynamic of DNA methylation in response to heat stress revealed epigenetic mechanism of heat acclimation in Saccharina japonica. J Phycol 2023; 59:249-263. [PMID: 36453855 DOI: 10.1111/jpy.13305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
Saccharina japonica is an ecologically and economically important kelp in cold-temperate regions. When it is cultivated on a large scale in the temperate and even subtropical zones, heat stress is a frequent abiotic stress. This study is the first attempt to reveal the regulatory mechanism of the response to heat stress from the perspective of DNA methylation in S. japonica. We firstly obtained the characteristics of variation in the methylome under heat stress, and observed that heat stress caused a slight increase in the overall methylation level and methylation rate, especially in the non-coding regions of the genome. Secondly, we noted that methylation was probably one of factors affecting the expression of genes, and that methylation within the gene body was positively correlated with the gene expression (rho = 0.0784). Moreover, it was found that among the differentially expressed genes regulated by methylation, many genes were related to heat stress response, such as HSP gene family, genes of antioxidant enzymes, genes related to proteasome-ubiquitination pathway, and plant cell signaling pathways. This study demonstrated that DNA methylation is involved in regulating the response to heat stress, laying a foundation for studying the acclimation and adaptation of S. japonica to heat stress from an epigenetic perspective.
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Affiliation(s)
- Fuli Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education; College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Pengyan Zhang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Zhourui Liang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yanmin Yuan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yi Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yukun Wu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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14
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Li L, He S, Lin MH, Zhang YP, Kuhl H, Liang XF. Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish ( Siniperca chuatsi). Front Genet 2023; 13:1088081. [PMID: 36712873 PMCID: PMC9878154 DOI: 10.3389/fgene.2022.1088081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023] Open
Abstract
Mandarin fish (Siniperca chuatsi) is one of the most economically important fish in China. However, it has the peculiar feeding habit that it feeds solely on live prey fish since first-feeding, while refuses dead prey fish or artificial diets. After the specific training procedure, partial individuals could accept dead prey fish and artificial diets. The genetic basis of individual difference in artificial diet feeding habit is still unknown. In the present study, the resequencing was performed between 10 individuals which could be domesticated to accept artificial diets and 10 individuals which could not. Through the selective sweep analysis based on heterozygosity (Hp) and population differentiation coefficient (Fst), 57 candidate windows were identified as the putative selected regions for feeding habit domestication of mandarin fish, involved in 149 genes. These genes were related to memory, vision and olfaction function, which could be potential targets of molecular marker assistant breeding of artificial diet feeding trait. Beside of the DNA sequence, we also explored the potential role of DNA methylation in feeding habit domestication in mandarin fish. Whole-genome bisulfite sequencing was performed between the individuals which could be domesticated to accept artificial diets and those could not. 5,976 differentially methylated regions were identified, referring to 3,522 genes, such as the genes involved in cAMP signaling pathway. The DNA methylation changes of these genes might contribute to the adaption of artificial diets in mandarin fish. In conclusion, the putative selected regions and the differentially methylated regions were identified in the whole genome, providing new insights into the feeding habit domestication from live prey fish to artificial diets in mandarin fish. And the involved genes were identified as the candidate genes for molecular breeding of artificial diet utilization in mandarin fish.
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Affiliation(s)
- Ling Li
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Shan He
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Ming-Hui Lin
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Yan-Peng Zhang
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany,*Correspondence: Xu-Fang Liang, ; Heiner Kuhl,
| | - Xu-Fang Liang
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China,*Correspondence: Xu-Fang Liang, ; Heiner Kuhl,
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15
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Jamshidi A, Liu MC, Klein EA, Venn O, Hubbell E, Beausang JF, Gross S, Melton C, Fields AP, Liu Q, Zhang N, Fung ET, Kurtzman KN, Amini H, Betts C, Civello D, Freese P, Calef R, Davydov K, Fayzullina S, Hou C, Jiang R, Jung B, Tang S, Demas V, Newman J, Sakarya O, Scott E, Shenoy A, Shojaee S, Steffen KK, Nicula V, Chien TC, Bagaria S, Hunkapiller N, Desai M, Dong Z, Richards DA, Yeatman TJ, Cohn AL, Thiel DD, Berry DA, Tummala MK, McIntyre K, Sekeres MA, Bryce A, Aravanis AM, Seiden MV, Swanton C. Evaluation of cell-free DNA approaches for multi-cancer early detection. Cancer Cell 2022; 40:1537-1549.e12. [PMID: 36400018 DOI: 10.1016/j.ccell.2022.10.022] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 08/03/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022]
Abstract
In the Circulating Cell-free Genome Atlas (NCT02889978) substudy 1, we evaluate several approaches for a circulating cell-free DNA (cfDNA)-based multi-cancer early detection (MCED) test by defining clinical limit of detection (LOD) based on circulating tumor allele fraction (cTAF), enabling performance comparisons. Among 10 machine-learning classifiers trained on the same samples and independently validated, when evaluated at 98% specificity, those using whole-genome (WG) methylation, single nucleotide variants with paired white blood cell background removal, and combined scores from classifiers evaluated in this study show the highest cancer signal detection sensitivities. Compared with clinical stage and tumor type, cTAF is a more significant predictor of classifier performance and may more closely reflect tumor biology. Clinical LODs mirror relative sensitivities for all approaches. The WG methylation feature best predicts cancer signal origin. WG methylation is the most promising technology for MCED and informs development of a targeted methylation MCED test.
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Affiliation(s)
| | - Minetta C Liu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | | | | | | | | | | | - Nan Zhang
- GRAIL, LLC, Menlo Park, CA 94025, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Zhao Dong
- GRAIL, LLC, Menlo Park, CA 94025, USA
| | | | - Timothy J Yeatman
- Gibbs Cancer Center and Research Institute, Spartanburg, SC 29303, USA; Department of Surgery, University of Utah, Salt Lake City, UT 84112, USA
| | - Allen L Cohn
- Rocky Mountain Cancer Center, Denver, CO 80218, USA
| | - David D Thiel
- Department of Urology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Donald A Berry
- Department of Biostatistics, MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | | | | | | | | | | | - Charles Swanton
- Francis Crick Institute, London, NW1 1AT, UK; UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, London, WC1E 6DD, UK
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16
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Ehrlich KC, Lacey M, Baribault C, Sen S, Esteve PO, Pradhan S, Ehrlich M. Promoter-Adjacent DNA Hypermethylation Can Downmodulate Gene Expression: TBX15 in the Muscle Lineage. Epigenomes 2022; 6. [PMID: 36547252 DOI: 10.3390/epigenomes6040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
TBX15, which encodes a differentiation-related transcription factor, displays promoter-adjacent DNA hypermethylation in myoblasts and skeletal muscle (psoas) that is absent from non-expressing cells in other lineages. By whole-genome bisulfite sequencing (WGBS) and enzymatic methyl-seq (EM-seq), these hypermethylated regions were found to border both sides of a constitutively unmethylated promoter. To understand the functionality of this DNA hypermethylation, we cloned the differentially methylated sequences (DMRs) in CpG-free reporter vectors and tested them for promoter or enhancer activity upon transient transfection. These cloned regions exhibited strong promoter activity and, when placed upstream of a weak promoter, strong enhancer activity specifically in myoblast host cells. In vitro CpG methylation targeted to the DMR sequences in the plasmids resulted in 86−100% loss of promoter or enhancer activity, depending on the insert sequence. These results as well as chromatin epigenetic and transcription profiles for this gene in various cell types support the hypothesis that DNA hypermethylation immediately upstream and downstream of the unmethylated promoter region suppresses enhancer/extended promoter activity, thereby downmodulating, but not silencing, expression in myoblasts and certain kinds of skeletal muscle. This promoter-border hypermethylation was not found in cell types with a silent TBX15 gene, and these cells, instead, exhibit repressive chromatin in and around the promoter. TBX18, TBX2, TBX3 and TBX1 display TBX15-like hypermethylated DMRs at their promoter borders and preferential expression in myoblasts. Therefore, promoter-adjacent DNA hypermethylation for downmodulating transcription to prevent overexpression may be used more frequently for transcription regulation than currently appreciated.
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17
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Nwanade CF, Wang Z, Bai R, Wang R, Zhang T, Liu J, Yu Z. DNA Methylation Variation Is a Possible Mechanism in the Response of Haemaphysalis longicornis to Low-Temperature Stress. Int J Mol Sci 2022; 23. [PMID: 36499526 DOI: 10.3390/ijms232315207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Ticks are notorious ectoparasites and transmit the greatest variety of pathogens than any other arthropods. Cold tolerance is a key determinant of tick abundance and distribution. While studies have shown that DNA methylation is one of the important epigenetic regulations found across many species and plays a significant role in their response to low-temperature stress, its role in the response of ticks to low-temperature stress remains unexplored. Herein, we explored the DNA methylation profile of the tick, Haemaphysalis longicornis, exposed to low-temperature stress (4 °C) using whole-genome bisulfite sequencing (WGBS). We found that approximately 0.95% and 0.94% of the genomic C sites were methylated in the control and low-temperature groups, respectively. Moreover, the methylation level under the CG context was about 3.86% and 3.85% in the control and low-temperature groups, respectively. In addition, a total of 6087 differentially methylated regions (DMRs) were identified between the low-temperature and control groups, including 3288 hypermethylated and 2799 hypomethylated DMRs. Further, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially methylated genes revealed that most of the DMGs were significantly enriched in binding and RNA transport pathways. Taken together, this research confirmed, for the first time, the whole genome DNA methylation profile of H. longicornis and provided new insights into the DNA methylation changes relating to low-temperature stress in H. longicornis, as well as provided a foundation for future studies on the epigenetic mechanism underlying the responses of ticks to abiotic stress.
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18
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Fonseca PAS, Alonso-García M, Pelayo R, Marina H, Esteban-Blanco C, Mateo J, Gutiérrez-Gil B, Arranz JJ, Suárez-Vega A. Integrated analyses of the methylome and transcriptome to unravel sex differences in the perirenal fat from suckling lambs. Front Genet 2022; 13:1035063. [PMID: 36386829 PMCID: PMC9663842 DOI: 10.3389/fgene.2022.1035063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/18/2022] [Indexed: 11/25/2022] Open
Abstract
In sheep, differences were observed regarding fat accumulation and fatty acid (FA) composition between males and females, which may impact the quality and organoleptic characteristics of the meat. The integration of different omics technologies is a relevant approach for investigating biological and genetic mechanisms associated with complex traits. Here, the perirenal tissue of six male and six female Assaf suckling lambs was evaluated using RNA sequencing and whole-genome bisulfite sequencing (WGBS). A multiomic discriminant analysis using multiblock (s)PLS-DA allowed the identification of 314 genes and 627 differentially methylated regions (within these genes), which perfectly discriminate between males and females. These candidate genes overlapped with previously reported QTLs for carcass fat volume and percentage of different FAs in milk and meat from sheep. Additionally, differentially coexpressed (DcoExp) modules of genes between males (nine) and females (three) were identified that harbour 22 of these selected genes. Interestingly, these DcoExp were significantly correlated with fat percentage in different deposits (renal, pelvic, subcutaneous and intramuscular) and were associated with relevant biological processes for adipogenesis, adipocyte differentiation, fat volume and FA composition. Consequently, these genes may potentially impact adiposity and meat quality traits in a sex-specific manner, such as juiciness, tenderness and flavour.
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Affiliation(s)
- Pablo A. S. Fonseca
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - María Alonso-García
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Rocio Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Hector Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Javier Mateo
- Departamento de Higiene y Tecnología de Los Alimentos, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Juan-José Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain,*Correspondence: Juan-José Arranz,
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
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19
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Gao Y, Zhao H, An K, Liu Z, Hai L, Li R, Zhou Y, Zhao W, Jia Y, Wu N, Li L, Ying J, Wang J, Xu B, Wu Z, Tong Z, He J, Sun Y. Whole-genome bisulfite sequencing analysis of circulating tumour DNA for the detection and molecular classification of cancer. Clin Transl Med 2022; 12:e1014. [PMID: 35998020 PMCID: PMC9398227 DOI: 10.1002/ctm2.1014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Background Cancer cell–specific variation and circulating tumour DNA (ctDNA) methylation are promising biomarkers for non‐invasive cancer detection and molecular classification. Nevertheless, the applications of ctDNA to the early detection and screening of cancer remain highly challenging due to the scarcity of cancer cell–specific ctDNA, the low signal‐to‐noise ratio of DNA variation, and the lack of non‐locus‐specific DNA methylation technologies. Methods We enrolled three cohorts of breast cancer (BC) patients from two hospitals in China (BC: n = 123; healthy controls: n = 40). We developed a ctDNA whole‐genome bisulfite sequencing technology employing robust trace ctDNA capture from up to 200 μL plasma, mini‐input (1 ng) library preparation, unbiased genome‐wide coverage and comprehensive computational methods. Results A diagnostic signature comprising 15 ctDNA methylation markers exhibited high accuracy in the early (area under the curve [AUC] of 0.967) and advanced (AUC of 0.971) BC stages in multicentre patient cohorts. Furthermore, we revealed a ctDNA methylation signature that discriminates estrogen receptor status (Training set: AUC of 0.984 and Test set: AUC of 0.780). Different cancer types, including hepatocellular carcinoma and lung cancer, could also be well distinguished. Conclusions Our study provides a toolset to generate unbiased whole‐genome ctDNA methylomes with a minimal amount of plasma to develop highly specific and sensitive biomarkers for the early diagnosis and molecular subtyping of cancer.
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Affiliation(s)
- Yibo Gao
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.,Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Laboratory of Translational Medicine, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ke An
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zongzhi Liu
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.,Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Luo Hai
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Renda Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weipeng Zhao
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China
| | - Yongsheng Jia
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lingyu Li
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Jianming Ying
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Binghe Xu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhihong Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhongsheng Tong
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China
| | - Jie He
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.,Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yingli Sun
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
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20
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Leung C, Grulois D, Chevin LM. Plasticity across levels: relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga. Mol Ecol 2022; 31:4672-4687. [PMID: 35593517 PMCID: PMC9543585 DOI: 10.1111/mec.16542] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/12/2022] [Indexed: 12/01/2022]
Abstract
Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and investigating how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in Dunaliella salina, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain‐ and environment‐specific variation in gene expression levels, but a relative low—albeit significant—effect of strain × environment interaction. We also found an important genotype effect on the genome‐wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits.
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Affiliation(s)
- Christelle Leung
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Daphné Grulois
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
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21
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Zhao X, Hao Y, Wang Q, Shen Y, Cheng Y, Li B, Gao Y, Wang T, Qiu Y. Novel deoxyribonucleic acid methylation perturbations in workers exposed to vinyl chloride. Toxicol Ind Health 2022; 38:377-388. [PMID: 35548910 DOI: 10.1177/07482337221098600] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To explore the epigenetic mechanism of deoxyribonucleic acid (DNA) damage induced by vinyl chloride (VC), we studied the micronuclei of peripheral blood lymphocytes in 193 subjects (92 in a VC exposure group employed in a chlorine-alkali plant; 101 in a control group employed in a power plant) and selected three pairs from the subjects (exposed and control) for whole-genome bisulfite sequencing (WGBS). The results showed that the rate of micronucleus formation in the VC exposure group was higher than that of control group (6.05 ± 3.28‰ vs. 2.01 ± 1.79‰). A total of 9534 differentially methylated regions (DMRs) were identified by WGBS, of which 4816 were hypomethylated and 4718 were hypermethylated. The Kyoto encyclopedia of genes and genomes (KEGG) pathway and gene ontology (GO) analyses showed the top three KEGG pathways were cancer , neuroactive ligand-receptor interaction, and axon guidance, and the top three GO-BP pathways enriched were multicellular organismal process, developmental process, and anatomical structure development. In the most enriched DMR pathway (pathways in cancer), we found that BCL2, TJP2, TAOK1, PFKFB3, LIPI, and LIPH were hypermethylated, and the methylation levels of BNIP1 and GRPEL2 were decreased. The methylation of differentially methylated genes (DMGs) mentioned above were verified by methylation-specific PCR (MSP) and agarose gel electrophoresis (AGE) in 50 pairs of subjects, where the coincidence rate was 60-100%. In conclusion, the epigenetic perturbations of specific DMGs (BCL2, TJP2, TAOK1, PFKFB3, LIPI, LIPH, BNIP1, and GRPEL2) may be associated with DNA damage from vinyl chloride exposure.
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Affiliation(s)
- Xiaotian Zhao
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yan Hao
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Qian Wang
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yongmei Shen
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Ying Cheng
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Ben Li
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yi Gao
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Tong Wang
- Department of Statistics, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yulan Qiu
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
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22
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Mordaunt CE, Mouat JS, Schmidt RJ, LaSalle JM. Comethyl: a network-based methylome approach to investigate the multivariate nature of health and disease. Brief Bioinform 2022; 23:bbab554. [PMID: 35037016 PMCID: PMC8921619 DOI: 10.1093/bib/bbab554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/15/2021] [Accepted: 12/04/2021] [Indexed: 11/14/2022] Open
Abstract
Health outcomes are frequently shaped by difficult to dissect inter-relationships between biological, behavioral, social and environmental factors. DNA methylation patterns reflect such multivariate intersections, providing a rich source of novel biomarkers and insight into disease etiologies. Recent advances in whole-genome bisulfite sequencing enable investigation of DNA methylation over all genomic CpGs, but existing bioinformatic approaches lack accessible system-level tools. Here, we develop the R package Comethyl, for weighted gene correlation network analysis of user-defined genomic regions that generates modules of comethylated regions, which are then tested for correlations with multivariate sample traits. First, regions are defined by CpG genomic location or regulatory annotation and filtered based on CpG count, sequencing depth and variability. Next, correlation networks are used to find modules of interconnected nodes using methylation values within the selected regions. Each module containing multiple comethylated regions is reduced in complexity to a single eigennode value, which is then tested for correlations with experimental metadata. Comethyl has the ability to cover the noncoding regulatory regions of the genome with high relevance to interpretation of genome-wide association studies and integration with other types of epigenomic data. We demonstrate the utility of Comethyl on a dataset of male cord blood samples from newborns later diagnosed with autism spectrum disorder (ASD) versus typical development. Comethyl successfully identified an ASD-associated module containing regions mapped to genes enriched for brain glial functions. Comethyl is expected to be useful in uncovering the multivariate nature of health disparities for a variety of common disorders. Comethyl is available at github.com/cemordaunt/comethyl with complete documentation and example analyses.
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Affiliation(s)
- Charles E Mordaunt
- Department of Medical Microbiology and Immunology, Genome Center, Perinatal Origins of Disparities Center, and MIND Institute, University of California, Davis, CA, USA
| | - Julia S Mouat
- Department of Medical Microbiology and Immunology, Genome Center, Perinatal Origins of Disparities Center, and MIND Institute, University of California, Davis, CA, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences, Perinatal Origins of Disparities Center, and MIND Institute, University of California, Davis, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, Perinatal Origins of Disparities Center, and MIND Institute, University of California, Davis, CA, USA
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23
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Laufer BI, Neier K, Valenzuela AE, Yasui DH, Schmidt RJ, Lein PJ, LaSalle JM. Placenta and fetal brain share a neurodevelopmental disorder DNA methylation profile in a mouse model of prenatal PCB exposure. Cell Rep 2022; 38:110442. [PMID: 35235788 PMCID: PMC8941983 DOI: 10.1016/j.celrep.2022.110442] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/19/2021] [Accepted: 02/03/2022] [Indexed: 12/27/2022] Open
Abstract
Polychlorinated biphenyls (PCBs) are developmental neurotoxicants implicated as environmental risk factors for neurodevelopmental disorders (NDDs). Here, we report the effects of prenatal exposure to a human-relevant mixture of PCBs on the DNA methylation profiles of mouse placenta and fetal brain. Thousands of differentially methylated regions (DMRs) distinguish placenta and fetal brain from PCB-exposed mice from sex-matched vehicle controls. In both placenta and fetal brain, PCB-associated DMRs are enriched for functions related to neurodevelopment and cellular signaling and enriched within regions of bivalent chromatin. The placenta and brain PCB DMRs overlap significantly and map to a shared subset of genes enriched for Wnt signaling, Slit/Robo signaling, and genes differentially expressed in NDD models. The consensus PCB DMRs also significantly overlap with DMRs from human NDD brain and placenta. These results demonstrate that PCB-exposed placenta contains a subset of DMRs that overlap fetal brain DMRs relevant to an NDD.
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Affiliation(s)
- Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Kari Neier
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA 95616, USA
| | - Anthony E Valenzuela
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Rebecca J Schmidt
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA 95616, USA; Department of Public Health Sciences, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Pamela J Lein
- MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95616, USA; MIND Institute, School of Medicine, University of California, Davis, Sacramento, CA 95817, USA; Perinatal Origins of Disparities Center, University of California, Davis, Davis, CA 95616, USA.
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24
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Zhang J, Han B, Zheng W, Lin S, Li H, Gao Y, Sun D. Genome-Wide DNA Methylation Profile in Jejunum Reveals the Potential Genes Associated With Paratuberculosis in Dairy Cattle. Front Genet 2021; 12:735147. [PMID: 34721525 PMCID: PMC8554095 DOI: 10.3389/fgene.2021.735147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/23/2021] [Indexed: 12/04/2022] Open
Abstract
Paratuberculosis in cattle causes substantial economic losses to the dairy industry. Exploring functional genes and corresponding regulatory pathways related to resistance or susceptibility to paratuberculosis is essential to the breeding of disease resistance in cattle. Co-analysis of genome-wide DNA methylation and transcriptome profiles is a critically important approach to understand potential regulatory mechanism underlying the development of diseases. In this study, we characterized the profiles of DNA methylation of jejunum from nine Holstein cows in clinical, subclinical, and healthy groups using whole-genome bisulfite sequencing (WGBS). The average methylation level in functional regions was 29.95% in the promoter, 29.65% in the 5’ untranslated region (UTR), 68.24% in exons, 71.55% in introns, and 72.81% in the 3’ UTR. A total of 3,911, 4,336, and 4,094 differentially methylated genes (DMGs) were detected in clinical vs. subclinical, clinical vs. healthy, and subclinical vs. healthy comparative group, respectively. Gene ontology (GO) and analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that these DMGs were significantly enriched in specific biological processes related to immune response, such as Th1 and Th2 cell differentiation, wnt, TNF, MAPK, ECM-receptor interaction, cellular senescence, calcium, and chemokine signaling pathways (q value <0.05). The integration of information about DMGs, differentially expressed genes (DEGs), and biological functions suggested nine genes CALCRL, TNC, GATA4, CD44, TGM3, CXCL9, CXCL10, PPARG, and NFATC1 as promising candidates related to resistance/susceptibility to Mycobacterium avium subspecies paratuberculosis (MAP). This study reports on the high-resolution DNA methylation landscapes of the jejunum methylome across three conditions (clinical, subclinical, and healthy) in dairy cows. Our investigations integrated different sources of information about DMGs, DEGs, and pathways, enabling us to find nine functional genes that might have potential application in resisting paratuberculosis in dairy cattle.
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Affiliation(s)
- Junnan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Bo Han
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Weijie Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shan Lin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Houcheng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yahui Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
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25
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Ahn J, Hwang IS, Park MR, Hwang S, Lee K. Genomic Imprinting at the Porcine DIRAS3 Locus. Animals (Basel) 2021; 11:ani11051315. [PMID: 34063661 PMCID: PMC8147596 DOI: 10.3390/ani11051315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary DNA methylation associated with one of the two alleles from parents is an important mechanism that causes a silencing of that allele, leading to expression of another allele only. There has been a lack of detailed studies on DNA methylation and expression patterns that are related to the DIRAS3 gene in pigs. The objective of this study was to provide a comprehensive overview of DNA methylation and expression associated with the DIRAS3 gene in pigs by generating an embryonic pig model and analyzing next-generation sequencing using pig embryos and adult pigs. Our results clearly showed the presence of DNA methylation near the DIRAS3 gene in pigs and high expression of DIRAS3 in the hypothalamus from adult pigs and expression of only one allele in all the tested tissues including the hypothalamus. In summary, our findings suggested DNA methylation might be related to those unique gene expression patterns during the development of pigs. Abstract The epigenetic mechanisms underlying genomic imprinting include DNA methylation and monoallelic expression of genes in close proximity. Although genes imprinted in humans and mice have been widely characterized, there is a lack of detailed and comprehensive studies in livestock species including pigs. The purpose of this study was to investigate a detailed methylation status and parent-of-origin-specific gene expression within the genomic region containing an underexamined porcine DIRAS3 locus. Through whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) of porcine parthenogenetic embryos and analyses of public RNA-seq data from adult pigs, DNA methylation and monoallelic expression pattern were investigated. As a result, maternal hypermethylation at the DIRAS3 locus and hypothalamus-specific and monoallelic expression of the DIRAS3 gene were found in pigs. In conclusion, the findings from this study suggest that the presence of maternal hypermethylation, or imprints, might be maintained and related to monoallelic expression of DIRAS3 during pig development.
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Affiliation(s)
- Jinsoo Ahn
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA;
| | - In-Sul Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea; (I.-S.H.); (M.-R.P.); (S.H.)
| | - Mi-Ryung Park
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea; (I.-S.H.); (M.-R.P.); (S.H.)
| | - Seongsoo Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea; (I.-S.H.); (M.-R.P.); (S.H.)
| | - Kichoon Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA;
- Correspondence: ; Tel.: +1-614-688-7963
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26
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Zheng X, Wu Q, Wu H, Leung KS, Wong MH, Liu X, Cheng L. Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data. Front Cell Dev Biol 2021; 9:671302. [PMID: 33996828 PMCID: PMC8116545 DOI: 10.3389/fcell.2021.671302] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/06/2021] [Indexed: 01/07/2023] Open
Abstract
Bisulfite sequencing is considered as the gold standard approach for measuring DNA methylation, which acts as a pivotal part in regulating a variety of biological processes without changes in DNA sequences. In this study, we introduced the most prevalent methods for processing bisulfite sequencing data and evaluated the consistency of the data acquired from different measurements in liver cancer. Firstly, we introduced three commonly used bisulfite sequencing assays, i.e., reduced-representation bisulfite sequencing (RRBS), whole-genome bisulfite sequencing (WGBS), and targeted bisulfite sequencing (targeted BS). Next, we discussed the principles and compared different methods for alignment, quality assessment, methylation level scoring, and differentially methylated region identification. After that, we screened differential methylated genes in liver cancer through the three bisulfite sequencing assays and evaluated the consistency of their results. Ultimately, we compared bisulfite sequencing to 450 k beadchip and assessed the statistical similarity and functional association of differentially methylated genes (DMGs) among the four assays. Our results demonstrated that the DMGs measured by WGBS, RRBS, targeted BS and 450 k beadchip are consistently hypo-methylated in liver cancer with high functional similarity.
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Affiliation(s)
- Xubin Zheng
- Department of Critical Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, China.,Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Qiong Wu
- Department of Critical Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Haonan Wu
- Department of Critical Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Kwong-Sak Leung
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Man-Hon Wong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Xueyan Liu
- Department of Critical Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, China
| | - Lixin Cheng
- Department of Critical Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, China
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27
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Bao X, Zhang X, Wang L, Wang Z, Huang J, Zhang Q, Ye Y, Liu Y, Chen D, Zuo Y, Liu Q, Xu P, Huang B, Fang J, Lao J, Feng X, Li Y, Kurita R, Nakamura Y, Yu W, Ju C, Huang C, Mohandas N, Li D, Zhao C, Xu X. Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia. Am J Hum Genet 2021; 108:709-721. [PMID: 33735615 DOI: 10.1016/j.ajhg.2021.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/01/2021] [Indexed: 12/16/2022] Open
Abstract
The fetal-to-adult hemoglobin switch is regulated in a developmental stage-specific manner and reactivation of fetal hemoglobin (HbF) has therapeutic implications for treatment of β-thalassemia and sickle cell anemia, two major global health problems. Although significant progress has been made in our understanding of the molecular mechanism of the fetal-to-adult hemoglobin switch, the mechanism of epigenetic regulation of HbF silencing remains to be fully defined. Here, we performed whole-genome bisulfite sequencing and RNA sequencing analysis of the bone marrow-derived GYPA+ erythroid cells from β-thalassemia-affected individuals with widely varying levels of HbF groups (HbF ≥ 95th percentile or HbF ≤ 5th percentile) to screen epigenetic modulators of HbF and phenotypic diversity of β-thalassemia. We identified an ETS2 repressor factor encoded by ERF, whose promoter hypermethylation and mRNA downregulation are associated with high HbF levels in β-thalassemia. We further observed that hypermethylation of the ERF promoter mediated by enrichment of DNMT3A leads to demethylation of γ-globin genes and attenuation of binding of ERF on the HBG promoter and eventually re-activation of HbF in β-thalassemia. We demonstrated that ERF depletion markedly increased HbF production in human CD34+ erythroid progenitor cells, HUDEP-2 cell lines, and transplanted NCG-Kit-V831M mice. ERF represses γ-globin expression by directly binding to two consensus motifs regulating γ-globin gene expression. Importantly, ERF depletion did not affect maturation of erythroid cells. Identification of alterations in DNA methylation of ERF as a modulator of HbF synthesis opens up therapeutic targets for β-hemoglobinopathies.
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28
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Singh D, Sun D, King AG, Alquezar-Planas DE, Johnson RN, Alvarez-Ponce D, Yi SV. Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation. Proc Biol Sci 2021; 288:20202244. [PMID: 33622136 PMCID: PMC7934952 DOI: 10.1098/rspb.2020.2244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
X chromosome inactivation (XCI) mediated by differential DNA methylation between sexes is an iconic example of epigenetic regulation. Although XCI is shared between eutherians and marsupials, the role of DNA methylation in marsupial XCI remains contested. Here, we examine genome-wide signatures of DNA methylation across fives tissues from a male and female koala (Phascolarctos cinereus), and present the first whole-genome, multi-tissue marsupial ‘methylome atlas’. Using these novel data, we elucidate divergent versus common features of representative marsupial and eutherian DNA methylation. First, tissue-specific differential DNA methylation in koalas primarily occurs in gene bodies. Second, females show significant global reduction (hypomethylation) of X chromosome DNA methylation compared to males. We show that this pattern is also observed in eutherians. Third, on average, promoter DNA methylation shows little difference between male and female koala X chromosomes, a pattern distinct from that of eutherians. Fourth, the sex-specific DNA methylation landscape upstream of Rsx, the primary lncRNA associated with marsupial XCI, is consistent with the epigenetic regulation of female-specific (and presumably inactive X chromosome-specific) expression. Finally, we use the prominent female X chromosome hypomethylation and classify 98 previously unplaced scaffolds as X-linked, contributing an additional 14.6 Mb (21.5%) to genomic data annotated as the koala X chromosome. Our work demonstrates evolutionarily divergent pathways leading to functionally conserved patterns of XCI in two deep branches of mammals.
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Affiliation(s)
- Devika Singh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Dan Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Andrew G King
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | | | - Rebecca N Johnson
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia.,National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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Gong P, Jing Y, Liu Y, Wang L, Wu C, Du Z, Li H. Whole-genome bisulfite sequencing of abdominal adipose reveals DNA methylation pattern variations in broiler lines divergently selected for fatness. J Anim Sci 2021; 99:skaa408. [PMID: 33373456 PMCID: PMC8611762 DOI: 10.1093/jas/skaa408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/23/2020] [Indexed: 11/14/2022] Open
Abstract
The methylation status of pivotal genes involved in fat deposition in chickens has been extensively studied. However, the whole-genome DNA methylation profiles of broiler abdominal adipose tissue remain poorly understood. Using whole-genome bisulfite sequencing, we generated DNA methylation profiles of chicken abdominal adipose tissue from Northeast Agricultural University broiler lines divergently selected for abdominal fat content. We aimed to explore whether DNA methylation was associated with abdominal fat deposition in broilers. The whole-genome DNA methylation profiles of fat- and lean-line broilers abdominal adipose tissue were constructed. The DNA methylation levels of functional genomic regions in the fat broiler were higher than those in the lean broiler, especially in the 3' untranslated regions (UTRs) and exons in the non-CG contexts. Additionally, we identified 29,631 differentially methylated regions and, subsequently, annotated 6,484 and 2,016 differentially methylated genes (DMGs) in the gene body and promoter regions between the two lines, respectively. Functional annotation showed that the DMGs in promoter regions were significantly enriched mainly in the triglyceride catabolic process, lipid metabolism-related pathways, and extracellular matrix signal pathways. When the DMG in promoter regions and differentially expressed genes were integrated, we identified 30 genes with DNA methylation levels that negatively correlated with their messenger RNA (mRNA) expression, of which CMSS1 reached significant levels (false discovery rate < 0.05). These 30 genes were mainly involved in fatty acid metabolism, peroxisome-proliferator-activated receptor signaling, Wnt signaling pathways, transmembrane transport, RNA degradation, and glycosaminoglycan degradation. Comparing the DNA methylation profiles between fat- and lean-line broilers demonstrated that DNA methylation is involved in regulating broiler abdominal fat deposition. Our study offers a basis for further exploring the underlying mechanisms of abdominal adipose deposition in broilers.
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Affiliation(s)
- Pengfei Gong
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Yang Jing
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Yumeng Liu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Lijian Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Chunyan Wu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Zhiqiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
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Ahn J, Hwang IS, Park MR, Cho IC, Hwang S, Lee K. The Landscape of Genomic Imprinting at the Porcine SGCE/ PEG10 Locus from Methylome and Transcriptome of Parthenogenetic Embryos. G3 (Bethesda) 2020; 10:4037-47. [PMID: 32878957 DOI: 10.1534/g3.120.401425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In mammals, imprinted genes often exist in the form of clusters in specific chromosome regions. However, in pigs, genomic imprinting of a relatively few genes and clusters has been identified, and genes within or adjacent to putative imprinted clusters need to be investigated including those at the SGCE/PEG10 locus. The objective of this study was to, using porcine parthenogenetic embryos, investigate imprinting status of genes within the genomic region spans between the COL1A2 and ASB4 genes in chromosome 9. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) were conducted with normal and parthenogenetic embryos, and methylome and transcriptome were analyzed. As a result, differentially methylated regions (DMRs) between the embryos were identified, and parental allele-specific expressions of the SGCE and PEG10 genes were verified. The pig imprinted interval was limited between SGCE and PEG10, since both the COL1A2 and CASD1 genes at the centromere-proximal region and the genes between PPP1R9A and ASB4 toward the telomere were non-imprinted and biallelically expressed. Consequently, our combining analyses of methylome, transcriptome, and informative polymorphisms revealed the boundary of imprinting cluster at the SGCE/PEG10 locus in pig chromosome 9 and consolidated the landscape of genomic imprinting in pigs.
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Cuypers B, Dumetz F, Meysman P, Laukens K, De Muylder G, Dujardin JC, Domagalska MA. The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples. Microorganisms 2020; 8:E1252. [PMID: 32824654 DOI: 10.3390/microorganisms8081252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 11/21/2022] Open
Abstract
Cytosine C5 methylation is an important epigenetic control mechanism in a wide array of eukaryotic organisms and generally carried out by proteins of the C-5 DNA methyltransferase family (DNMTs). In several protozoans, the status of this mechanism remains elusive, such as in Leishmania, the causative agent of the disease leishmaniasis in humans and a wide array of vertebrate animals. In this work, we showed that the Leishmania donovani genome contains a C-5 DNA methyltransferase (DNMT) from the DNMT6 subfamily, whose function is still unclear, and verified its expression at the RNA level. We created viable overexpressor and knock-out lines of this enzyme and characterized their genome-wide methylation patterns using whole-genome bisulfite sequencing, together with promastigote and amastigote control lines. Interestingly, despite the DNMT6 presence, we found that methylation levels were equal to or lower than 0.0003% at CpG sites, 0.0005% at CHG sites, and 0.0126% at CHH sites at the genomic scale. As none of the methylated sites were retained after manual verification, we conclude that there is no evidence for DNA methylation in this species. We demonstrated that this difference in DNA methylation between the parasite (no detectable DNA methylation) and the vertebrate host (DNA methylation) allowed enrichment of parasite vs. host DNA using methyl-CpG-binding domain columns, readily available in commercial kits. As such, we depleted methylated DNA from mixes of Leishmania promastigote and amastigote DNA with human DNA, resulting in average Leishmania:human enrichments from 62× up to 263×. These results open a promising avenue for unmethylated DNA enrichment as a pre-enrichment step before sequencing Leishmania clinical samples.
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Yuan L, Wang D, Cao L, Yu N, Liu K, Guo Y, Gan S, Chen L. Regulation of Leaf Longevity by DML3-Mediated DNA Demethylation. Mol Plant 2020; 13:1149-1161. [PMID: 32561358 DOI: 10.1016/j.molp.2020.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/25/2019] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Leaf senescence is driven by the expression of senescence-associated genes (SAGs). Development-specific genes often undergo DNA demethylation in their promoter and other regions, which regulates gene expression. Whether and how DNA demethylation regulates the expression of SAGs and thus leaf senescence remain elusive. Whole-genome bisulfite sequencing (WGBS) analyses of wild-type (WT) and demeter-like 3 (dml3) Arabidopsis leaves at three developmental stages revealed hypermethylation during leaf senescence in dml3 compared with WT, and 20 556 differentially methylated regions (DMRs) were identified by comparing the methylomes of dml3 and WT in the CG, CHG, and CHH contexts. Furthermore, we identified that 335 DMR-associated genes (DMGs), such as NAC016 and SEN1, are upregulated during leaf senescence, and found an inverse correlation between the DNA methylation levels (especially in the promoter regions) and the transcript abundances of the related SAGs in WT. In contrast, in dml3 the promoters of SAGs were hypermethylated and their transcript levels were remarkably reduced, and leaf senescence was significantly delayed. Collectively, our study unraveled a novel epigenetic regulatory mechanism underlying leaf senescence in which DML3 is expressed at the onset of and during senescence to demethylate promoter, gene body or 3' UTR regions to activate a set of SAGs.
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Affiliation(s)
- Lu Yuan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Dan Wang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Liwen Cao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ningning Yu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ke Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Susheng Gan
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Liping Chen
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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Perzel Mandell KA, Price AJ, Wilton R, Collado-Torres L, Tao R, Eagles NJ, Szalay AS, Hyde TM, Weinberger DR, Kleinman JE, Jaffe AE. Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex. Epigenetics 2020; 16:1-13. [PMID: 32602773 DOI: 10.1080/15592294.2020.1786304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
DNA methylation (DNAm) is a key epigenetic regulator of gene expression across development. The developing prenatal brain is a highly dynamic tissue, but our understanding of key drivers of epigenetic variability across development is limited. We, therefore, assessed genomic methylation at over 39 million sites in the prenatal cortex using whole-genome bisulfite sequencing and found loci and regions in which methylation levels are dynamic across development. We saw that DNAm at these loci was associated with nearby gene expression and enriched for enhancer chromatin states in prenatal brain tissue. Additionally, these loci were enriched for genes associated with neuropsychiatric disorders and genes involved with neurogenesis. We also found autosomal differences in DNAm between the sexes during prenatal development, though these have less clear functional consequences. We lastly confirmed that the dynamic methylation at this critical period is specifically CpG methylation, with generally low levels of CpH methylation. Our findings provide detailed insight into prenatal brain development as well as clues to the pathogenesis of psychiatric traits seen later in life.
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Affiliation(s)
- Kira A Perzel Mandell
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM) , Baltimore, MD, USA
| | - Amanda J Price
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM) , Baltimore, MD, USA
| | - Richard Wilton
- Department of Physics and Astronomy, Krieger School of Arts and Sciences, Johns Hopkins University , Baltimore, MD, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University , Baltimore, MD, USA
| | - Ran Tao
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA
| | - Nicholas J Eagles
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA
| | - Alexander S Szalay
- Department of Physics and Astronomy, Krieger School of Arts and Sciences, Johns Hopkins University , Baltimore, MD, USA.,Department of Computer Science, Whiting School of Engineering, Johns Hopkins University , Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Neurology, JHSOM , Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, JHSOM , Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM) , Baltimore, MD, USA.,Department of Neurology, JHSOM , Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, JHSOM , Baltimore, MD, USA.,Department of Neuroscience, JHSOM , Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, JHSOM , Baltimore, MD, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM) , Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University , Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, JHSOM , Baltimore, MD, USA.,Department of Neuroscience, JHSOM , Baltimore, MD, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health (JHBSPH) , Baltimore, MD, USA.,Department of Biostatistics, JHBSPH , Baltimore, MD, USA
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34
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Huang W, Hu H, Zhang Q, Wang N, Yang X, Guo AY. Genome-Wide DNA Methylation Enhances Stemness in the Mechanical Selection of Tumor-Repopulating Cells. Front Bioeng Biotechnol 2020; 8:88. [PMID: 32258002 PMCID: PMC7090028 DOI: 10.3389/fbioe.2020.00088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
Background DNA methylation plays essential roles in tumor occurrence and stemness maintenance. Tumor-repopulating cells (TRCs) are cancer stem cell (CSC)-like cells with highly tumorigenic and self-renewing abilities, which were selected from tumor cells in soft three-dimensional (3D) fibrin gels. Methods Here, we presented a genome-wide map of methylated cytosines for time-series samples in TRC selection, in a 3D culture using whole-genome bisulfite sequencing (WGBS). Results A comparative analysis revealed that the methylation degrees of many differentially methylated genes (DMGs) were increased by the mechanical environment and changed from 2D rigid to 3D soft. DMGs were significantly enriched in stemness-related terms. In 1-day, TRCs had the highest non-CG methylation rate indicating its strong stemness. We found that genes with continuously increasing or decreasing methylation like CREB5/ADAMTS6/LMX1A may also affect the TRC screening process. Furthermore, results showed that stage-specific/common CSCs markers were biased toward changing their methylation in non-CG (CHG and CHH, where H corresponds to A, T, or C) methylation and enriched in gene body region. Conclusions WGBS provides DNA methylome in TRC screening. It was confirmed that non-CG DNA methylation plays an important role in TRC selection, which indicates that it is more sensitive to mechanical microenvironments and affects TRCs by regulating the expression of stemness genes in tumor cells.
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Affiliation(s)
- Wei Huang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Hu
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qiong Zhang
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ning Wang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - An-Yuan Guo
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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35
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Lin C, Peng B, Li Y, Wang P, Zhao G, Ding X, Li R, Zhao L, Zhang C. Cytoplasm Types Affect DNA Methylation among Different Cytoplasmic Male Sterility Lines and Their Maintainer Line in Soybean ( Glycine max L.). Plants (Basel) 2020; 9:E385. [PMID: 32245080 PMCID: PMC7155767 DOI: 10.3390/plants9030385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 11/18/2022]
Abstract
Cytoplasmic male sterility (CMS) lines and their maintainer line have the same nucleus but different cytoplasm types. We used three soybean (Glycine max L.) CMS lines, JLCMS9A, JLCMSZ9A, and JLCMSPI9A, and their maintainer line, JLCMS9B, to explore whether methylation levels differed in their nuclei. Whole-genome bisulfite sequencing of these four lines was performed. The results show that the cytosine methylation level in the maintainer line was lower than in the CMS lines. Compared with JLCMS9B, the Gene Ontology (GO) enrichment analysis of DMR (differentially methylated region, DMR)-related genes of JLCMS9A revealed that their different 5-methylcytosine backgrounds were enriched in molecular function, whereas JLCMSZ9A and JLCMSPI9A were enriched in biological process and cellular component. The Kyoto Encyclopedia of Genes and Genome (KEGG) analysis of DMR-related genes and different methylated promoter regions in different cytosine contexts, hypomethylation or hypermethylation, showed that the numbers of DMR-related genes and promoter regions were clearly different. According to the DNA methylation and genetic distances separately, JLCMS9A clustered with JLCMS9B, and JLCMSPI9A with JLCMSZ9A. Thus, the effects of different cytoplasm types on DNA methylation were significantly different. This may be related to their genetic distances revealed by re-sequencing these lines. The detected DMR-related genes and pathways that are probably associated with CMS are also discussed.
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Affiliation(s)
| | | | | | | | | | | | | | - Limei Zhao
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China; (C.L.); (B.P.); (Y.L.); (P.W.); (G.Z.); (X.D.); (R.L.)
| | - Chunbao Zhang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China; (C.L.); (B.P.); (Y.L.); (P.W.); (G.Z.); (X.D.); (R.L.)
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Teng H, Xue M, Liang J, Wang X, Wang L, Wei W, Li C, Zhang Z, Li Q, Ran X, Shi X, Cai W, Wang W, Gao H, Sun Z. Inter- and intratumor DNA methylation heterogeneity associated with lymph node metastasis and prognosis of esophageal squamous cell carcinoma. Am J Cancer Res 2020; 10:3035-3048. [PMID: 32194853 PMCID: PMC7053185 DOI: 10.7150/thno.42559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/22/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Esophageal squamous cell carcinoma (ESCC), one of the leading causes of cancer mortality worldwide, is a heterogeneous cancer with diverse clinical manifestations. However, little is known about the epigenetic heterogeneity and its clinical relevance for this prevalent cancer. Methods: We generated 7.56 Tb single-base resolution whole-genome bisulfite sequencing data for 84 ESCC and paired paraneoplastic tissues. The analysis identified inter- and intratumor DNA methylation (DNAm) heterogeneity, epigenome-wide DNAm alterations together with the functional regulators involved in the hyper- or hypomethylated regions, and their association with clinical features. We then validated the correlation between the methylation level of specific regions and clinical outcomes of 96 ESCC patients in an independent cohort. Results: ESCC manifested substantial inter- and intratumor DNAm heterogeneity. The high intratumor DNAm heterogeneity was associated with lymph node metastasis and worse overall survival. Interestingly, hypermethylated regions in ESCC were enriched in promoters of numerous transcription factors, and demethylated noncoding regions related to RXR transcription factor binding appeared to contribute to the development of ESCC. Furthermore, we identified numerous DNAm alterations associated with carcinogenesis and lymph node metastasis of ESCC. We also validated three novel prognostic markers for ESCC, including one each in the promoter of CLK1, the 3' untranslated region of ZEB2, and the intergenic locus surrounded by several lncRNAs. Conclusions: This study presents the first population-level resource for dissecting base-resolution DNAm variation in ESCC and provides novel insights into the ESCC pathogenesis and progression, which might facilitate diagnosis and prognosis for this prevalent malignancy.
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Araki H, Miura F, Watanabe A, Morinaga C, Kitaoka F, Kitano Y, Sakai N, Shibata Y, Terada M, Goto S, Yamanaka S, Takahashi M, Ito T. Base-Resolution Methylome of Retinal Pigment Epithelial Cells Used in the First Trial of Human Induced Pluripotent Stem Cell-Based Autologous Transplantation. Stem Cell Reports 2019; 13:761-774. [PMID: 31564644 PMCID: PMC6829753 DOI: 10.1016/j.stemcr.2019.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 12/19/2022] Open
Abstract
The first-in-human trial of induced pluripotent stem cell (iPSC)-based autologous transplantation was successfully performed on a female patient with age-related macular degeneration. Here we delineated the base-resolution methylome of the iPSC-derived retinal pigment epithelium (iRPE) used in this trial. The methylome of iRPE closely resembled that of native RPE (nRPE), although partially methylated domains (PMDs) emerged in iRPE but not nRPE. Most differentially methylated regions between iRPE and nRPE appeared to originate from (de)methylation errors during differentiation, whereas errors at reprogramming resulted in aberrant genomic imprinting and X chromosome reactivation. Moreover, non-CpG methylation was prominent in nRPE but not iRPE. Intriguingly, xenotransplantation to mouse remodeled the iRPE methylome to demethylate a subset of suppressed genes and accumulate non-CpG methylation, but failed to resolve PMDs and hypermethylated CpG islands. Although the impacts of these alterations remain elusive, our findings should provide a useful guide for methylome analyses of other iPSC-derived cells. The methylome of iPSC-derived RPE closely resembled that of native RPE Most methylomic differences originated from errors during differentiation Errors at reprogramming induced loss of imprinting and X chromosome reactivation Some of the differences were mitigated by xenotransplantation to mouse
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Affiliation(s)
- Hiromitsu Araki
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Akira Watanabe
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Chikako Morinaga
- Laboratory for Retinal Regeneration, Center for Biosystems Dynamics Research, RIKEN, Kobe 650-0047, Japan
| | - Fumiyo Kitaoka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yuko Kitano
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Noriko Sakai
- Laboratory for Retinal Regeneration, Center for Biosystems Dynamics Research, RIKEN, Kobe 650-0047, Japan
| | - Yumiko Shibata
- Laboratory for Retinal Regeneration, Center for Biosystems Dynamics Research, RIKEN, Kobe 650-0047, Japan
| | - Motoki Terada
- Laboratory for Retinal Regeneration, Center for Biosystems Dynamics Research, RIKEN, Kobe 650-0047, Japan
| | - So Goto
- Laboratory for Retinal Regeneration, Center for Biosystems Dynamics Research, RIKEN, Kobe 650-0047, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Masayo Takahashi
- Laboratory for Retinal Regeneration, Center for Biosystems Dynamics Research, RIKEN, Kobe 650-0047, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan.
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Xiu Y, Shao C, Zhu Y, Li Y, Gan T, Xu W, Piferrer F, Chen S. Differences in DNA Methylation Between Disease-Resistant and Disease-Susceptible Chinese Tongue Sole ( Cynoglossus semilaevis) Families. Front Genet 2019; 10:847. [PMID: 31572451 PMCID: PMC6753864 DOI: 10.3389/fgene.2019.00847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/14/2019] [Indexed: 12/12/2022] Open
Abstract
DNA methylation, the most widely studied and most well-understood epigenetic modification, has been reported to play crucial roles in diverse processes. Although it has been found that DNA methylation can modulate the expression of immune-related genes in teleosts, a systemic analysis of epigenetic regulation on teleost immunity has rarely been performed. In this research, we employed whole-genome bisulfite sequencing to investigate the genome-wide DNA methylation profiles in select disease-resistant Cynoglossus semilaevis (DR-CS, family 14L006) and disease-susceptible C. semilaevis (DS-CS, family 14L104) against Vibrio harveyi infection. The results showed that following selective breeding, DR-CS had higher DNA methylation levels and different DNA methylation patterns, with 3,311 differentially methylated regions and 6,456 differentially methylated genes. Combining these data with the corresponding transcriptome data, we identified several immune-related genes that exhibited differential expression levels that were modulated by DNA methylation. Specifically, DNA methylation of tumor necrosis factor–like and lipopolysaccharide-binding protein-like was significantly correlated with their expression and significantly contributed to the disease resistance of the selected C. semilaevis family. In conclusion, we suggest that artificial selection for disease resistance in Chinese tongue sole causes changes in DNA methylation levels in important immune-related genes and that these epigenetic changes are potentially involved in multiple immune responses in Chinese tongue sole.
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Affiliation(s)
- Yunji Xiu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Zhu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yangzhen Li
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tian Gan
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wenteng Xu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Francesc Piferrer
- Institut de Ciències del Mar (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Songlin Chen
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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39
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Anacleto R, Badoni S, Parween S, Butardo VM, Misra G, Cuevas RP, Kuhlmann M, Trinidad TP, Mallillin AC, Acuin C, Bird AR, Morell MK, Sreenivasulu N. Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice. Plant Biotechnol J 2019; 17:1261-1275. [PMID: 30549178 PMCID: PMC6575982 DOI: 10.1111/pbi.13051] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 11/15/2018] [Accepted: 11/25/2018] [Indexed: 05/19/2023]
Abstract
Reliably generating rice varieties with low glycaemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa ) explained the intermediate-to-high GI variation. A SNP (C˃T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non-starch polysaccharide pathway in lowering GI.
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Affiliation(s)
| | - Saurabh Badoni
- International Rice Research InstituteLos BañosPhilippines
| | - Sabiha Parween
- International Rice Research InstituteLos BañosPhilippines
| | - Vito M. Butardo
- International Rice Research InstituteLos BañosPhilippines
- Department of Chemistry and BiotechnologyFaculty of Science, Engineering and TechnologySwinburne University of TechnologyHawthornVic.Australia
| | - Gopal Misra
- International Rice Research InstituteLos BañosPhilippines
| | | | - Markus Kuhlmann
- The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | | | | | - Cecilia Acuin
- International Rice Research InstituteLos BañosPhilippines
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40
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Dai X, Lin N, Li D, Wang T. A non-randomized procedure for large-scale heterogeneous multiple discrete testing based on randomized tests. Biometrics 2019; 75:638-649. [PMID: 30387496 PMCID: PMC6565503 DOI: 10.1111/biom.12996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/16/2018] [Indexed: 11/28/2022]
Abstract
In the analysis of next-generation sequencing technology, massive discrete data are generated from short read counts with varying biological coverage. Conducting conditional hypothesis testing such as Fisher's Exact Test at every genomic region of interest thus leads to a heterogeneous multiple discrete testing problem. However, most existing multiple testing procedures for controlling the false discovery rate (FDR) assume that test statistics are continuous and become conservative for discrete tests. To overcome the conservativeness, in this article, we propose a novel multiple testing procedure for better FDR control on heterogeneous discrete tests. Our procedure makes decisions based on the marginal critical function (MCF) of randomized tests, which enables achieving a powerful and non-randomized multiple testing procedure. We provide upper bounds of the positive FDR (pFDR) and the positive false non-discovery rate (pFNR) corresponding to our procedure. We also prove that the set of detections made by our method contains every detection made by a naive application of the widely-used q-value method. We further demonstrate the improvement of our method over other existing multiple testing procedures by simulations and a real example of differentially methylated region (DMR) detection using whole-genome bisulfite sequencing (WGBS) data.
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Affiliation(s)
- Xiaoyu Dai
- Department of Mathematics, Washington University in St.
Louis, Saint Louis, MO 63130, USA
| | - Nan Lin
- Department of Mathematics, Washington University in St.
Louis, Saint Louis, MO 63130, USA
- Division of Biostatistics, Washington University in St.
Louis, Saint Louis, MO 63130, USA
| | - Daofeng Li
- Department of Genetics, Washington University in St. Louis,
Saint Louis, MO 63130, USA
| | - Ting Wang
- Department of Genetics, Washington University in St. Louis,
Saint Louis, MO 63130, USA
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41
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Wang Z, Wu X, Wu Z, An H, Yi B, Wen J, Ma C, Shen J, Fu T, Tu J. Genome-Wide DNA Methylation Comparison between Brassica napus Genic Male Sterile Line and Restorer Line. Int J Mol Sci 2018; 19:E2689. [PMID: 30201884 DOI: 10.3390/ijms19092689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/30/2018] [Accepted: 09/04/2018] [Indexed: 12/29/2022] Open
Abstract
DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during plant development. However, few studies have determined the DNA methylation profiles of male-sterile rapeseed. Here, we conducted a global comparison of DNA methylation patterns between the rapeseed genic male sterile line 7365A and its near-isogenic fertile line 7365B by whole-genome bisulfite sequencing (WGBS). Profiling of the genome-wide DNA methylation showed that the methylation level in floral buds was lower than that in leaves and roots. Besides, a total of 410 differentially methylated region-associated genes (DMGs) were identified in 7365A relative to 7365B. Traditional bisulfite sequencing polymerase chain reaction (PCR) was performed to validate the WGBS data. Eleven DMGs were found to be involved in anther and pollen development, which were analyzed by quantitative PCR. In particular, Bnams4 was hypo-methylated in 7365A, and its expression was up-regulated, which might affect other DMGs and thus control the male sterility. This study provided genome-wide DNA methylation profiles of floral buds and important clues for revealing the molecular mechanism of genic male sterility in rapeseed.
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42
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Fonseca Balvís N, Garcia-Martinez S, Pérez-Cerezales S, Ivanova E, Gomez-Redondo I, Hamdi M, Rizos D, Coy P, Kelsey G, Gutierrez-Adan A. Cultured bovine embryo biopsy conserves methylation marks from original embryo. Biol Reprod 2018; 97:189-196. [PMID: 29044423 DOI: 10.1093/biolre/iox077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/15/2017] [Indexed: 11/14/2022] Open
Abstract
A major limitation of embryo epigenotyping by chromatin immunoprecipitation analysis is the reduced amount of sample available from an embryo biopsy. We developed an in vitro system to expand trophectoderm cells from an embryo biopsy to overcome this limitation. This work analyzes whether expanded trophectoderm (EX) is representative of the trophectoderm (TE) methylation or adaptation to culture has altered its epigenome. We took a small biopsy from the trophectoderm (30-40 cells) of in vitro produced bovine-hatched blastocysts and cultured it on fibronectin-treated plates until we obtained ∼4 × 104 cells. The rest of the embryo was allowed to recover its spherical shape and, subsequently, TE and inner cell mass were separated. We examined whether there were DNA methylation differences between TE and EX of three bovine embryos using whole-genome bisulfite sequencing. As a consequence of adaptation to culture, global methylation, including transposable elements, was higher in EX, with 5.3% of quantified regions showing significant methylation differences between TE and EX. Analysis of individual embryos indicated that TE methylation is more similar to its EX counterpart than to TE from other embryos. Interestingly, these similarly methylated regions are enriched in CpG islands, promoters and transcription units near genes involved in biological processes important for embryo development. Our results indicate that EX is representative of the embryo in terms of DNA methylation, thus providing an informative proxy for embryo epigenotyping.
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Affiliation(s)
- Noelia Fonseca Balvís
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Soledad Garcia-Martinez
- Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Serafín Pérez-Cerezales
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Isabel Gomez-Redondo
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Meriem Hamdi
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Dimitrios Rizos
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Pilar Coy
- Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Alfonso Gutierrez-Adan
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
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Dong X, Shi M, Lee M, Toro R, Gravina S, Han W, Yasuda S, Wang T, Zhang Z, Vijg J, Suh Y, Spivack SD. Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung. Epigenetics 2018; 13:264-274. [PMID: 29465290 DOI: 10.1080/15592294.2018.1441650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Gene regulatory analysis of highly diverse human tissues in vivo is essentially constrained by the challenge of performing genome-wide, integrated epigenetic and transcriptomic analysis in small selected groups of specific cell types. Here we performed genome-wide bisulfite sequencing and RNA-seq from the same small groups of bronchial and alveolar cells isolated by laser capture microdissection from flash-frozen lung tissue of 12 donors and their peripheral blood T cells. Methylation and transcriptome patterns differed between alveolar and bronchial cells, while each of these epithelia showed more differences from mesodermally-derived T cells. Differentially methylated regions (DMRs) between alveolar and bronchial cells tended to locate at regulatory regions affecting promoters of 4,350 genes. A large number of pathways enriched for these DMRs including GTPase signal transduction, cell death, and skeletal muscle. Similar patterns of transcriptome differences were observed: 4,108 differentially expressed genes (DEGs) enriched in GTPase signal transduction, inflammation, cilium assembly, and others. Prioritizing using DMR-DEG regulatory network, we highlighted genes, e.g., ETS1, PPARG, and RXRG, at prominent alveolar vs. bronchial cell discriminant nodes. Our results show that multi-omic analysis of small, highly specific cells is feasible and yields unique physiologic loci distinguishing human lung cell types in situ.
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Affiliation(s)
- Xiao Dong
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Miao Shi
- b Department of Medicine , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Moonsook Lee
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Rafael Toro
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Silvia Gravina
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Weiguo Han
- b Department of Medicine , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Shoya Yasuda
- c Department of Computational Intelligence and Systems Science , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku, Yokohama , Kanagawa 226-8502 , Japan
| | - Tao Wang
- d Department of Epidemiology & Population Health , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Zhengdong Zhang
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Jan Vijg
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA.,e Department of Ophthalmology & Visual Sciences , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Yousin Suh
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA.,b Department of Medicine , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA.,e Department of Ophthalmology & Visual Sciences , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Simon D Spivack
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA.,b Department of Medicine , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA.,d Department of Epidemiology & Population Health , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
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Abstract
Evolutionary studies of DNA methylation offer insights into the mechanisms governing the variation of genomic DNA methylation across different species. Comparisons of gross levels of DNA methylation between distantly related species indicate that the size of the genome and the level of genomic DNA methylation are positively correlated. In plant genomes, this can be reliably explained by the genomic contents of repetitive sequences. In animal genomes, the role of repetitive sequences on genomic DNA methylation is less clear. On a shorter timescale, population-level comparisons demonstrate that genetic variation can explain the observed variability of DNA methylation to some degree. The amount of DNA methylation variation that has been attributed to genetic variation in the human population studies so far is substantially lower than that from Arabidopsis population studies, but this disparity might reflect the differences in the computational and experimental techniques used. The effect of genetic variation on DNA methylation has been directly examined in mammalian systems, revealing several causative factors that govern DNA methylation. On the other hand, studies from Arabidopsis have furthered our understanding of spontaneous mutations of DNA methylation, termed “epimutations.” Arabidopsis has an extremely high rate of spontaneous epimutations, which may play a major role in shaping the global DNA methylation landscape in this genome. Key missing information includes the frequencies of spontaneous epimutations in other lineages, in particular animal genomes, and how population-level variation of DNA methylation leads to species-level differences.
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Affiliation(s)
- Soojin V Yi
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
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45
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Aberg KA, Chan RF, Shabalin AA, Zhao M, Turecki G, Staunstrup NH, Starnawska A, Mors O, Xie LY, van den Oord EJ. A MBD-seq protocol for large-scale methylome-wide studies with (very) low amounts of DNA. Epigenetics 2017; 12:743-750. [PMID: 28703682 DOI: 10.1080/15592294.2017.1335849] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
We recently showed that, after optimization, our methyl-CpG binding domain sequencing (MBD-seq) application approximates the methylome-wide coverage obtained with whole-genome bisulfite sequencing (WGB-seq), but at a cost that enables adequately powered large-scale association studies. A prior drawback of MBD-seq is the relatively large amount of genomic DNA (ideally >1 µg) required to obtain high-quality data. Biomaterials are typically expensive to collect, provide a finite amount of DNA, and may simply not yield sufficient starting material. The ability to use low amounts of DNA will increase the breadth and number of studies that can be conducted. Therefore, we further optimized the enrichment step. With this low starting material protocol, MBD-seq performed equally well, or better, than the protocol requiring ample starting material (>1 µg). Using only 15 ng of DNA as input, there is minimal loss in data quality, achieving 93% of the coverage of WGB-seq (with standard amounts of input DNA) at similar false/positive rates. Furthermore, across a large number of genomic features, the MBD-seq methylation profiles closely tracked those observed for WGB-seq with even slightly larger effect sizes. This suggests that MBD-seq provides similar information about the methylome and classifies methylation status somewhat more accurately. Performance decreases with <15 ng DNA as starting material but, even with as little as 5 ng, MBD-seq still achieves 90% of the coverage of WGB-seq with comparable genome-wide methylation profiles. Thus, the proposed protocol is an attractive option for adequately powered and cost-effective methylome-wide investigations using (very) low amounts of DNA.
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Affiliation(s)
- Karolina A Aberg
- a Center for Biomarker Research and Precision Medicine , Virginia Commonwealth University , Richmond , VA , USA
| | - Robin F Chan
- a Center for Biomarker Research and Precision Medicine , Virginia Commonwealth University , Richmond , VA , USA
| | - Andrey A Shabalin
- a Center for Biomarker Research and Precision Medicine , Virginia Commonwealth University , Richmond , VA , USA
| | - Min Zhao
- a Center for Biomarker Research and Precision Medicine , Virginia Commonwealth University , Richmond , VA , USA
| | - Gustavo Turecki
- b Douglas Mental Health University Institute and Department of Psychiatry , McGill University , Montreal , Quebec , Canada
| | - Nicklas Heine Staunstrup
- c Department of Biomedicine , Aarhus University , Aarhus C , 8000 , Denmark.,d Translational Neuropsychiatric Unit , Aarhus University Hospital , Risskov , 8240 , Denmark.,f The Lundbeck Foundation Initiative for Integrative Psychiatric Research , iPSYCH , Denmark.,g Center for Integrative Sequencing , iSEQ, Aarhus University , Aarhus C , 8000 , Denmark
| | - Anna Starnawska
- c Department of Biomedicine , Aarhus University , Aarhus C , 8000 , Denmark.,f The Lundbeck Foundation Initiative for Integrative Psychiatric Research , iPSYCH , Denmark.,g Center for Integrative Sequencing , iSEQ, Aarhus University , Aarhus C , 8000 , Denmark
| | - Ole Mors
- d Translational Neuropsychiatric Unit , Aarhus University Hospital , Risskov , 8240 , Denmark.,e Psychosis Research Unit , Aarhus University Hospital , Risskov , 8240 , Denmark.,f The Lundbeck Foundation Initiative for Integrative Psychiatric Research , iPSYCH , Denmark
| | - Lin Y Xie
- a Center for Biomarker Research and Precision Medicine , Virginia Commonwealth University , Richmond , VA , USA
| | - Edwin Jcg van den Oord
- a Center for Biomarker Research and Precision Medicine , Virginia Commonwealth University , Richmond , VA , USA
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Liu H, Wu Y, Cao A, Mao B, Zhao B, Wang J. Genome-Wide Analysis of DNA Methylation During Ovule Development of Female-Sterile Rice fsv1. G3 (Bethesda) 2017; 7:3621-35. [PMID: 28877971 DOI: 10.1534/g3.117.300243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The regulation of female fertility is an important field of rice sexual reproduction research. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during development processes. However, few reports have described the methylation profiles of female-sterile rice during ovule development. In this study, ovules were continuously acquired from the beginning of megaspore mother cell meiosis until the mature female gametophyte formation period, and global DNA methylation patterns were compared in the ovules of a high-frequency female-sterile line (fsv1) and a wild-type rice line (Gui99) using whole-genome bisulfite sequencing (WGBS). Profiling of the global DNA methylation revealed hypo-methylation, and 3471 significantly differentially methylated regions (DMRs) were observed in fsv1 ovules compared with Gui99. Based on functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis of differentially methylated genes (DMGs), we observed more DMGs enriched in cellular component, reproduction regulation, metabolic pathway, and other pathways. In particular, many ovule development genes and plant hormone-related genes showed significantly different methylation patterns in the two rice lines, and these differences may provide important clues for revealing the mechanism of female gametophyte abortion.
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47
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Crary-Dooley FK, Tam ME, Dunaway KW, Hertz-Picciotto I, Schmidt RJ, LaSalle JM. A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies. Epigenetics 2017; 12:206-214. [PMID: 28055307 PMCID: PMC5406214 DOI: 10.1080/15592294.2016.1276680] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
DNA methylation is an epigenetic mark at the interface of genetic and environmental factors relevant to human disease. Quantitative assessments of global DNA methylation levels have therefore become important tools in epidemiology research, particularly for understanding effects of environmental exposures in complex diseases. Among the available methods of quantitative DNA methylation measurements, bisulfite sequencing is considered the gold standard, but whole-genome bisulfite sequencing (WGBS) has previously been considered too costly for epidemiology studies with high sample numbers. Pyrosequencing of repetitive sequences within bisulfite-treated DNA has been routinely used as a surrogate for global DNA methylation, but a comparison of pyrosequencing to WGBS for accuracy and reproducibility of methylation levels has not been performed. This study compared the global methylation levels measured from uniquely mappable (non-repetitive) WGBS sequences to pyrosequencing assays of several repeat sequences and repeat assay-matched WGBS data and determined uniquely mappable WGBS data to be the most reproducible and accurate measurement of global DNA methylation levels. We determined sources of variation in repetitive pyrosequencing assays to be PCR amplification bias, PCR primer selection bias in methylation levels of targeted sequences, and inherent variability in methylation levels of repeat sequences. Low-coverage, uniquely mappable WGBS showed the strongest correlation between replicates of all assays. By using multiplexing by indexed bar codes, the cost of WGBS can be lowered significantly to improve the accuracy of global DNA methylation assessments for human studies.
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Affiliation(s)
- Florence K Crary-Dooley
- a Department of Medical Microbiology and Immunology , Genome Center , University of California , Davis , CA , USA
| | - Mitchell E Tam
- a Department of Medical Microbiology and Immunology , Genome Center , University of California , Davis , CA , USA
| | - Keith W Dunaway
- a Department of Medical Microbiology and Immunology , Genome Center , University of California , Davis , CA , USA
| | - Irva Hertz-Picciotto
- b Department of Public Health Sciences , University of California , Davis , CA , USA.,c MIND Institute , University of California , Davis , CA , USA
| | - Rebecca J Schmidt
- b Department of Public Health Sciences , University of California , Davis , CA , USA.,c MIND Institute , University of California , Davis , CA , USA
| | - Janine M LaSalle
- a Department of Medical Microbiology and Immunology , Genome Center , University of California , Davis , CA , USA.,c MIND Institute , University of California , Davis , CA , USA
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48
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Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JHA, Pourfarzad F, Kuijpers TW, Burden F, Farrow S, Downes K, Ouwehand WH, Clarke L, Datta A, Lowy E, Flicek P, Frontini M, Stunnenberg HG, Martín-Subero JI, Gut I, Heath S. Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems. Cell Rep 2016; 17:2101-2111. [PMID: 27851971 PMCID: PMC5889099 DOI: 10.1016/j.celrep.2016.10.054] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/17/2016] [Accepted: 09/12/2016] [Indexed: 01/15/2023] Open
Abstract
DNA methylation and the localization and post-translational modification of nucleosomes are interdependent factors that contribute to the generation of distinct phenotypes from genetically identical cells. With 112 whole-genome bisulfite sequencing datasets from the BLUEPRINT Epigenome Project, we analyzed the global development of DNA methylation patterns during lineage commitment and maturation of a range of immune system effector cells and the cancers that arise from them. We show clear trends in methylation patterns that are distinct in the innate and adaptive arms of the human immune system, both globally and in relation to consistently positioned nucleosomes. Most notable are a progressive loss of methylation in developing lymphocytes and the consistent occurrence of non-CG methylation in specific cell types. Cancer samples from the two lineages are further polarized, suggesting the involvement of distinct lineage-specific epigenetic mechanisms. We anticipate broad utility for this resource as a basis for further comparative epigenetic analyses.
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Affiliation(s)
- Ronald P Schuyler
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Angelika Merkel
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Emanuele Raineri
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Lucia Altucci
- Dipartimento di Biochimica Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, Vico Luigi de Crecchio 7, Napoli 80138, Italy
| | - Edo Vellenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Radboud University, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Farzin Pourfarzad
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, the Netherlands
| | - Taco W Kuijpers
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, the Netherlands; Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; British Heart Foundation Centre of Excellence, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0QQ Cambridge, UK; Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH Cambridge, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; British Heart Foundation Centre of Excellence, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0QQ Cambridge, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Radboud University, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - José I Martín-Subero
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain.
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49
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Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJG, Wilson WH, Datta A, Flicek P, Royo R, Martens J, Giné E, Lopez-Guillermo A, Stunnenberg HG, Klapper W, Pott C, Heath S, Gut IG, Siebert R, Campo E, Martín-Subero JI. Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage. Cancer Cell 2016; 30:806-821. [PMID: 27846393 PMCID: PMC5805090 DOI: 10.1016/j.ccell.2016.09.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/18/2016] [Accepted: 09/19/2016] [Indexed: 01/17/2023]
Abstract
We analyzed the in silico purified DNA methylation signatures of 82 mantle cell lymphomas (MCL) in comparison with cell subpopulations spanning the entire B cell lineage. We identified two MCL subgroups, respectively carrying epigenetic imprints of germinal-center-inexperienced and germinal-center-experienced B cells, and we found that DNA methylation profiles during lymphomagenesis are largely influenced by the methylation dynamics in normal B cells. An integrative epigenomic approach revealed 10,504 differentially methylated regions in regulatory elements marked by H3K27ac in MCL primary cases, including a distant enhancer showing de novo looping to the MCL oncogene SOX11. Finally, we observed that the magnitude of DNA methylation changes per case is highly variable and serves as an independent prognostic factor for MCL outcome.
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Affiliation(s)
- Ana C Queirós
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Renée Beekman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Roser Vilarrasa-Blasi
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Martí Duran-Ferrer
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Angelika Merkel
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Emanuele Raineri
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Nuria Russiñol
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Giancarlo Castellano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Alba Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Marta Kulis
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Núria Verdaguer-Dot
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Pedro Jares
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Unidad de Genómica, IDIBAPS, Barcelona 08036, Spain
| | | | | | - Anke Bergmann
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany; Department of Pediatrics, Christian-Albrechts University & University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Inga Vater
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany
| | - Itziar Salaverría
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Harmen J G van de Werken
- Department of Cell Biology, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Cancer Computational Biology Center, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Department of Urology, Erasmus MC, Rotterdam 3015 CN, the Netherlands
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Romina Royo
- Joint Program on Computational Biology, Barcelona Supercomputing Center (BSC) and Institute of Research in Biomedicine (IRB), Barcelona Science Park, Barcelona 08034, Spain
| | - Joost Martens
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen 6500 HB, the Netherlands
| | - Eva Giné
- Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona 08036, Spain
| | | | - Hendrik G Stunnenberg
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen 6500 HB, the Netherlands
| | - Wolfram Klapper
- Hematopathology Section and Lymph Node Registry, Christian-Albrecht University, Kiel 24105, Germany
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel 24116, Germany
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany
| | - Elías Campo
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain; Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Barcelona 08036, Spain
| | - José I Martín-Subero
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain.
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50
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Hamada H, Okae H, Toh H, Chiba H, Hiura H, Shirane K, Sato T, Suyama M, Yaegashi N, Sasaki H, Arima T. Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta. Am J Hum Genet 2016; 99:1045-1058. [PMID: 27843122 DOI: 10.1016/j.ajhg.2016.08.021] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/31/2016] [Indexed: 10/20/2022] Open
Abstract
DNA methylation is globally reprogrammed after fertilization, and as a result, the parental genomes have similar DNA-methylation profiles after implantation except at the germline differentially methylated regions (gDMRs). We and others have previously shown that human blastocysts might contain thousands of transient maternally methylated gDMRs (transient mDMRs), whose maternal methylation is lost in embryonic tissues after implantation. In this study, we performed genome-wide allelic DNA methylation analyses of purified trophoblast cells from human placentas and, surprisingly, found that more than one-quarter of the transient-in-embryo mDMRs maintained their maternally biased DNA methylation. RNA-sequencing-based allelic expression analyses revealed that some of the placenta-specific mDMRs were associated with expression of imprinted genes (e.g., TIGAR, SLC4A7, PROSER2-AS1, and KLHDC10), and three imprinted gene clusters were identified. This approach also identified some X-linked gDMRs. Comparisons of the data with those from other mammals revealed that genomic imprinting in the placenta is highly variable. These findings highlight the incomplete erasure of germline DNA methylation in the human placenta; understanding this erasure is important for understanding normal placental development and the pathogenesis of developmental disorders with imprinting effects.
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