1
|
Luo Y, Zhou T, Liu D, Wang F, Zhao Q. AIMER: A SNP-independent software for identifying imprinting-like allelic methylated regions from DNA methylome. Comput Struct Biotechnol J 2024; 23:566-576. [PMID: 38274999 PMCID: PMC10809074 DOI: 10.1016/j.csbj.2023.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024] Open
Abstract
Genomic imprinting is essential for mammalian growth and embryogenesis. High-throughput bisulfite sequencing accompanied with parental haplotype-specific information allows analysis of imprinted genes and imprinting control regions (ICRs) on a large scale. Currently, although several allelic methylated regions (AMRs) detection software were developed, methods for detecting imprinted AMRs is still limited. Here, we developed a SNP-independent statistical approach, AIMER, to detect imprinting-like AMRs. By using the mouse frontal cortex methylome as input, we demonstrated that AIMER performs very well in detecting known germline ICRs compared with other methods. Furthermore, we found the putative parental AMRs AIMER detected could be distinguished from sequence-dependent AMRs. Finally, we found a novel germline imprinting-like AMR using WGBS data from 17 distinct mouse tissue samples. The results indicate that AIMER is a good choice for detecting imprinting-like (parent-of-origin-dependent) AMRs. We hope this method will be helpful for future genomic imprinting studies. The Python source code for our project is now publicly available on both GitHub (https://github.com/ZhaoLab-TMU/AIMER) and Gitee (https://gitee.com/zhaolab_tmu/AIMER).
Collapse
Affiliation(s)
| | | | - Deng Liu
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Fan Wang
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qian Zhao
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| |
Collapse
|
2
|
Rendek T, Pos O, Duranova T, Saade R, Budis J, Repiska V, Szemes T. Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics. Cancers (Basel) 2024; 16:2001. [PMID: 38893121 PMCID: PMC11171112 DOI: 10.3390/cancers16112001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In current clinical practice, effective cancer testing and screening paradigms are limited to specific types of cancer, exhibiting varying efficiency, acceptance, and adherence. Cell-free DNA (cfDNA) methylation profiling holds promise in providing information about the presence of malignity regardless of its type and location while leveraging blood-based liquid biopsies as a method to obtain analytical samples. However, technical difficulties, costs and challenges resulting from biological variations, tumor heterogeneity, and exogenous factors persist. This method exploits the mechanisms behind cfDNA release but faces issues like fragmentation, low concentrations, and high background noise. This review explores cfDNA methylation's origins, means of detection, and profiling for cancer diagnostics. The critical evaluation of currently available multi-cancer early detection methods (MCEDs) as well as tests targeting single genes, emphasizing their potential and limits to refine strategies for early cancer detection, are explained. The current methodology limitations, workflows, comparisons of clinically approved liquid biopsy-based methylation tests for cancer, their utilization in companion diagnostics as well as the biological limitations of the epigenetics approach are discussed, aiming to help healthcare providers as well as researchers to orient themselves in this increasingly complex and evolving field of diagnostics.
Collapse
Affiliation(s)
- Tomas Rendek
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Ondrej Pos
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | | | - Rami Saade
- 2nd Department of Gynaecology and Obstetrics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Tomas Szemes
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| |
Collapse
|
3
|
Rengifo Rojas C, Cercy J, Perillous S, Gonthier-Guéret C, Montibus B, Maupetit-Méhouas S, Espinadel A, Dupré M, Hong CC, Hata K, Nakabayashi K, Plagge A, Bouschet T, Arnaud P, Vaillant I, Court F. Biallelic non-productive enhancer-promoter interactions precede imprinted expression of Kcnk9 during mouse neural commitment. HGG ADVANCES 2024; 5:100271. [PMID: 38297831 PMCID: PMC10869267 DOI: 10.1016/j.xhgg.2024.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
It is only partially understood how constitutive allelic methylation at imprinting control regions (ICRs) interacts with other regulation levels to drive timely parental allele-specific expression along large imprinted domains. The Peg13-Kcnk9 domain is an imprinted domain with important brain functions. To gain insights into its regulation during neural commitment, we performed an integrative analysis of its allele-specific epigenetic, transcriptomic, and cis-spatial organization using a mouse stem cell-based corticogenesis model that recapitulates the control of imprinted gene expression during neurodevelopment. We found that, despite an allelic higher-order chromatin structure associated with the paternally CTCF-bound Peg13 ICR, enhancer-Kcnk9 promoter contacts occurred on both alleles, although they were productive only on the maternal allele. This observation challenges the canonical model in which CTCF binding isolates the enhancer and its target gene on either side and suggests a more nuanced role for allelic CTCF binding at some ICRs.
Collapse
Affiliation(s)
- Cecilia Rengifo Rojas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jil Cercy
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sophie Perillous
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Céline Gonthier-Guéret
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bertille Montibus
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Stéphanie Maupetit-Méhouas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Astrid Espinadel
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Marylou Dupré
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan; Department of Human Molecular Genetics, Gunma University Graduate School of Medicine 3-39-22 Showa, Maebashi, Gunma 371-8511, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Antonius Plagge
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Philippe Arnaud
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Isabelle Vaillant
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Franck Court
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| |
Collapse
|
4
|
Lin Y, Li J, Gu Y, Jin L, Bai J, Zhang J, Wang Y, Liu P, Long K, He M, Li D, Liu C, Han Z, Zhang Y, Li X, Zeng B, Lu L, Kong F, Sun Y, Fan Y, Wang X, Wang T, Jiang A, Ma J, Shen L, Zhu L, Jiang Y, Tang G, Fan X, Liu Q, Li H, Wang J, Chen L, Ge L, Li X, Tang Q, Li M. Haplotype-resolved 3D chromatin architecture of the hybrid pig. Genome Res 2024; 34:310-325. [PMID: 38479837 PMCID: PMC10984390 DOI: 10.1101/gr.278101.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter-enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.
Collapse
Affiliation(s)
- Yu Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
| | - Yiren Gu
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingyi Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yujie Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Pengliang Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mengnan He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Can Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ziyin Han
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaokai Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Zeng
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lu Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Fanli Kong
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ying Sun
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Geriatric Health, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yongliang Fan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - An'an Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jideng Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanzhi Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoqing Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaolan Fan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qingyou Liu
- Animal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Hua Li
- Animal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jinyong Wang
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Li Chen
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Liangpeng Ge
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Xuewei Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianzi Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
| |
Collapse
|
5
|
Zhan Y, Lou H, Shou R, Li A, Shang J, Jin Y, Li L, Zhu L, Lu X, Fan X. Maternal exposure to E 551 during pregnancy leads to genome-wide DNA methylation changes and metabolic disorders in the livers of pregnant mice and their fetuses. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133233. [PMID: 38118196 DOI: 10.1016/j.jhazmat.2023.133233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/09/2023] [Accepted: 12/10/2023] [Indexed: 12/22/2023]
Abstract
The widespread use of nanoparticles in the food industry has raised concerns regarding their potential adverse effects on human health, particularly in vulnerable populations, including pregnant mothers and fetuses. However, studies evaluating the reproductive and developmental toxicity of food-grade nanomaterials are limited. This study investigated the potential risks of prenatal dietary exposure to food-grade silica nanoparticles (E 551) on maternal health and fetal growth using conventional toxicological and epigenetic methods. The results showed that prenatal exposure to a high-dose of E 551 induces fetal resorption. Moreover, E 551 significantly accumulates in maternal and fetal livers, triggering a hepatic inflammatory response. At the epigenetic level, global DNA methylation is markedly altered in the maternal and fetal livers. Genome-wide DNA methylation sequencing revealed affected mCG, mCHG, and mCHH methylation landscapes. Subsequent bioinformatic analysis of the differentially methylated genes suggests that E 551 poses a risk of inducing metabolic disorders in maternal and fetal livers. This is further evidenced by impaired glucose tolerance in pregnant mice and altered expression of key metabolism-related genes and proteins in maternal and fetal livers. Collectively, the results of this study highlighted the importance of epigenetics in characterizing the potential toxicity of maternal exposure to food-grade nanomaterials during pregnancy.
Collapse
Affiliation(s)
- Yingqi Zhan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - He Lou
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rongshang Shou
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Anyao Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiaxin Shang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanyan Jin
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lu Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314102, China
| | - Lidan Zhu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyan Lu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China; Jinhua Institute of Zhejiang University, Jinhua, Zhejiang 321016, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314102, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China; Jinhua Institute of Zhejiang University, Jinhua, Zhejiang 321016, China.
| |
Collapse
|
6
|
Martinez D, Jiang E, Zhou Z. Overcoming genetic and cellular complexity to study the pathophysiology of X-linked intellectual disabilities. J Neurodev Disord 2024; 16:5. [PMID: 38424476 PMCID: PMC10902969 DOI: 10.1186/s11689-024-09517-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/04/2024] [Indexed: 03/02/2024] Open
Abstract
X-linked genetic causes of intellectual disability (ID) account for a substantial proportion of cases and remain poorly understood, in part due to the heterogeneous expression of X-linked genes in females. This is because most genes on the X chromosome are subject to random X chromosome inactivation (XCI) during early embryonic development, which results in a mosaic pattern of gene expression for a given X-linked mutant allele. This mosaic expression produces substantial complexity, especially when attempting to study the already complicated neural circuits that underly behavior, thus impeding the understanding of disease-related pathophysiology and the development of therapeutics. Here, we review a few selected X-linked forms of ID that predominantly affect heterozygous females and the current obstacles for developing effective therapies for such disorders. We also propose a genetic strategy to overcome the complexity presented by mosaicism in heterozygous females and highlight specific tools for studying synaptic and circuit mechanisms, many of which could be shared across multiple forms of intellectual disability.
Collapse
Affiliation(s)
- Dayne Martinez
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Evan Jiang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Intellectual and Developmental Disabilities Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
| |
Collapse
|
7
|
Routh S, Manickam V. Epigenetic alterations dictating the inflammation: A view through pancreatitis. Life Sci 2024; 338:122383. [PMID: 38158041 DOI: 10.1016/j.lfs.2023.122383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Pancreatitis is a severe inflammation in the pancreas and accounts for one of the leading gastrointestinal disorders worldwide, and presently pacing up with the morbidity and mortality rates. It has been noted that severe recurrences of acute pancreatitis lead to chronic inflammation and fibrosis of the pancreas which may further result to a long-term risk of pancreatic carcinogenesis which has a lower survival rate and worse prognosis. Several genetic and epigenetic mechanisms have been reported to orchestrate disease development. Intriguingly, concurrent epigenetic alterations can also control the genes responsible for the pathophysiology of several inflammatory pathways. Deciphering how epigenetic changes affect the inflammatory processes in pancreatitis and body's response to various therapeutic modalities may help to manage the condition more effectively. The current review will concentrate on several epigenetic changes in general and how specifically they are implicated in pancreatitis pathogenesis. Further, this review summarizes the involvement of inflammation in pancreatitis from an epigenetic perspective.
Collapse
Affiliation(s)
- Sreyoshi Routh
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Venkatraman Manickam
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| |
Collapse
|
8
|
Best C, Mennigen JA, Gilmour KM. Exploring transcriptional and post-transcriptional epigenetic regulation of crf and 11βhsd2 in rainbow trout brain during chronic social stress. Comp Biochem Physiol A Mol Integr Physiol 2024; 288:111557. [PMID: 38043640 DOI: 10.1016/j.cbpa.2023.111557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Using dominance hierarchies in juvenile rainbow trout (Oncorhynchus mykiss) as a model of chronic social stress in fish, we explored whether epigenetic transcriptional and post-transcriptional mechanisms are involved in the gene expression of corticotropin-releasing factor (crf) and 11β-hydroxysteroid dehydrogenase (11βhsd2), key factors involved in the regulation of the endocrine stress axis response. In juvenile rainbow trout pairs, subordinate individuals display sustained elevation of circulating cortisol concentrations. Cortisol production is controlled by the hypothalamic-pituitary-interrenal (HPI) axis in fish and initiated by CRF release from the preoptic area (POA). Given that crf is modulated during chronic social stress, and that such stress has been implicated in the epigenetic regulation of crf in other taxa, we probed a role for epigenetic regulation of crf transcript abundance in chronically stressed rainbow trout. We also investigated the regulation of the cortisol-metabolising enzyme 11βhsd2 in the POA, which is upregulated in subordinates. The potential involvement of DNA methylation and microRNAs (miRNAs) in the regulation of crf transcript abundance was investigated during social stress in the POA of fish, as was the potential involvement of miRNAs in 11βhsd2 regulation. Although transcript abundances of crf were elevated in subordinate fish after 4 days, DNA methylation profiles within putative promoter sequences upstream of the crf gene were not significantly affected by chronic stress. An inverse relationship between crf and its predicted posttranscriptional regulator miR-103a-3p in the POA suggests that miRNAs may be involved in mediating the effects of chronic social stress on key components of the endocrine stress axis.
Collapse
Affiliation(s)
- Carol Best
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.
| | | |
Collapse
|
9
|
Yin Q, Yang CH, Strelkova OS, Wu J, Sun Y, Gopalan S, Yang L, Dekker J, Fazzio TG, Li XZ, Gibcus J, Rando OJ. Revisiting chromatin packaging in mouse sperm. Genome Res 2023; 33:gr.277845.123. [PMID: 38129076 PMCID: PMC10760523 DOI: 10.1101/gr.277845.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/31/2023] [Indexed: 12/23/2023]
Abstract
Mammalian sperm show an unusual and heavily compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, nucleosome localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis, we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, and appropriate lysis conditions, are together required to reveal a sperm chromatin state distinct from most previous reports. Using ATAC-seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with early development and transcriptional control. Histone modification and chromosome folding profiles also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies show that our knowledge of chromosome packaging in mammalian sperm remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.
Collapse
Affiliation(s)
- Qiangzong Yin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Chih-Hsiang Yang
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Olga S Strelkova
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Jingyi Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yu Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Sneha Gopalan
- Department of Molecular Cellular and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Liyan Yang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
- Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Thomas G Fazzio
- Department of Molecular Cellular and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Johan Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA;
| |
Collapse
|
10
|
Zhou Y, Xiong L, Chen✉ J, Wang✉ Q. Integrative Analyses of scRNA-seq, Bulk mRNA-seq, and DNA Methylation Profiling in Depressed Suicide Brain Tissues. Int J Neuropsychopharmacol 2023; 26:840-855. [PMID: 37774423 PMCID: PMC10726413 DOI: 10.1093/ijnp/pyad057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/27/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Suicidal behaviors have become a serious public health concern globally due to the economic and human cost of suicidal behavior to individuals, families, communities, and society. However, the underlying etiology and biological mechanism of suicidal behavior remains poorly understood. METHODS We collected different single omic data, including single-cell RNA sequencing (scRNA-seq), bulk mRNA-seq, DNA methylation microarrays from the cortex of Major Depressive Disorder (MDD) in suicide subjects' studies, as well as fluoxetine-treated rats brains. We matched subject IDs that overlapped between the transcriptome dataset and the methylation dataset. The differential expression genes and differentially methylated regions were calculated with a 2-group comparison analysis. Cross-omics analysis was performed to calculate the correlation between the methylated and transcript levels of differentially methylated CpG sites and mapped transcripts. Additionally, we performed a deconvolution analysis for bulk mRNA-seq and DNA methylation profiling with scRNA-seq as the reference profiles. RESULTS Difference in cell type proportions among 7 cell types. Meanwhile, our analysis of single-cell sequence from the antidepressant-treated rats found that drug-specific differential expression genes were enriched into biological pathways, including ion channels and glutamatergic receptors. CONCLUSIONS This study identified some important dysregulated genes influenced by DNA methylation in 2 brain regions of depression and suicide patients. Interestingly, we found that oligodendrocyte precursor cells (OPCs) have the most contributors for cell-type proportions related to differential expression genes and methylated sites in suicidal behavior.
Collapse
Affiliation(s)
- Yalan Zhou
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lan Xiong
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Jianhua Chen✉
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingzhong Wang✉
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
11
|
Ahn J, Hwang IS, Park MR, Hwang S, Lee K. Imprinting at the KBTBD6 locus involves species-specific maternal methylation and monoallelic expression in livestock animals. J Anim Sci Biotechnol 2023; 14:131. [PMID: 37817239 PMCID: PMC10565993 DOI: 10.1186/s40104-023-00931-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/21/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The primary differentially methylated regions (DMRs) which are maternally hypermethylated serve as imprinting control regions (ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of imprinting. RESULTS Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter CpG island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter CpG islands were methylated in oocytes and/or allelically methylated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these CpG islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent imprinting. CONCLUSIONS In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting.
Collapse
Affiliation(s)
- Jinsoo Ahn
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - In-Sul Hwang
- Animal Biotechnology Division, Rural Development Administration, National Institute of Animal Science, Jeonbuk, 55365 Republic of Korea
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, Columbia University, New York, NY 10032 USA
| | - Mi-Ryung Park
- Animal Biotechnology Division, Rural Development Administration, National Institute of Animal Science, Jeonbuk, 55365 Republic of Korea
| | - Seongsoo Hwang
- Animal Welfare Research Team, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Jeollabuk-do, 55365 Republic of Korea
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
| |
Collapse
|
12
|
Watanabe R, Nakachi Y, Matsubara H, Ueda J, Ishii T, Ukai W, Hashimoto E, Kasai K, Simizu S, Kato T, Bundo M, Iwamoto K. Identification of epigenetically active L1 promoters in the human brain and their relationship with psychiatric disorders. Neurosci Res 2023; 195:37-51. [PMID: 37141946 DOI: 10.1016/j.neures.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/09/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023]
Abstract
Long interspersed nuclear element-1 (LINE-1, L1) affects the transcriptome landscape in multiple ways. Promoter activity within its 5'UTR plays a critical role in regulating diverse L1 activities. However, the epigenetic status of L1 promoters in adult brain cells and their relationship with psychiatric disorders remain poorly understood. Here, we examined DNA methylation and hydroxymethylation of the full-length L1s in neurons and nonneurons and identified "epigenetically active" L1s. Notably, some of epigenetically active L1s were retrotransposition competent, which even had chimeric transcripts from the antisense promoters at their 5'UTRs. We also identified differentially methylated L1s in the prefrontal cortices of patients with psychiatric disorders. In nonneurons of bipolar disorder patients, one L1 was significantly hypomethylated and showed an inverse correlation with the expression level of the overlapping gene NREP. Finally, we observed that altered DNA methylation levels of L1 in patients with psychiatric disorders were not affected by the surrounding genomic regions but originated from the L1 sequences. These results suggested that altered epigenetic regulation of the L1 5'UTR in the brain was involved in the pathophysiology of psychiatric disorders.
Collapse
Affiliation(s)
- Risa Watanabe
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hikari Matsubara
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Junko Ueda
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takao Ishii
- Department of Occupational Therapy, Sapporo Medical University School of Health Sciences, Sapporo, Japan
| | - Wataru Ukai
- Department of Neuropsychiatry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Eri Hashimoto
- Department of Neuropsychiatry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; The International Research Center for Neurointelligence (WPI-IRCN), University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo, Japan; University of Tokyo Institute for Diversity and Adaptation of Human Mind (UTIDAHM), The University of Tokyo, Tokyo, Japan; UTokyo Center for Integrative Science of Human Behaviour (CiSHuB), The University of Tokyo, Tokyo, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan.
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan.
| |
Collapse
|
13
|
Loftus D, Bae B, Whilden CM, Whipple AJ. Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis. Genes Dev 2023; 37:829-843. [PMID: 37821107 PMCID: PMC10620047 DOI: 10.1101/gad.350896.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brains from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we showed that imprinted chromatin structure precedes imprinted expression at the locus. Additionally, activation of a distal enhancer induced imprinted expression of Kcnk9 in an allelic chromatin structure-dependent manner. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.
Collapse
Affiliation(s)
- Daniel Loftus
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Bongmin Bae
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Courtney M Whilden
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Amanda J Whipple
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
14
|
Liu R, Zhao E, Yu H, Yuan C, Abbas MN, Cui H. Methylation across the central dogma in health and diseases: new therapeutic strategies. Signal Transduct Target Ther 2023; 8:310. [PMID: 37620312 PMCID: PMC10449936 DOI: 10.1038/s41392-023-01528-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 08/26/2023] Open
Abstract
The proper transfer of genetic information from DNA to RNA to protein is essential for cell-fate control, development, and health. Methylation of DNA, RNAs, histones, and non-histone proteins is a reversible post-synthesis modification that finetunes gene expression and function in diverse physiological processes. Aberrant methylation caused by genetic mutations or environmental stimuli promotes various diseases and accelerates aging, necessitating the development of therapies to correct the disease-driver methylation imbalance. In this Review, we summarize the operating system of methylation across the central dogma, which includes writers, erasers, readers, and reader-independent outputs. We then discuss how dysregulation of the system contributes to neurological disorders, cancer, and aging. Current small-molecule compounds that target the modifiers show modest success in certain cancers. The methylome-wide action and lack of specificity lead to undesirable biological effects and cytotoxicity, limiting their therapeutic application, especially for diseases with a monogenic cause or different directions of methylation changes. Emerging tools capable of site-specific methylation manipulation hold great promise to solve this dilemma. With the refinement of delivery vehicles, these new tools are well positioned to advance the basic research and clinical translation of the methylation field.
Collapse
Affiliation(s)
- Ruochen Liu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Erhu Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Huijuan Yu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Chaoyu Yuan
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
15
|
Shao Z, Han Y, Zhou D. Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA. BMC Genomics 2023; 24:439. [PMID: 37542258 PMCID: PMC10403921 DOI: 10.1186/s12864-023-09541-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND DNA methylation is one of the best characterized epigenetic modifications in the mammalian nuclear genome and is known to play a significant role in various biological processes. Nonetheless, the presence of 5-methylcytosine (5mC) in mitochondrial DNA remains controversial, as data ranging from the lack of 5mC to very extensive 5mC have been reported. RESULTS By conducting comprehensive bioinformatic analyses of both published and our own data, we reveal that previous observations of extensive and strand-biased mtDNA-5mC are likely artifacts due to a combination of factors including inefficient bisulfite conversion, extremely low sequencing reads in the L strand, and interference from nuclear mitochondrial DNA sequences (NUMTs). To reduce false positive mtDNA-5mC signals, we establish an optimized procedure for library preparation and data analysis of bisulfite sequencing. Leveraging our modified workflow, we demonstrate an even distribution of 5mC signals across the mtDNA and an average methylation level ranging from 0.19% to 0.67% in both cell lines and primary cells, which is indistinguishable from the background noise. CONCLUSIONS We have developed a framework for analyzing mtDNA-5mC through bisulfite sequencing, which enables us to present multiple lines of evidence for the lack of extensive 5mC in mammalian mtDNA. We assert that the data available to date do not support the reported presence of mtDNA-5mC.
Collapse
Affiliation(s)
- Zhenyu Shao
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yang Han
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University & Chinese Academy of Medical Sciences (RU069), Shanghai, 200032, China
| | - Dan Zhou
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University & Chinese Academy of Medical Sciences (RU069), Shanghai, 201399, China.
| |
Collapse
|
16
|
Sun T, Xu Y, Xiang Y, Ou J, Soderblom EJ, Diao Y. Crosstalk between RNA m 6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells. Nat Genet 2023; 55:1324-1335. [PMID: 37474847 PMCID: PMC10766344 DOI: 10.1038/s41588-023-01452-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
Transposable elements (TEs) are parasitic DNA sequences accounting for over half of the human genome. Tight control of the repression and activation states of TEs is critical for genome integrity, development, immunity and diseases, including cancer. However, precisely how this regulation is achieved remains unclear. Here we develop a targeted proteomic proximity labeling approach to capture TE-associated proteins in human embryonic stem cells (hESCs). We find that the RNA N6-methyladenosine (m6A) reader, YTHDC2, occupies genomic loci of the primate-specific TE, LTR7/HERV-H, specifically through its interaction with m6A-modified HERV-H RNAs. Unexpectedly, YTHDC2 recruits the DNA 5-methylcytosine (5mC)-demethylase, TET1, to remove 5mC from LTR7/HERV-H and prevent epigenetic silencing. Functionally, the YTHDC2/LTR7 axis inhibits neural differentiation of hESCs. Our results reveal both an underappreciated crosstalk between RNA m6A and DNA 5mC, the most abundant regulatory modifications of RNA and DNA in eukaryotes, and the fact that in hESCs this interplay controls TE activity and cell fate.
Collapse
Affiliation(s)
- Tongyu Sun
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Yueyuan Xu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Yu Xiang
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
| | - Jianhong Ou
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
| | - Erik J Soderblom
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Proteomics and Metabolomics Shared Resource, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.
- Department of Orthopaedics Surgery, Duke University Medical Center, Durham, NC, USA.
- Department of Pathology, Duke University Medical Center, Durham, NC, USA.
| |
Collapse
|
17
|
Esnault C, Magat T, Zine El Aabidine A, Garcia-Oliver E, Cucchiarini A, Bouchouika S, Lleres D, Goerke L, Luo Y, Verga D, Lacroix L, Feil R, Spicuglia S, Mergny JL, Andrau JC. G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions. Nat Genet 2023; 55:1359-1369. [PMID: 37400615 DOI: 10.1038/s41588-023-01437-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/31/2023] [Indexed: 07/05/2023]
Abstract
Metazoan promoters are enriched in secondary DNA structure-forming motifs, such as G-quadruplexes (G4s). Here we describe 'G4access', an approach to isolate and sequence G4s associated with open chromatin via nuclease digestion. G4access is antibody- and crosslinking-independent and enriches for computationally predicted G4s (pG4s), most of which are confirmed in vitro. Using G4access in human and mouse cells, we identify cell-type-specific G4 enrichment correlated with nucleosome exclusion and promoter transcription. G4access allows measurement of variations in G4 repertoire usage following G4 ligand treatment, HDAC and G4 helicases inhibitors. Applying G4access to cells from reciprocal hybrid mouse crosses suggests a role for G4s in the control of active imprinting regions. Consistently, we also observed that G4access peaks are unmethylated, while methylation at pG4s correlates with nucleosome repositioning on DNA. Overall, our study provides a new tool for studying G4s in cellular dynamics and highlights their association with open chromatin, transcription and their antagonism to DNA methylation.
Collapse
Affiliation(s)
- Cyril Esnault
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Talha Magat
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Amal Zine El Aabidine
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Encar Garcia-Oliver
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France
| | - Soumya Bouchouika
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - David Lleres
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Lutz Goerke
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Yu Luo
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France
- Université Paris-Saclay, Institut Curie, Orsay, France
| | - Daniela Verga
- Université Paris-Saclay, Institut Curie, Orsay, France
| | - Laurent Lacroix
- Institut de Biologie de l'École Normale Supérieure, ENS, CNRS UMR8197, Inserm U1024, Paris, France
| | - Robert Feil
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Salvatore Spicuglia
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France.
| |
Collapse
|
18
|
Singh A, Rappolee DA, Ruden DM. Epigenetic Reprogramming in Mice and Humans: From Fertilization to Primordial Germ Cell Development. Cells 2023; 12:1874. [PMID: 37508536 PMCID: PMC10377882 DOI: 10.3390/cells12141874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
In this review, advances in the understanding of epigenetic reprogramming from fertilization to the development of primordial germline cells in a mouse and human embryo are discussed. To gain insights into the molecular underpinnings of various diseases, it is essential to comprehend the intricate interplay between genetic, epigenetic, and environmental factors during cellular reprogramming and embryonic differentiation. An increasing range of diseases, including cancer and developmental disorders, have been linked to alterations in DNA methylation and histone modifications. Global epigenetic reprogramming occurs in mammals at two stages: post-fertilization and during the development of primordial germ cells (PGC). Epigenetic reprogramming after fertilization involves rapid demethylation of the paternal genome mediated through active and passive DNA demethylation, and gradual demethylation in the maternal genome through passive DNA demethylation. The de novo DNA methyltransferase enzymes, Dnmt3a and Dnmt3b, restore DNA methylation beginning from the blastocyst stage until the formation of the gastrula, and DNA maintenance methyltransferase, Dnmt1, maintains methylation in the somatic cells. The PGC undergo a second round of global demethylation after allocation during the formative pluripotent stage before gastrulation, where the imprints and the methylation marks on the transposable elements known as retrotransposons, including long interspersed nuclear elements (LINE-1) and intracisternal A-particle (IAP) elements are demethylated as well. Finally, DNA methylation is restored in the PGC at the implantation stage including sex-specific imprints corresponding to the sex of the embryo. This review introduces a novel perspective by uncovering how toxicants and stress stimuli impact the critical period of allocation during formative pluripotency, potentially influencing both the quantity and quality of PGCs. Furthermore, the comprehensive comparison of epigenetic events between mice and humans breaks new ground, empowering researchers to make informed decisions regarding the suitability of mouse models for their experiments.
Collapse
Affiliation(s)
- Aditi Singh
- CS Mott Center, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48202, USA; (A.S.); (D.A.R.)
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48202, USA
| | - Daniel A. Rappolee
- CS Mott Center, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48202, USA; (A.S.); (D.A.R.)
- Reproductive Stress Measurement, Mechanisms and Management, Corp., 135 Lake Shore Rd., Grosse Pointe Farms, MI 48236, USA
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA
- Department of Physiology, Wayne State University, Detroit, MI 48202, USA
| | - Douglas M. Ruden
- CS Mott Center, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48202, USA; (A.S.); (D.A.R.)
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48202, USA
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA
| |
Collapse
|
19
|
Loftus D, Bae B, Whilden CM, Whipple AJ. Allelic chromatin structure primes imprinted expression of Kcnk9 during neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544389. [PMID: 37333073 PMCID: PMC10274912 DOI: 10.1101/2023.06.09.544389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brain from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we show that on the maternal allele enhancer-promoter contacts formed early in development prime the brain-specific potassium leak channel Kcnk9 for maternal expression prior to neurogenesis. In contrast, these enhancer-promoter contacts are blocked by CTCF on the paternal allele, preventing paternal Kcnk9 activation. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.
Collapse
Affiliation(s)
- Daniel Loftus
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Bongmin Bae
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Courtney M. Whilden
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Amanda J. Whipple
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| |
Collapse
|
20
|
Tyler AL, Spruce C, Kursawe R, Haber A, Ball RL, Pitman WA, Fine AD, Raghupathy N, Walker M, Philip VM, Baker CL, Mahoney JM, Churchill GA, Trowbridge JJ, Stitzel ML, Paigen K, Petkov PM, Carter GW. Variation in histone configurations correlates with gene expression across nine inbred strains of mice. Genome Res 2023; 33:857-871. [PMID: 37217254 PMCID: PMC10519406 DOI: 10.1101/gr.277467.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
The Diversity Outbred (DO) mice and their inbred founders are widely used models of human disease. However, although the genetic diversity of these mice has been well documented, their epigenetic diversity has not. Epigenetic modifications, such as histone modifications and DNA methylation, are important regulators of gene expression and, as such, are a critical mechanistic link between genotype and phenotype. Therefore, creating a map of epigenetic modifications in the DO mice and their founders is an important step toward understanding mechanisms of gene regulation and the link to disease in this widely used resource. To this end, we performed a strain survey of epigenetic modifications in hepatocytes of the DO founders. We surveyed four histone modifications (H3K4me1, H3K4me3, H3K27me3, and H3K27ac), as well as DNA methylation. We used ChromHMM to identify 14 chromatin states, each of which represents a distinct combination of the four histone modifications. We found that the epigenetic landscape is highly variable across the DO founders and is associated with variation in gene expression across strains. We found that epigenetic state imputed into a population of DO mice recapitulated the association with gene expression seen in the founders, suggesting that both histone modifications and DNA methylation are highly heritable mechanisms of gene expression regulation. We illustrate how DO gene expression can be aligned with inbred epigenetic states to identify putative cis-regulatory regions. Finally, we provide a data resource that documents strain-specific variation in the chromatin state and DNA methylation in hepatocytes across nine widely used strains of laboratory mice.
Collapse
Affiliation(s)
- Anna L Tyler
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Catrina Spruce
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Romy Kursawe
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Annat Haber
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Robyn L Ball
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Wendy A Pitman
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Alexander D Fine
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - Michael Walker
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Vivek M Philip
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - J Matthew Mahoney
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Gary A Churchill
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | | | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Kenneth Paigen
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| | - Petko M Petkov
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA;
| | - Gregory W Carter
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine 04609, USA
| |
Collapse
|
21
|
Budkina A, Medvedeva YA, Stupnikov A. Assessing the Differential Methylation Analysis Quality for Microarray and NGS Platforms. Int J Mol Sci 2023; 24:ijms24108591. [PMID: 37239934 DOI: 10.3390/ijms24108591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/28/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Differential methylation (DM) is actively recruited in different types of fundamental and translational studies. Currently, microarray- and NGS-based approaches for methylation analysis are the most widely used with multiple statistical models designed to extract differential methylation signatures. The benchmarking of DM models is challenging due to the absence of gold standard data. In this study, we analyze an extensive number of publicly available NGS and microarray datasets with divergent and widely utilized statistical models and apply the recently suggested and validated rank-statistic-based approach Hobotnica to evaluate the quality of their results. Overall, microarray-based methods demonstrate more robust and convergent results, while NGS-based models are highly dissimilar. Tests on the simulated NGS data tend to overestimate the quality of the DM methods and therefore are recommended for use with caution. Evaluation of the top 10 DMC and top 100 DMC in addition to the not-subset signature also shows more stable results for microarray data. Summing up, given the observed heterogeneity in NGS methylation data, the evaluation of newly generated methylation signatures is a crucial step in DM analysis. The Hobotnica metric is coordinated with previously developed quality metrics and provides a robust, sensitive, and informative estimation of methods' performance and DM signatures' quality in the absence of gold standard data solving a long-existing problem in DM analysis.
Collapse
Affiliation(s)
- Anna Budkina
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Yulia A Medvedeva
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia
| | - Alexey Stupnikov
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| |
Collapse
|
22
|
Liu F, Wang Y, Gu H, Wang X. Technologies and applications of single-cell DNA methylation sequencing. Theranostics 2023; 13:2439-2454. [PMID: 37215576 PMCID: PMC10196823 DOI: 10.7150/thno.82582] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/09/2023] [Indexed: 05/24/2023] Open
Abstract
DNA methylation is the most stable epigenetic modification. In mammals, it usually occurs at the cytosine of CpG dinucleotides. DNA methylation is essential for many physiological and pathological processes. Aberrant DNA methylation has been observed in human diseases, particularly cancer. Notably, conventional DNA methylation profiling technologies require a large amount of DNA, often from a heterogeneous cell population, and provide an average methylation level of many cells. It is often not realistic to collect sufficient numbers of cells, such as rare cells and circulating tumor cells in peripheral blood, for bulk sequencing assays. It is therefore essential to develop sequencing technologies that can accurately profile DNA methylation using small numbers of cells or even single cells. Excitingly, many single-cell DNA methylation sequencing and single-cell omics sequencing technologies have been developed, and applications of these methods have greatly expanded our understanding of the molecular mechanism of DNA methylation. Here, we summaries single-cell DNA methylation and multi-omics sequencing methods, delineate their applications in biomedical sciences, discuss technical challenges, and present our perspective on future research directions.
Collapse
Affiliation(s)
- Fang Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230026, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech. Ltd, Hangzhou, 310000, China
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230026, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Xiaoxue Wang
- Department of Hematology, the First Hospital of China Medical University, Shenyang, 110001, China
| |
Collapse
|
23
|
Martin S, Poppe D, Olova N, O'Leary C, Ivanova E, Pflueger J, Dechka J, Simmons RK, Cooper HM, Reik W, Lister R, Wolvetang EJ. Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development. Genes (Basel) 2023; 14:genes14050957. [PMID: 37239317 DOI: 10.3390/genes14050957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
DNA methylation in neurons is directly linked to neuronal genome regulation and maturation. Unlike other tissues, vertebrate neurons accumulate high levels of atypical DNA methylation in the CH sequence context (mCH) during early postnatal brain development. Here, we investigate to what extent neurons derived in vitro from both mouse and human pluripotent stem cells recapitulate in vivo DNA methylation patterns. While human ESC-derived neurons did not accumulate mCH in either 2D culture or 3D organoid models even after prolonged culture, cortical neurons derived from mouse ESCs acquired in vivo levels of mCH over a similar time period in both primary neuron cultures and in vivo development. mESC-derived neuron mCH deposition was coincident with a transient increase in Dnmt3a, preceded by the postmitotic marker Rbfox3 (NeuN), was enriched at the nuclear lamina, and negatively correlated with gene expression. We further found that methylation patterning subtly differed between in vitro mES-derived and in vivo neurons, suggesting the involvement of additional noncell autonomous processes. Our findings show that mouse ESC-derived neurons, in contrast to those of humans, can recapitulate the unique DNA methylation landscape of adult neurons in vitro over experimentally tractable timeframes, which allows their use as a model system to study epigenome maturation over development.
Collapse
Affiliation(s)
- Sally Martin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel Poppe
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Nelly Olova
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Conor O'Leary
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Elena Ivanova
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Jennifer Dechka
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rebecca K Simmons
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Helen M Cooper
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Wolf Reik
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
- The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
24
|
Yang A, Yan S, Yin Y, Chen C, Tang X, Ran M, Chen B. FZD7, Regulated by Non-CpG Methylation, Plays an Important Role in Immature Porcine Sertoli Cell Proliferation. Int J Mol Sci 2023; 24:ijms24076179. [PMID: 37047150 PMCID: PMC10094452 DOI: 10.3390/ijms24076179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
The regulatory role of non-CpG methylation in mammals has been important in whole-genome bisulfite sequencing. It has also been suggested that non-CpG methylation regulates gene expression to affect the development and health of mammals. However, the dynamic regulatory mechanisms of genome-wide, non-CpG methylation during testicular development still require intensive study. In this study, we analyzed the dataset from the whole-genome bisulfite sequencing (WGBS) and the RNA-seq of precocious porcine testicular tissues across two developmental stages (1 and 75 days old) in order to explore the regulatory roles of non-CpG methylation. Our results showed that genes regulated by non-CpG methylation affect the development of testes in multiple pathways. Furthermore, several hub genes that are regulated by non-CpG methylation during testicular development-such as VEGFA, PECAM1, and FZD7-were also identified. We also found that the relative expression of FZD7 was downregulated by the zebularine-induced demethylation of the first exon of FZD7. This regulatory relationship was consistent with the results of the WGBS and RNA-seq analysis. The immature porcine Sertoli cells were transfected with RNAi to mimic the expression patterns of FZD7 during testicular development. The results of the simulation test showed that cell proliferation was significantly impeded and that cell cycle arrest at the G2 phase was caused by the siRNA-induced FZD7 inhibition. We also found that the percentage of early apoptotic Sertoli cells was decreased by transfecting them with the RNAi for FZD7. This indicates that FZD7 is an important factor in linking the proliferation and apoptosis of Sertoli cells. We further demonstrated that Sertoli cells that were treated with the medium collected from apoptotic cells could stimulate proliferation. These findings will contribute to the exploration of the regulatory mechanisms of non-CpG methylation in testicular development and of the relationship between the proliferation and apoptosis of normal somatic cells.
Collapse
Affiliation(s)
- Anqi Yang
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Saina Yan
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Yanfei Yin
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Chujie Chen
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Xiangwei Tang
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Maoliang Ran
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Bin Chen
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| |
Collapse
|
25
|
Fu H, Zheng H, Chen X, Weirauch MT, Muglia LJ, Wang L, Liu Y. NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. Genome Biol 2023; 24:50. [PMID: 36927507 PMCID: PMC10018866 DOI: 10.1186/s13059-023-02889-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
Cis-regulatory elements are coordinated to regulate the expression of their targeted genes. However, the joint measurement of cis-regulatory elements' activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single-nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.
Collapse
Affiliation(s)
- Hailu Fu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Haizi Zheng
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Xiaoting Chen
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Matthew T Weirauch
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Present address: Burroughs Wellcome Fund, Research Triangle Park, NC, 27614, USA
| | - Li Wang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Biology, Xavier University, Cincinnati, OH, 45207, USA.
| | - Yaping Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- Department of Electrical Engineering and Computing Sciences, University of Cincinnati College of Engineering and Applied Science, Cincinnati, OH, 45229, USA.
- University of Cincinnati Cancer Center, Cincinnati, OH, 45219, USA.
| |
Collapse
|
26
|
Tan B, Zhou C, Zang X, Zhao X, Xiao L, Zeng J, Hong L, Wu Z, Gu T. Integrated Analysis of DNA Methylation and Gene Expression in Porcine Placental Development. Int J Mol Sci 2023; 24:ijms24065169. [PMID: 36982243 PMCID: PMC10049215 DOI: 10.3390/ijms24065169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Proper placental development is crucial for the conceptus to grow and survive, because the placenta is responsible for transporting nutrients and oxygen from the pregnant female to the developing fetus. However, the processes of placental morphogenesis and fold formation remain to be fully elucidated. In this study, we used whole-genome bisulfite sequencing and RNA sequencing to produce a global map of DNA methylation and gene expression changes in placentas from Tibetan pig fetuses 21, 28, and 35 days post-coitus. Substantial changes in morphology and histological structures at the uterine-placental interface were revealed via hematoxylin-eosin staining. Transcriptome analysis identified 3959 differentially expressed genes (DEGs) and revealed the key transcriptional properties in three stages. The DNA methylation level in the gene promoter was negatively correlated with gene expression. We identified a set of differentially methylated regions associated with placental developmental genes and transcription factors. The decrease in DNA methylation level in the promoter was associated with the transcriptional activation of 699 DEGs that were functionally enriched in cell adhesion and migration, extracellular matrix remodeling, and angiogenesis. Our analysis provides a valuable resource for understanding the mechanisms of DNA methylation in placental development. The methylation status of different genomic regions plays a key role in establishing transcriptional patterns from placental morphogenesis to fold formation.
Collapse
Affiliation(s)
- Baohua Tan
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Chen Zhou
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xupeng Zang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xinming Zhao
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Liyao Xiao
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiekang Zeng
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
27
|
Kreibich E, Kleinendorst R, Barzaghi G, Kaspar S, Krebs AR. Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation. Mol Cell 2023; 83:787-802.e9. [PMID: 36758546 DOI: 10.1016/j.molcel.2023.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/21/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023]
Abstract
Enhancers are cis-regulatory elements that control the establishment of cell identities during development. In mammals, enhancer activation is tightly coupled with DNA demethylation. However, whether this epigenetic remodeling is necessary for enhancer activation is unknown. Here, we adapted single-molecule footprinting to measure chromatin accessibility and transcription factor binding as a function of the presence of methylation on the same DNA molecules. We leveraged natural epigenetic heterogeneity at active enhancers to test the impact of DNA methylation on their chromatin accessibility in multiple cell lineages. Although reduction of DNA methylation appears dispensable for the activity of most enhancers, we identify a class of cell-type-specific enhancers where DNA methylation antagonizes the binding of transcription factors. Genetic perturbations reveal that chromatin accessibility and transcription factor binding require active demethylation at these loci. Thus, in addition to safeguarding the genome from spurious activation, DNA methylation directly controls transcription factor occupancy at active enhancers.
Collapse
Affiliation(s)
- Elisa Kreibich
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Rozemarijn Kleinendorst
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Guido Barzaghi
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Sarah Kaspar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Arnaud R Krebs
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| |
Collapse
|
28
|
Genes and pathways associated with fear discrimination identified by genome-wide DNA methylation and RNA-seq analyses in nucleus accumbens in mice. Prog Neuropsychopharmacol Biol Psychiatry 2023; 120:110643. [PMID: 36152737 DOI: 10.1016/j.pnpbp.2022.110643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/21/2022]
Abstract
Fear memory is critical for individual survival. However, the maladaptive fear response is one of the hallmarks of fear-related disorders, which is characterized by the failure to discriminate threatening signals from neutral or safe cues. The biological mechanisms of fear discrimination remain to be clarified. In this study, we found that the nucleus accumbens (NAc) was indispensable for the formation of cued fear memory in mice, during which the expression of DNA methyltransferase 3a gene (DNMT3a) increased. Injection of Zebularine, a nonspecific DNMT inhibitor, into NAc immediately after conditioning induced a maladaptive fear response to neutral cue (CS-). Using whole-genome bisulfite sequencing (WGBS), differentially methylated sites and methylated regions (DMRs) were investigated. 16,226 DMRs in the genenome were identified, in which, 214 genes with significant differences in their methylation levels and mRNA expression profiles were identified through correlation analysis. Notably, 15 genes were synaptic function-related and 8 genes were enriched in the cGMP-PKG signaling pathway. Moreover, inhibition of PKG impaired fear discrimination. Together, our results revealed the profile and role of genome-wide DNA methylation in NAc in the regulation of fear discrimination.
Collapse
|
29
|
Akbari V, Hanlon VC, O’Neill K, Lefebvre L, Schrader KA, Lansdorp PM, Jones SJ. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq. CELL GENOMICS 2022; 3:100233. [PMID: 36777186 PMCID: PMC9903809 DOI: 10.1016/j.xgen.2022.100233] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/08/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Hundreds of loci in human genomes have alleles that are methylated differentially according to their parent of origin. These imprinted loci generally show little variation across tissues, individuals, and populations. We show that such loci can be used to distinguish the maternal and paternal homologs for all human autosomes without the need for the parental DNA. We integrate methylation-detecting nanopore sequencing with the long-range phase information in Strand-seq data to determine the parent of origin of chromosome-length haplotypes for both DNA sequence and DNA methylation in five trios with diverse genetic backgrounds. The parent of origin was correctly inferred for all autosomes with an average mismatch error rate of 0.31% for SNVs and 1.89% for insertions or deletions (indels). Because our method can determine whether an inherited disease allele originated from the mother or the father, we predict that it will improve the diagnosis and management of many genetic diseases.
Collapse
Affiliation(s)
- Vahid Akbari
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Kieran O’Neill
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Louis Lefebvre
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kasmintan A. Schrader
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Peter M. Lansdorp
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada,Corresponding author
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada,Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Corresponding author
| |
Collapse
|
30
|
Aversano S, Caiazza C, Caiazzo M. Induced pluripotent stem cell-derived and directly reprogrammed neurons to study neurodegenerative diseases: The impact of aging signatures. Front Aging Neurosci 2022; 14:1069482. [PMID: 36620769 PMCID: PMC9810544 DOI: 10.3389/fnagi.2022.1069482] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Many diseases of the central nervous system are age-associated and do not directly result from genetic mutations. These include late-onset neurodegenerative diseases (NDDs), which represent a challenge for biomedical research and drug development due to the impossibility to access to viable human brain specimens. Advancements in reprogramming technologies have allowed to obtain neurons from induced pluripotent stem cells (iPSCs) or directly from somatic cells (iNs), leading to the generation of better models to understand the molecular mechanisms and design of new drugs. Nevertheless, iPSC technology faces some limitations due to reprogramming-associated cellular rejuvenation which resets the aging hallmarks of donor cells. Given the prominent role of aging for the development and manifestation of late-onset NDDs, this suggests that this approach is not the most suitable to accurately model age-related diseases. Direct neuronal reprogramming, by which a neuron is formed via direct conversion from a somatic cell without going through a pluripotent intermediate stage, allows the possibility to generate patient-derived neurons that maintain aging and epigenetic signatures of the donor. This aspect may be advantageous for investigating the role of aging in neurodegeneration and for finely dissecting underlying pathological mechanisms. Here, we will compare iPSC and iN models as regards the aging status and explore how this difference is reported to affect the phenotype of NDD in vitro models.
Collapse
Affiliation(s)
- Simona Aversano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Carmen Caiazza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Massimiliano Caiazzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy,Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, Netherlands,*Correspondence: Massimiliano Caiazzo,
| |
Collapse
|
31
|
Wei A, Wu H. Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers. Development 2022; 149:dev182683. [PMID: 36519514 PMCID: PMC10108609 DOI: 10.1242/dev.182683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA methylation is a highly conserved epigenetic modification that plays essential roles in mammalian gene regulation, genome stability and development. Despite being primarily considered a stable and heritable epigenetic silencing mechanism at heterochromatic and repetitive regions, whole genome methylome analysis reveals that DNA methylation can be highly cell-type specific and dynamic within proximal and distal gene regulatory elements during early embryonic development, stem cell differentiation and reprogramming, and tissue maturation. In this Review, we focus on the mechanisms and functions of regulated DNA methylation and demethylation, highlighting how these dynamics, together with crosstalk between DNA methylation and histone modifications at distinct regulatory regions, contribute to mammalian development and tissue maturation. We also discuss how recent technological advances in single-cell and long-read methylome sequencing, along with targeted epigenome-editing, are enabling unprecedented high-resolution and mechanistic dissection of DNA methylome dynamics.
Collapse
Affiliation(s)
- Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
32
|
Claxton M, Pulix M, Seah MKY, Bernardo R, Zhou P, Aljuraysi S, Liloglou T, Arnaud P, Kelsey G, Messerschmidt DM, Plagge A. Variable allelic expression of imprinted genes at the Peg13, Trappc9, Ago2 cluster in single neural cells. Front Cell Dev Biol 2022; 10:1022422. [PMID: 36313557 PMCID: PMC9596773 DOI: 10.3389/fcell.2022.1022422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is an epigenetic process through which genes are expressed in a parent-of-origin specific manner resulting in mono-allelic or strongly biased expression of one allele. For some genes, imprinted expression may be tissue-specific and reliant on CTCF-influenced enhancer-promoter interactions. The Peg13 imprinting cluster is associated with neurodevelopmental disorders and comprises canonical imprinted genes, which are conserved between mouse and human, as well as brain-specific imprinted genes in mouse. The latter consist of Trappc9, Chrac1 and Ago2, which have a maternal allelic expression bias of ∼75% in brain. Findings of such allelic expression biases on the tissue level raise the question of how they are reflected in individual cells and whether there is variability and mosaicism in allelic expression between individual cells of the tissue. Here we show that Trappc9 and Ago2 are not imprinted in hippocampus-derived neural stem cells (neurospheres), while Peg13 retains its strong bias of paternal allele expression. Upon analysis of single neural stem cells and in vitro differentiated neurons, we find not uniform, but variable states of allelic expression, especially for Trappc9 and Ago2. These ranged from mono-allelic paternal to equal bi-allelic to mono-allelic maternal, including biased bi-allelic transcriptional states. Even Peg13 expression deviated from its expected paternal allele bias in a small number of cells. Although the cell populations consisted of a mosaic of cells with different allelic expression states, as a whole they reflected bulk tissue data. Furthermore, in an attempt to identify potential brain-specific regulatory elements across the Trappc9 locus, we demonstrate tissue-specific and general silencer activities, which might contribute to the regulation of its imprinted expression bias.
Collapse
Affiliation(s)
- Michael Claxton
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Michela Pulix
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michelle K. Y. Seah
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ralph Bernardo
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Peng Zhou
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sultan Aljuraysi
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Department of Physiology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Triantafillos Liloglou
- Faculty of Health, Social Care and Medicine, Edge Hill University, Ormskirk, Lancashire, United Kingdom
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Cambridge, United Kingdom
| | - Daniel M. Messerschmidt
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Antonius Plagge
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
33
|
Wang M, Chen Z, Zhang Y. CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos. EMBO J 2022; 41:e112012. [PMID: 36215692 PMCID: PMC9670200 DOI: 10.15252/embj.2022112012] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 01/13/2023] Open
Abstract
Epigenome reprogramming after fertilization enables transcriptionally quiescent maternal and paternal chromatin to acquire a permissive state for subsequent zygotic genome activation (ZGA). H3K27 acetylation (H3K27ac) is a well-established chromatin marker of active enhancers and promoters. However, reprogramming dynamics of H3K27ac during maternal-to-zygotic transition (MZT) in mammalian embryos are not well-studied. By profiling the allelic landscape of H3K27ac during mouse MZT, we show that H3K27ac undergoes three waves of rapid global transitions between oocyte stage and 2-cell stage. Notably, germinal vesicle oocyte and zygote chromatin are globally hyperacetylated, with noncanonical, broad H3K27ac domains that correlate with broad H3K4 trimethylation (H3K4me3) and open chromatin. H3K27ac marks genomic regions primed for activation including ZGA genes, retrotransposons, and active alleles of imprinted genes. We show that CBP/p300 and HDAC activities play important roles in regulating H3K27ac dynamics and are essential for preimplantation development. Specifically, CBP/p300 acetyltransferase broadly deposits H3K27ac in zygotes to induce the opening of condensed chromatin at putative enhancers and ensure proper ZGA. On the contrary, HDACs revert broad H3K27ac domains to canonical domains and safeguard ZGA by preventing premature expression of developmental genes. In conclusion, coordinated activities of CBP/p300 and HDACs during mouse MZT are essential for ZGA and preimplantation development.
Collapse
Affiliation(s)
- Meng Wang
- Howard Hughes Medical InstituteBoston Children's HospitalBostonMAUSA,Program in Cellular and Molecular MedicineBoston Children's HospitalBostonMAUSA,Division of Hematology/Oncology, Department of PediatricsBoston Children's HospitalBostonMAUSA
| | - Zhiyuan Chen
- Howard Hughes Medical InstituteBoston Children's HospitalBostonMAUSA,Program in Cellular and Molecular MedicineBoston Children's HospitalBostonMAUSA,Division of Hematology/Oncology, Department of PediatricsBoston Children's HospitalBostonMAUSA
| | - Yi Zhang
- Howard Hughes Medical InstituteBoston Children's HospitalBostonMAUSA,Program in Cellular and Molecular MedicineBoston Children's HospitalBostonMAUSA,Division of Hematology/Oncology, Department of PediatricsBoston Children's HospitalBostonMAUSA,Department of GeneticsHarvard Medical SchoolBostonMAUSA,Harvard Stem Cell InstituteBostonMAUSA
| |
Collapse
|
34
|
Samara A, Spildrejorde M, Sharma A, Falck M, Leithaug M, Modafferi S, Bjørnstad PM, Acharya G, Gervin K, Lyle R, Eskeland R. A multi-omics approach to visualize early neuronal differentiation from hESCs in 4D. iScience 2022; 25:105279. [PMID: 36304110 PMCID: PMC9593815 DOI: 10.1016/j.isci.2022.105279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/22/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022] Open
Abstract
Neuronal differentiation of pluripotent stem cells is an established method to study physiology, disease, and medication safety. However, the sequence of events in human neuronal differentiation and the ability of in vitro models to recapitulate early brain development are poorly understood. We developed a protocol optimized for the study of early human brain development and neuropharmacological applications. We comprehensively characterized gene expression and epigenetic profiles at four timepoints, because the cells differentiate from embryonic stem cells towards a heterogeneous population of progenitors, immature and mature neurons bearing telencephalic signatures. A multi-omics roadmap of neuronal differentiation, combined with searchable interactive gene analysis tools, allows for extensive exploration of early neuronal development and the effect of medications. Multi-omics charting a new neuronal differentiation protocol for human ES cells Single-cell analyses reveal marker genes during neuronal differentiation Identified transcriptional waves similar to early human brain development Searchable tools to visualize single-cell gene expression and chromatin state
Collapse
Affiliation(s)
- Athina Samara
- Division of Clinical Paediatrics, Department of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden,Astrid Lindgren Children′s Hospital Karolinska University Hospital, Stockholm, Sweden,Corresponding author
| | - Mari Spildrejorde
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway,Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ankush Sharma
- Department of Informatics, University of Oslo, Oslo, Norway,Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway,Department of Biosciences, University of Oslo, Oslo, Norway
| | - Martin Falck
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway,Department of Biosciences, University of Oslo, Oslo, Norway
| | - Magnus Leithaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Stefania Modafferi
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Pål Marius Bjørnstad
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ganesh Acharya
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Alfred Nobels Allé 8, SE-14152 Stockholm, Sweden,Center for Fetal Medicine, Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
| | - Kristina Gervin
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway,Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, School of Pharmacy, University of Oslo, Oslo, Norway,Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, Oslo, Norway
| | - Robert Lyle
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway,Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway,Corresponding author
| | - Ragnhild Eskeland
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway,Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway,Corresponding author
| |
Collapse
|
35
|
Imprinting fidelity in mouse iPSCs depends on sex of donor cell and medium formulation. Nat Commun 2022; 13:5432. [PMID: 36114205 PMCID: PMC9481624 DOI: 10.1038/s41467-022-33013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Reprogramming of somatic cells into induced Pluripotent Stem Cells (iPSCs) is a major leap towards personalised approaches to disease modelling and cell-replacement therapies. However, we still lack the ability to fully control the epigenetic status of iPSCs, which is a major hurdle for their downstream applications. Epigenetic fidelity can be tracked by genomic imprinting, a phenomenon dependent on DNA methylation, which is frequently perturbed in iPSCs by yet unknown reasons. To try to understand the causes underlying these defects, we conducted a thorough imprinting analysis using IMPLICON, a high-throughput method measuring DNA methylation levels, in multiple female and male murine iPSC lines generated under different experimental conditions. Our results show that imprinting defects are remarkably common in iPSCs, but their nature depends on the sex of donor cells and their response to culture conditions. Imprints in female iPSCs resist the initial genome-wide DNA demethylation wave during reprogramming, but ultimately cells accumulate hypomethylation defects irrespective of culture medium formulations. In contrast, imprinting defects on male iPSCs depends on the experimental conditions and arise during reprogramming, being mitigated by the addition of vitamin C (VitC). Our findings are fundamental to further optimise reprogramming strategies and generate iPSCs with a stable epigenome. Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) is associated with epigenetic alterations. Here the authors assess DNA methylation in detail in multiple female and male mouse iPSC lines generated with different protocols and find that defects depend on the sex of donor cells and can be partially mitigated by Vitamin C.
Collapse
|
36
|
Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei MS, Vander Schaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. CELL GENOMICS 2022; 2:100144. [PMID: 35873672 PMCID: PMC9306256 DOI: 10.1016/j.xgen.2022.100144] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 05/20/2022] [Indexed: 05/21/2023]
Abstract
We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc Min/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.
Collapse
Affiliation(s)
- Wanding Zhou
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
| | - Toshinori Hinoue
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bret Barnes
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | - Owen Mitchell
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Waleed Iqbal
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kelly K. Foy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kwang-Ho Lee
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ethan J. Moyer
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra VanderArk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Julie M. Koeman
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Wubin Ding
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Manpreet Kalkat
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Nathan J. Spix
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bryn Eagleson
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Liang Kang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Peter A. Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Connie M. Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Rishi Porecha
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | | | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
| |
Collapse
|
37
|
Akbari V, Garant JM, O'Neill K, Pandoh P, Moore R, Marra MA, Hirst M, Jones SJM. Genome-wide detection of imprinted differentially methylated regions using nanopore sequencing. eLife 2022; 11:77898. [PMID: 35787786 PMCID: PMC9255983 DOI: 10.7554/elife.77898] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/16/2022] [Indexed: 01/02/2023] Open
Abstract
Imprinting is a critical part of normal embryonic development in mammals, controlled by defined parent-of-origin (PofO) differentially methylated regions (DMRs) known as imprinting control regions. Direct nanopore sequencing of DNA provides a means to detect allelic methylation and to overcome the drawbacks of methylation array and short-read technologies. Here, we used publicly available nanopore sequencing data for 12 standard B-lymphocyte cell lines to acquire the genome-wide mapping of imprinted intervals in humans. Using the sequencing data, we were able to phase 95% of the human methylome and detect 94% of the previously well-characterized, imprinted DMRs. In addition, we found 42 novel imprinted DMRs (16 germline and 26 somatic), which were confirmed using whole-genome bisulfite sequencing (WGBS) data. Analysis of WGBS data in mouse (Mus musculus), rhesus monkey (Macaca mulatta), and chimpanzee (Pan troglodytes) suggested that 17 of these imprinted DMRs are conserved. Some of the novel imprinted intervals are within or close to imprinted genes without a known DMR. We also detected subtle parental methylation bias, spanning several kilobases at seven known imprinted clusters. At these blocks, hypermethylation occurs at the gene body of expressed allele(s) with mutually exclusive H3K36me3 and H3K27me3 allelic histone marks. These results expand upon our current knowledge of imprinting and the potential of nanopore sequencing to identify imprinting regions using only parent-offspring trios, as opposed to the large multi-generational pedigrees that have previously been required.
Collapse
Affiliation(s)
- Vahid Akbari
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jean-Michel Garant
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| |
Collapse
|
38
|
Fang J, Jiang J, Leichter SM, Liu J, Biswal M, Khudaverdyan N, Zhong X, Song J. Mechanistic basis for maintenance of CHG DNA methylation in plants. Nat Commun 2022; 13:3877. [PMID: 35790763 PMCID: PMC9256654 DOI: 10.1038/s41467-022-31627-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 06/26/2022] [Indexed: 11/08/2022] Open
Abstract
DNA methylation is an evolutionarily conserved epigenetic mechanism essential for transposon silencing and heterochromatin assembly. In plants, DNA methylation widely occurs in the CG, CHG, and CHH (H = A, C, or T) contexts, with the maintenance of CHG methylation mediated by CMT3 chromomethylase. However, how CMT3 interacts with the chromatin environment for faithful maintenance of CHG methylation is unclear. Here we report structure-function characterization of the H3K9me2-directed maintenance of CHG methylation by CMT3 and its Zea mays ortholog ZMET2. Base-specific interactions and DNA deformation coordinately underpin the substrate specificity of CMT3 and ZMET2, while a bivalent readout of H3K9me2 and H3K18 allosterically stimulates substrate binding. Disruption of the interaction with DNA or H3K9me2/H3K18 led to loss of CMT3/ZMET2 activity in vitro and impairment of genome-wide CHG methylation in vivo. Together, our study uncovers how the intricate interplay of CMT3, repressive histone marks, and DNA sequence mediates heterochromatic CHG methylation.
Collapse
Affiliation(s)
- Jian Fang
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Jianjun Jiang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Sarah M Leichter
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Jie Liu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Mahamaya Biswal
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Nelli Khudaverdyan
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA.
| |
Collapse
|
39
|
Small regulatory RNAs in rice epigenetic regulation. Biochem Soc Trans 2022; 50:1215-1225. [PMID: 35579290 DOI: 10.1042/bst20210336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/17/2022]
Abstract
Plant small RNAs (sRNAs) are short non-coding RNAs that are implicated in various regulatory processes involving post-transcriptional gene silencing and epigenetic gene regulation. In epigenetic regulation, sRNAs are primarily involved in RNA-directed DNA methylation (RdDM) pathways. sRNAs in the RdDM pathways play a role not only in the suppression of transposable element (TE) activity but also in gene expression regulation. Although the major components of the RdDM pathways have been well studied in Arabidopsis, recent studies have revealed that the RdDM pathways in rice have important biological functions in stress response and developmental processes. In this review, we summarize and discuss recent literature on sRNA-mediated epigenetic regulation in rice. First, we describe the RdDM mechanisms in plants. We then introduce recent discoveries on the biological roles of rice genes involved in the RdDM pathway and TE-derived sRNAs working at specific genomic loci for epigenetic control in rice.
Collapse
|
40
|
Yang H, Bai D, Li Y, Yu Z, Wang C, Sheng Y, Liu W, Gao S, Zhang Y. Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo. Nat Cell Biol 2022; 24:783-792. [PMID: 35484247 DOI: 10.1038/s41556-022-00900-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 03/16/2022] [Indexed: 12/13/2022]
Abstract
Parental DNA methylation and histone modifications undergo distinct global reprogramming in mammalian pre-implantation embryos, but the landscape of epigenetic crosstalk and its effects on embryogenesis are largely unknown. Here we comprehensively analyse the association between DNA methylation and H3K9me3 reprogramming in mouse pre-implantation embryos and reveal that CpG-rich genomic loci with high H3K9me3 signal and DNA methylation level (CHM) are hotspots of DNA methylation maintenance during pre-implantation embryogenesis. We further profile the allele-specific epigenetic map with unprecedented resolution in gynogenetic and androgenetic embryos, respectively, and identify 1,279 allele-specific CHMs, including 19 known imprinting control regions (ICRs). Our study suggests that 22 ICR-like regions (ICRLRs) may regulate allele-specific transcription similarly to known ICRs, and five of them are confirmed to be important for mouse embryo development. Taken together, our study reveals the widespread existence of allele-specific CHMs and largely extends the scope of allele-specific regulation in mammalian pre-implantation embryos.
Collapse
Affiliation(s)
- Hui Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Dandan Bai
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Yanhe Li
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Zhaowei Yu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Chenfei Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yifan Sheng
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Wenqiang Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. .,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China. .,Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. .,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China. .,Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. .,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China.
| |
Collapse
|
41
|
Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation. Cell Res 2022; 32:801-813. [PMID: 35428874 PMCID: PMC9437020 DOI: 10.1038/s41422-022-00652-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/10/2022] [Indexed: 12/13/2022] Open
Abstract
AbstractChromatin remodeling is essential for epigenome reprogramming after fertilization. However, the underlying mechanisms of chromatin remodeling remain to be explored. Here, we investigated the dynamic changes in nucleosome occupancy and positioning in pronucleus-stage zygotes using ultra low-input MNase-seq. We observed distinct features of inheritance and reconstruction of nucleosome positioning in both paternal and maternal genomes. Genome-wide de novo nucleosome occupancy in the paternal genome was observed as early as 1 h after the injection of sperm into ooplasm. The nucleosome positioning pattern was continually rebuilt to form nucleosome-depleted regions (NDRs) at promoters and transcription factor (TF) binding sites with differential dynamics in paternal and maternal genomes. NDRs formed more quickly on the promoters of genes involved in zygotic genome activation (ZGA), and this formation is closely linked to histone acetylation, but not transcription elongation or DNA replication. Importantly, we found that NDR establishment on the binding motifs of specific TFs might be associated with their potential pioneer functions in ZGA. Further investigations suggested that the predicted factors MLX and RFX1 played important roles in regulating minor and major ZGA, respectively. Our data not only elucidate the nucleosome positioning dynamics in both male and female pronuclei following fertilization, but also provide an efficient method for identifying key transcription regulators during development.
Collapse
|
42
|
Mattei AL, Bailly N, Meissner A. DNA methylation: a historical perspective. Trends Genet 2022; 38:676-707. [DOI: 10.1016/j.tig.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
|
43
|
Shi C, Zhang J, Yan Z, Gao L, Gao C, Wu W, Liu J, Cui Y. Epigenetic effect of putrescine supplementation during in vitro maturation of oocytes on offspring in mice. J Assist Reprod Genet 2022; 39:681-694. [PMID: 35254568 PMCID: PMC8995222 DOI: 10.1007/s10815-022-02448-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/25/2022] [Indexed: 01/12/2023] Open
Abstract
PURPOSE To investigate the epigenetic safety of putrescine supplementation during in vitro maturation (IVM) to offspring. METHODS Germinal vesicle oocytes retrieved from 12-week-old mice were randomly divided into two groups and cultured in IVM medium with or without 1 mmol/L putrescine for 16 h. Then, in vitro fertilization and embryo transplantation were conducted to produce the F1 offspring. The F1 mated with ordinary mice and bred the F2 offspring. The DNA methylation patterns in the brain and heart of F1 were investigated by reduced representation bisulfite sequencing. Imprinted gene expression levels of F1 oocytes were tested. The global methylation of F2 was examined by dot blot. RESULTS The weight, organ coefficient, and histology were normal in the F1 and F2 offspring from the putrescine-treated oocytes. An overall methylation level of 31.23 to 32.53% was observed for all CpG sites in the brain and heart of the two groups. The DNA methylation patterns of the brain and heart in F1 were not altered in general, with subtle differences. The expression levels of imprinted genes including H19, Snrpn, Peg3, Igf2, and Igf2r did not statistically change. The global 5mC level of F2 was consistent with the control group. CONCLUSION Putrescine supplementation during IVM did not directly affect the development, health, and reproduction, and did not affect the genome and global epigenetics of mouse offspring derived from those oocytes. The transient putrescine treatment for improving oocyte maturation shows its long-term safety of genome and epigenetics in the offspring of mice.
Collapse
Affiliation(s)
- Chennan Shi
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Jingyi Zhang
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Zhengjie Yan
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Li Gao
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Chao Gao
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Wei Wu
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Jiayin Liu
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
| | - Yugui Cui
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China.
| |
Collapse
|
44
|
Romano R, Cillo F, Moracas C, Pignata L, Nannola C, Toriello E, De Rosa A, Cirillo E, Coppola E, Giardino G, Brunetti-Pierri N, Riccio A, Pignata C. Epigenetic Alterations in Inborn Errors of Immunity. J Clin Med 2022; 11:jcm11051261. [PMID: 35268351 PMCID: PMC8910960 DOI: 10.3390/jcm11051261] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 02/07/2023] Open
Abstract
The epigenome bridges environmental factors and the genome, fine-tuning the process of gene transcription. Physiological programs, including the development, maturation and maintenance of cellular identity and function, are modulated by intricate epigenetic changes that encompass DNA methylation, chromatin remodeling, histone modifications and RNA processing. The collection of genome-wide DNA methylation data has recently shed new light into the potential contribution of epigenetics in pathophysiology, particularly in the field of immune system and host defense. The study of patients carrying mutations in genes encoding for molecules involved in the epigenetic machinery has allowed the identification and better characterization of environment-genome interactions via epigenetics as well as paving the way for the development of new potential therapeutic options. In this review, we summarize current knowledge of the role of epigenetic modifications in the immune system and outline their potential involvement in the pathogenesis of inborn errors of immunity.
Collapse
Affiliation(s)
- Roberta Romano
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Francesca Cillo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Cristina Moracas
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Chiara Nannola
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Elisabetta Toriello
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Antonio De Rosa
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Emilia Cirillo
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Emma Coppola
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Giuliana Giardino
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Nicola Brunetti-Pierri
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
- Correspondence: (A.R.); (C.P.)
| | - Claudio Pignata
- Department of Translational Medical Sciences, Università degli Studi di Napoli “Federico II”, 80125 Naples, Italy; (R.R.); (F.C.); (C.M.); (C.N.); (E.T.); (A.D.R.); (E.C.); (E.C.); (G.G.); (N.B.-P.)
- Correspondence: (A.R.); (C.P.)
| |
Collapse
|
45
|
Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation Methods. Genes (Basel) 2022; 13:genes13020306. [PMID: 35205351 PMCID: PMC8872013 DOI: 10.3390/genes13020306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
DNA methylation plays essential roles in various cellular processes. Next-generation sequencing has enabled us to study the functional implication of DNA methylation across the whole genome. However, this approach usually requires a substantial amount of genomic DNA, which limits its application to defined cell types within a discrete brain region. Here, we applied two separate protocols, Accel-NGS Methyl-Seq (AM-seq) and Enzymatic Methyl-seq (EM-seq), to profile the methylome of D2 dopamine receptor-expressing medium spiny neurons (D2-MSNs) in mouse nucleus accumbens (NAc). Using 40 ng DNA extracted from FACS-isolated D2-MSNs, we found that both methods yielded comparably high-quality methylome data. Additionally, we identified numerous unmethylated regions (UMRs) as cell type-specific regulatory regions. By comparing the NAc D2-MSN methylome with the published methylomes of mouse prefrontal cortex excitatory neurons and neural progenitor cells (NPCs), we identified numerous differentially methylated CpG and non-CpG regions. Our study not only presents a comparison of these two low-input DNA whole genome methylation profiling protocols, but also provides a resource of DNA methylome of mouse accumbal D2-MSNs, a neuron type that has critical roles in addiction and other neuropsychiatric disorders.
Collapse
|
46
|
Kaplan G, Xu H, Abreu K, Feng J. DNA Epigenetics in Addiction Susceptibility. Front Genet 2022; 13:806685. [PMID: 35145550 PMCID: PMC8821887 DOI: 10.3389/fgene.2022.806685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
Addiction is a chronically relapsing neuropsychiatric disease that occurs in some, but not all, individuals who use substances of abuse. Relatively little is known about the mechanisms which contribute to individual differences in susceptibility to addiction. Neural gene expression regulation underlies the pathogenesis of addiction, which is mediated by epigenetic mechanisms, such as DNA modifications. A growing body of work has demonstrated distinct DNA epigenetic signatures in brain reward regions that may be associated with addiction susceptibility. Furthermore, factors that influence addiction susceptibility are also known to have a DNA epigenetic basis. In the present review, we discuss the notion that addiction susceptibility has an underlying DNA epigenetic basis. We focus on major phenotypes of addiction susceptibility and review evidence of cell type-specific, time dependent, and sex biased effects of drug use. We highlight the role of DNA epigenetics in these diverse processes and propose its contribution to addiction susceptibility differences. Given the prevalence and lack of effective treatments for addiction, elucidating the DNA epigenetic mechanism of addiction vulnerability may represent an expeditious approach to relieving the addiction disease burden.
Collapse
|
47
|
Glaser J, Iranzo J, Borensztein M, Marinucci M, Gualtieri A, Jouhanneau C, Teissandier A, Gaston-Massuet C, Bourc'his D. The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates. eLife 2022; 11:65641. [PMID: 35049495 PMCID: PMC8809892 DOI: 10.7554/elife.65641] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
Genomic imprinting refers to the mono-allelic and parent-specific expression of a subset of genes. While long recognized for their role in embryonic development, imprinted genes have recently emerged as important modulators of postnatal physiology, notably through hypothalamus-driven functions. Here, using mouse models of loss, gain and parental inversion of expression, we report that the paternally expressed Zdbf2 gene controls neonatal growth in mice, in a dose-sensitive but parent-of-origin-independent manner. We further found that Zdbf2-KO neonates failed to fully activate hypothalamic circuits that stimulate appetite, and suffered milk deprivation and diminished circulating Insulin Growth Factor 1 (IGF-1). Consequently, only half of Zdbf2-KO pups survived the first days after birth and those surviving were smaller. This study demonstrates that precise imprinted gene dosage is essential for vital physiological functions at the transition from intra- to extra-uterine life, here the adaptation to oral feeding and optimized body weight gain.
Collapse
Affiliation(s)
- Juliane Glaser
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Julian Iranzo
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Maud Borensztein
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Mattia Marinucci
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Angelica Gualtieri
- Centre for Endocrinology, Queen Mary University of London, London, United Kingdom
| | | | - Aurélie Teissandier
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | | | - Deborah Bourc'his
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| |
Collapse
|
48
|
Fanis P, Morrou M, Tomazou M, Michailidou K, Spyrou GM, Toumba M, Skordis N, Neocleous V, Phylactou LA. Methylation status of hypothalamic Mkrn3 promoter across puberty. Front Endocrinol (Lausanne) 2022; 13:1075341. [PMID: 36714607 PMCID: PMC9880154 DOI: 10.3389/fendo.2022.1075341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
Makorin RING finger protein 3 (MKRN3) is an important factor located on chromosome 15 in the imprinting region associated with Prader-Willi syndrome. Imprinted MKRN3 is expressed in hypothalamic regions essential for the onset of puberty and mutations in the gene have been found in patients with central precocious puberty. The pubertal process is largely controlled by epigenetic mechanisms that include, among other things, DNA methylation at CpG dinucleotides of puberty-related genes. In the present study, we investigated the methylation status of the Mkrn3 promoter in the hypothalamus of the female mouse before, during and after puberty. Initially, we mapped the 32 CpG dinucleotides in the promoter, the 5'UTR and the first 50 nucleotides of the coding region of the Mkrn3 gene. Moreover, we identified a short CpG island region (CpG islet) located within the promoter. Methylation analysis using bisulfite sequencing revealed that CpG dinucleotides were methylated regardless of developmental stage, with the lowest levels of methylation being found within the CpG islet region. In addition, the CpG islet region showed significantly lower methylation levels at the pre-pubertal stage when compared with the pubertal or post-pubertal stage. Finally, in silico analysis of transcription factor binding sites on the Mkrn3 CpG islet identified the recruitment of 29 transcriptional regulators of which 14 were transcriptional repressors. Our findings demonstrate the characterization and differential methylation of the CpG dinucleotides located in the Mkrn3 promoter that could influence the transcriptional activity in pre-pubertal compared to pubertal or post-pubertal period. Further studies are needed to clarify the possible mechanisms and effects of differential methylation of the Mkrn3 promoter.
Collapse
Affiliation(s)
- Pavlos Fanis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Maria Morrou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios Tomazou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M. Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Meropi Toumba
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Child Endocrine Care, Department of Pediatrics, Aretaeio Hospital, Nicosia, Cyprus
| | - Nicos Skordis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Division of Pediatric Endocrinology, Paedi Center for Specialized Pediatrics, Nicosia, Cyprus
- Medical School, University of Nicosia, Nicosia, Cyprus
| | - Vassos Neocleous
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Leonidas A. Phylactou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- *Correspondence: Leonidas A. Phylactou,
| |
Collapse
|
49
|
Collins BE, Neul JL. Rett Syndrome and MECP2 Duplication Syndrome: Disorders of MeCP2 Dosage. Neuropsychiatr Dis Treat 2022; 18:2813-2835. [PMID: 36471747 PMCID: PMC9719276 DOI: 10.2147/ndt.s371483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
Rett syndrome (RTT) is a neurodevelopmental disorder caused predominantly by loss-of-function mutations in the gene Methyl-CpG-binding protein 2 (MECP2), which encodes the MeCP2 protein. RTT is a MECP2-related disorder, along with MECP2 duplication syndrome (MDS), caused by gain-of-function duplications of MECP2. Nearly two decades of research have advanced our knowledge of MeCP2 function in health and disease. The following review will discuss MeCP2 protein function and its dysregulation in the MECP2-related disorders RTT and MDS. This will include a discussion of the genetic underpinnings of these disorders, specifically how sporadic X-chromosome mutations arise and manifest in specific populations. We will then review current diagnostic guidelines and clinical manifestations of RTT and MDS. Next, we will delve into MeCP2 biology, describing the dual landscapes of methylated DNA and its reader MeCP2 across the neuronal genome as well as the function of MeCP2 as a transcriptional modulator. Following this, we will outline common MECP2 mutations and genotype-phenotype correlations in both diseases, with particular focus on mutations associated with relatively mild disease in RTT. We will also summarize decades of disease modeling and resulting molecular, synaptic, and behavioral phenotypes associated with RTT and MDS. Finally, we list several therapeutics in the development pipeline for RTT and MDS and available evidence of their safety and efficacy.
Collapse
Affiliation(s)
- Bridget E Collins
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Jeffrey L Neul
- Vanderbilt Kennedy Center, Departments of Pediatrics, Pharmacology, and Special Education, Vanderbilt University Medical Center and Vanderbilt University, Nashville, TN, USA
| |
Collapse
|
50
|
Structure and Function of TET Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:239-267. [DOI: 10.1007/978-3-031-11454-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|