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Kubo N, Uehara R, Uemura S, Ohishi H, Shirane K, Sasaki H. Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells. Nat Commun 2024; 15:3266. [PMID: 38627502 PMCID: PMC11021467 DOI: 10.1038/s41467-024-47699-2] [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: 09/15/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
DNA methyltransferase 3A (DNMT3A) and its catalytically inactive cofactor DNA methyltransferase 3-Like (DNMT3L) proteins form functional heterotetramers to deposit DNA methylation in mammalian germ cells. While both proteins have an ATRX-DNMT3-DNMT3L (ADD) domain that recognizes histone H3 tail unmethylated at lysine-4 (H3K4me0), the combined and differential roles of the domains in the two proteins have not been fully defined in vivo. Here we investigate DNA methylation landscapes in female and male germ cells derived from mice with loss-of-function amino acid substitutions in the ADD domains of DNMT3A and/or DNMT3L. Mutations in either the DNMT3A-ADD or the DNMT3L-ADD domain moderately decrease global CG methylation levels, but to different degrees, in both germ cells. Furthermore, when the ADD domains of both DNMT3A and DNMT3L lose their functions, the CG methylation levels are much more reduced, especially in oocytes, comparable to the impact of the Dnmt3a/3L knockout. In contrast, aberrant accumulation of non-CG methylation occurs at thousands of genomic regions in the double mutant oocytes and spermatozoa. These results highlight the critical role of the ADD-H3K4me0 binding in proper CG and non-CG methylation in germ cells and the various impacts of the ADD domains of the two proteins.
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Affiliation(s)
- Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Ryuji Uehara
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shuhei Uemura
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Hiroaki Ohishi
- Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenjiro Shirane
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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Tibben BM, Rothbart SB. Mechanisms of DNA Methylation Regulatory Function and Crosstalk with Histone Lysine Methylation. J Mol Biol 2024; 436:168394. [PMID: 38092287 PMCID: PMC10957332 DOI: 10.1016/j.jmb.2023.168394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
DNA methylation is a well-studied epigenetic modification that has key roles in regulating gene expression, maintaining genome integrity, and determining cell fate. Precisely how DNA methylation patterns are established and maintained in specific cell types at key developmental stages is still being elucidated. However, research over the last two decades has contributed to our understanding of DNA methylation regulation by other epigenetic processes. Specifically, lysine methylation on key residues of histone proteins has been shown to contribute to the allosteric regulation of DNA methyltransferase (DNMT) activities. In this review, we discuss the dynamic interplay between DNA methylation and histone lysine methylation as epigenetic regulators of genome function by synthesizing key recent studies in the field. With a focus on DNMT3 enzymes, we discuss mechanisms of DNA methylation and histone lysine methylation crosstalk in the regulation of gene expression and the maintenance of genome integrity. Further, we discuss how alterations to the balance of various sites of histone lysine methylation and DNA methylation contribute to human developmental disorders and cancers. Finally, we provide perspectives on the current direction of the field and highlight areas for continued research and development.
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Affiliation(s)
- Bailey M Tibben
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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Yu M, Zhang X, Yan J, Guo J, Zhang F, Zhu K, Liu S, Sun Y, Shen W, Wang J. Transcriptional Specificity Analysis of Testis and Epididymis Tissues in Donkey. Genes (Basel) 2022; 13:genes13122339. [PMID: 36553607 PMCID: PMC9777602 DOI: 10.3390/genes13122339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Donkeys, with high economic value for meat, skin and milk production, are important livestock. However, the current insights into reproduction of donkeys are far from enough. To obtain a deeper understanding, the differential expression analysis and weighted gene co-expression network analysis (WGCNA) of transcriptomic data of testicular and epididymis tissues in donkeys were performed. In the result, there were 4313 differentially expressed genes (DEGs) in the two tissues, including 2047 enriched in testicular tissue and 2266 in epididymis tissue. WGCNA identified 1081 hub genes associated with testis development and 6110 genes with epididymal development. Next, the tissue-specific genes were identified with the above two methods, and the gene ontology (GO) analysis revealed that the epididymal-specific genes were associated with gonad development. On the other hand, the testis-specific genes were involved in the formation of sperm flagella, meiosis period, ciliary assembly, ciliary movement, etc. In addition, we found that eca-Mir-711 and eca-Mir-143 likely participated in regulating the development of epididymal tissue. Meanwhile, eca-Mir-429, eca-Mir-761, eca-Mir-200a, eca-Mir-191 and eca-Mir-200b potentially played an important role in regulating the development of testicular tissue. In short, these results will contribute to functional studies of the male reproductive trait in donkeys.
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Affiliation(s)
- Mubin Yu
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyuan Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jiamao Yan
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jianhua Guo
- Jiaozhou Agricultural and Rural Bureau, Jiaozhou 266300, China
| | - Fali Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Kexin Zhu
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Wei Shen
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao 266109, China
- Correspondence: (W.S.); (J.W.)
| | - Junjie Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
- Correspondence: (W.S.); (J.W.)
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Luo H, Mipam T, Wu S, Xu C, Yi C, Zhao W, Chai Z, Chen X, Wu Z, Wang J, Wang J, Wang H, Zhong J, Cai X. DNA methylome of primary spermatocyte reveals epigenetic dysregulation associated with male sterility of cattleyak. Theriogenology 2022; 191:153-167. [PMID: 35988507 DOI: 10.1016/j.theriogenology.2022.08.016] [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: 10/01/2021] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 10/15/2022]
Abstract
DNA cytosine methylation modification in the germline is of particular importance since it is a highly heritable epigenetic mark. Although cytosine methylation has been analyzed at the genome-scale for several mammalian species, our knowledge of DNA methylation patterns and the mechanisms underlying male hybrid sterility is still limited in domestic animals such as cattleyak. Here we for the first time show the genome-wide and single-base resolution landscape of methylcytosines (mC) in the primary spermatocyte (PSC) genome of yak with normal spermatogenesis and the inter-specific hybrid cattleyak with male infertility. A comparative investigation revealed that widespread differences are observed in the composition and patterning of DNA cytosine methylation between the two methylomes. Global CG or non-CG DNA methylation levels, as well as the number of mC sites, are increased in cattleyak compared to yak. Notably, the DNA methylome in cattleyak PSC exhibits promoter hypermethylation of meiosis-specific genes and piRNA pathway genes with respect to yak. Furthermore, major retrotransposonson classes are predominantly hypermethylated in cattleyak while those are fully hypomethylated in yak. KEGG pathway enrichment indicates Rap1 signaling and MAPK pathways may play potential roles in the spermatogenic arrest of cattleyak. Our present study not only provides valuable insights into distinct features of the cattleyak PSC methylome but also paves the way toward elucidating the complex, yet highly coordinated epigenetic modification during male germline development for inter-specific hybrid animals.
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Affiliation(s)
- Hui Luo
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - TserangDonko Mipam
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - Shixin Wu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - Chuanfei Xu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - Chuanping Yi
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - Wangsheng Zhao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - Xuemei Chen
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - Zhijuan Wu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China.
| | - Xin Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China.
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Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:111-136. [PMID: 36350508 PMCID: PMC9815518 DOI: 10.1007/978-3-031-11454-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cytosine methylation at the C5-position-generating 5-methylcytosine (5mC)-is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80%) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation and genetic alterations in enzymes and regulators involved in DNA methylation are associated with various human diseases, including cancer and developmental disorders. In mammals, DNA methylation is mediated by two families of DNA methyltransferases (Dnmts), namely Dnmt1 and Dnmt3 proteins. Over the last three decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and human diseases.
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Transposable Element Dynamics and Regulation during Zygotic Genome Activation in Mammalian Embryos and Embryonic Stem Cell Model Systems. Stem Cells Int 2021; 2021:1624669. [PMID: 34691189 PMCID: PMC8536462 DOI: 10.1155/2021/1624669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic sequences capable of duplicating and reintegrating at new regions within the genome. A growing body of evidence has demonstrated that these elements play important roles in host genome evolution, despite being traditionally viewed as parasitic elements. To prevent ectopic activation of TE transposition and transcription, they are epigenetically silenced in most somatic tissues. Intriguingly, a specific class of TEs-retrotransposons-is transiently expressed at discrete phases during mammalian development and has been linked to the establishment of totipotency during zygotic genome activation (ZGA). While mechanisms controlling TE regulation in somatic tissues have been extensively studied, the significance underlying the unique transcriptional reactivation of retrotransposons during ZGA is only beginning to be uncovered. In this review, we summarize the expression dynamics of key retrotransposons during ZGA, focusing on findings from in vivo totipotent embryos and in vitro totipotent-like embryonic stem cells (ESCs). We then dissect the functions of retrotransposons and discuss how their transcriptional activities are finetuned during early stages of mammalian development.
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Li Y, Chen X, Lu C. The interplay between DNA and histone methylation: molecular mechanisms and disease implications. EMBO Rep 2021; 22:e51803. [PMID: 33844406 PMCID: PMC8097341 DOI: 10.15252/embr.202051803] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Methylation of cytosine in CpG dinucleotides and histone lysine and arginine residues is a chromatin modification that critically contributes to the regulation of genome integrity, replication, and accessibility. A strong correlation exists between the genome-wide distribution of DNA and histone methylation, suggesting an intimate relationship between these epigenetic marks. Indeed, accumulating literature reveals complex mechanisms underlying the molecular crosstalk between DNA and histone methylation. These in vitro and in vivo discoveries are further supported by the finding that genes encoding DNA- and histone-modifying enzymes are often mutated in overlapping human diseases. Here, we summarize recent advances in understanding how DNA and histone methylation cooperate to maintain the cellular epigenomic landscape. We will also discuss the potential implication of these insights for understanding the etiology of, and developing biomarkers and therapies for, human congenital disorders and cancers that are driven by chromatin abnormalities.
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Affiliation(s)
- Yinglu Li
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Xiao Chen
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
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Sanusi KO, Ibrahim KG, Abubakar B, Malami I, Bello MB, Imam MU, Abubakar MB. Effect of maternal zinc deficiency on offspring health: The epigenetic impact. J Trace Elem Med Biol 2021; 65:126731. [PMID: 33610057 DOI: 10.1016/j.jtemb.2021.126731] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Zinc deficiency is associated with adverse effects on maternal health and pregnancy outcomes. These consequences have been reported over the years from zinc supplementation trials and observational studies whereby outcomes of maternal, foetal and infant health were measured. Owing to the importance of zinc in the functions of epigenetic enzymes, pre-clinical studies have shown that its deficiency could disrupt biological activities that involve epigenetic mechanisms in offspring. Thus, this review assessed the link between epigenetics and the effects of maternal zinc deficiency on the offspring's health in animal studies. METHODS Research articles were retrieved without date restriction from PubMed, Web of Science, ScienceDirect, and Google Scholar databases, as well as reference lists of relevant articles. The search terms used were "zinc deficiency", "maternal zinc deficiency", "epigenetics", and "offspring." Six studies met the eligibility criteria and were reviewed. RESULTS All the eligible studies reported maternal zinc deficiency and observed changes in epigenetic markers on the progeny during prenatal and postnatal stages of development. The main epigenetic markers reported were global and gene specific methylation and/ or acetylation. The epigenetic changes led to mortality, disruption in development, and risk of later life diseases. CONCLUSION Maternal zinc deficiency is associated with epigenetic modifications in offspring, which induce pathologies and increase the risk of later life diseases. More research and insight into the epigenetic mechanisms could spring up new approaches to combat the associated disease conditions.
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Affiliation(s)
- Kamaldeen Olalekan Sanusi
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria; Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria.
| | - Kasimu Ghandi Ibrahim
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria; Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria.
| | - Bilyaminu Abubakar
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria; Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria.
| | - Ibrahim Malami
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria; Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria.
| | - Muhammad Bashir Bello
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria; Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria.
| | - Mustapha Umar Imam
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria; Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria.
| | - Murtala Bello Abubakar
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria; Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University PMB, 2254, Sokoto, Nigeria.
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Yusuf AP, Abubakar MB, Malami I, Ibrahim KG, Abubakar B, Bello MB, Qusty N, Elazab ST, Imam MU, Alexiou A, Batiha GES. Zinc Metalloproteins in Epigenetics and Their Crosstalk. Life (Basel) 2021; 11:life11030186. [PMID: 33652690 PMCID: PMC7996840 DOI: 10.3390/life11030186] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
More than half a century ago, zinc was established as an essential micronutrient for normal human physiology. In silico data suggest that about 10% of the human proteome potentially binds zinc. Many proteins with zinc-binding domains (ZBDs) are involved in epigenetic modifications such as DNA methylation and histone modifications, which regulate transcription in physiological and pathological conditions. Zinc metalloproteins in epigenetics are mainly zinc metalloenzymes and zinc finger proteins (ZFPs), which are classified into writers, erasers, readers, editors, and feeders. Altogether, these classes of proteins engage in crosstalk that fundamentally maintains the epigenome's modus operandi. Changes in the expression or function of these proteins induced by zinc deficiency or loss of function mutations in their ZBDs may lead to aberrant epigenetic reprogramming, which may worsen the risk of non-communicable chronic diseases. This review attempts to address zinc's role and its proteins in natural epigenetic programming and artificial reprogramming and briefly discusses how the ZBDs in these proteins interact with the chromatin.
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Affiliation(s)
- Abdurrahman Pharmacy Yusuf
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
| | - Murtala Bello Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
- Correspondence: (M.B.A.); (A.A.); (G.E.-S.B.)
| | - Ibrahim Malami
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Kasimu Ghandi Ibrahim
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Bilyaminu Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria
| | - Naeem Qusty
- Medical Laboratories Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Mecca 21955, Saudi Arabia;
| | - Sara T. Elazab
- Department of Pharmacology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Dakahlia 35516, Egypt;
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346 Sokoto, Nigeria; (A.P.Y.); (I.M.); (K.G.I.); (B.A.); (M.U.I.)
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254 Sokoto, Nigeria
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
- AFNP Med, Haidingergasse 29, 1030 Vienna, Austria
- Correspondence: (M.B.A.); (A.A.); (G.E.-S.B.)
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, AlBeheira 22511, Egypt
- Correspondence: (M.B.A.); (A.A.); (G.E.-S.B.)
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Extensive sex differences at the initiation of genetic recombination. Nature 2018; 561:338-342. [PMID: 30185906 PMCID: PMC6364566 DOI: 10.1038/s41586-018-0492-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 07/18/2018] [Indexed: 12/28/2022]
Abstract
Meiotic recombination differs between males and females; however, when and how these differences are established is unknown. Here we identify extensive sex differences at recombination initiation by mapping hotspots of meiotic DNA double-strand breaks in male and female mice. Contrary to past findings in humans, few hotspots are used uniquely in either sex. Instead, grossly different recombination landscapes result from up to 15-fold differences in hotspot usage between males and females. Indeed, most recombination occurs at sex-biased hotspots. Sex-biased hotspots appear to be partly determined by chromosome structure, and DNA methylation, absent in females at the onset of meiosis, plays a substantial role. Sex differences are also evident later in meiosis as the repair frequency of distal meiotic breaks as crossovers diverges in males and females. Suppression of distal crossovers may help to minimize age-related aneuploidy that arises due to cohesion loss during dictyate arrest in females.
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11
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Zhu Q, Stöger R, Alberio R. A Lexicon of DNA Modifications: Their Roles in Embryo Development and the Germline. Front Cell Dev Biol 2018; 6:24. [PMID: 29637072 PMCID: PMC5880922 DOI: 10.3389/fcell.2018.00024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/27/2018] [Indexed: 12/12/2022] Open
Abstract
5-methylcytosine (5mC) on CpG dinucleotides has been viewed as the major epigenetic modification in eukaryotes for a long time. Apart from 5mC, additional DNA modifications have been discovered in eukaryotic genomes. Many of these modifications are thought to be solely associated with DNA damage. However, growing evidence indicates that some base modifications, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxylcytosine (5caC), and N6-methadenine (6mA), may be of biological relevance, particularly during early stages of embryo development. Although abundance of these DNA modifications in eukaryotic genomes can be low, there are suggestions that they cooperate with other epigenetic markers to affect DNA-protein interactions, gene expression, defense of genome stability and epigenetic inheritance. Little is still known about their distribution in different tissues and their functions during key stages of the animal lifecycle. This review discusses current knowledge and future perspectives of these novel DNA modifications in the mammalian genome with a focus on their dynamic distribution during early embryonic development and their potential function in epigenetic inheritance through the germ line.
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Affiliation(s)
- Qifan Zhu
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
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12
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Li Y, Li YH, Zhou X, Wu B, Chen JP, Wang ZK, Wang X, Shi HJ, Li RS. DNA hydroxymethylation rate in the AChE and HoxC4 promoter associated with human sperm quality. Andrologia 2018; 50:e12963. [PMID: 29430663 DOI: 10.1111/and.12963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2018] [Indexed: 12/23/2022] Open
Abstract
The relationship of altered DNA 5'-hydroxymethylation in human spermatozoa with seminal parameters remains unclear. The aim of the study was to investigate the association between the 5'-hydroxymethylcytosine (5hmC) rate in the promoters of acetylcholinesterase (AChE) and homeobox C4 (HoxC4) genes and human sperm concentration/motility. The study population consisted of three groups: asthenozoospermia (AZ), oligoasthenozoospermia (OAZ) and normozoospermia (NZ). The 5hmC rate in the promoter was measured by CCGG loci-dependent MspI/HpaII restriction mapping of glycosylation-modified sperm DNA combined with a hydroxymethylation-specific real-time polymerase chain reaction assay. The 5hmC rate in the AChE promoter in group AZ and OAZ was higher than that in group NZ (p < .05). A weak inverse correlation between 5hmC rate of AChE and sperm motility was observed in all subjects (r = -.172, p < .05). The 5hmC rate in the HoxC4 promoter in group OAZ was lower than that in group NZ (p < .05). These results indicated that altered 5hmC rates of AChE and HoxC4 promoters are associated with low sperm motility and sperm concentration respectively.
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Affiliation(s)
- Y Li
- School of Pharmacy, Fudan University, Shanghai, China
| | - Y H Li
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
| | - X Zhou
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
| | - B Wu
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
| | - J P Chen
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
| | - Z K Wang
- The hospital affiliated to Shanghai Institute of Planned Parenthood Research, Shanghai, China
| | - X Wang
- The hospital affiliated to Shanghai Institute of Planned Parenthood Research, Shanghai, China
| | - H J Shi
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
| | - R S Li
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, China
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13
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Stathopoulou A, Chhetri JB, Ambrose JC, Estève PO, Ji L, Erdjument-Bromage H, Zhang G, Neubert TA, Pradhan S, Herrero J, Schmitz RJ, Ooi SK. A novel requirement for DROSHA in maintenance of mammalian CG methylation. Nucleic Acids Res 2017; 45:9398-9412. [PMID: 28934503 PMCID: PMC5766157 DOI: 10.1093/nar/gkx695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/27/2017] [Indexed: 12/18/2022] Open
Abstract
In mammals, faithful inheritance of genomic methylation patterns ensures proper gene regulation and cell behaviour, impacting normal development and fertility. Following establishment, genomic methylation patterns are transmitted through S-phase by the maintenance methyltransferase Dnmt1. Using a protein interaction screen, we identify Microprocessor component DROSHA as a novel DNMT1-interactor. Drosha-deficient embryonic stem (ES) cells display genomic hypomethylation that is not accounted for by changes in the levels of DNMT proteins. DNMT1-mediated methyltransferase activity is also reduced in these cells. We identify two transcripts that are specifically upregulated in Drosha- but not Dicer-deficient ES cells. Regions within these transcripts predicted to form stem-loop structures are processed by Microprocessor and can inhibit DNMT1-mediated methylation in vitro. Our results highlight DROSHA as a novel regulator of mammalian DNA methylation and we propose that DROSHA-mediated processing of RNA is necessary to ensure full DNMT1 activity. This adds to the DROSHA repertoire of non-miRNA dependent functions as well as implicating RNA in regulating DNMT1 activity and correct levels of genomic methylation.
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Affiliation(s)
| | - Jyoti B. Chhetri
- Department of Cancer Biology, UCL Cancer Institute, London WC1E 6BT, UK
| | - John C. Ambrose
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK
| | | | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA
| | - Hediye Erdjument-Bromage
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Guoqiang Zhang
- New England Biolabs, 240 Country Road, Ipswich, MA 01938, USA
| | - Thomas A. Neubert
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute, NYU School of Medicine, New York, NY 10016, USA
| | | | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK
| | - Robert J. Schmitz
- Institute of Bioinformatics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA
| | - Steen K.T. Ooi
- Department of Cancer Biology, UCL Cancer Institute, London WC1E 6BT, UK
- To whom correspondence should be addressed. Tel: +44 2076 790717; Fax: +44 2076 796817;
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14
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Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RM, Cheng X. Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. Nucleic Acids Res 2017; 45:2503-2515. [PMID: 28158710 PMCID: PMC5389525 DOI: 10.1093/nar/gkx057] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/21/2017] [Indexed: 12/22/2022] Open
Abstract
Activator protein 1 (AP-1) is a transcription factor that recognizes two versions of a 7-base pair response element, either 5΄-TGAGTCA-3΄ or 5΄-MGAGTCA-3΄ (where M = 5-methylcytosine). These two elements share the feature that 5-methylcytosine and thymine both have a methyl group in the same position, 5-carbon of the pyrimidine, so each of them has two methyl groups at nucleotide positions 1 and 5 from the 5΄ end, resulting in four methyl groups symmetrically positioned in duplex DNA. Epstein-Barr Virus Zta is a key transcriptional regulator of the viral lytic cycle that is homologous to AP-1. Zta recognizes several methylated Zta-response elements, including meZRE1 (5΄-TGAGMCA-3΄) and meZRE2 (5΄-TGAGMGA-3΄), where a methylated cytosine occupies one of the inner thymine residues corresponding to the AP-1 element, resulting in the four spatially equivalent methyl groups. Here, we study how AP-1 and Zta recognize these methyl groups within their cognate response elements. These methyl groups are in van der Waals contact with a conserved di-alanine in AP-1 dimer (Ala265 and Ala266 in Jun), or with the corresponding Zta residues Ala185 and Ser186 (via its side chain carbon Cβ atom). Furthermore, the two ZRE elements differ at base pair 6 (C:G versus G:C), forming a pseudo-symmetric sequence (meZRE1) or an asymmetric sequence (meZRE2). In vitro DNA binding assays suggest that Zta has high affinity for all four sequences examined, whereas AP-1 has considerably reduced affinity for the asymmetric sequence (meZRE2). We ascribe this difference to Zta Ser186 (a unique residue for Zta) whose side chain hydroxyl oxygen atom interacts with the two half sites differently, whereas the corresponding Ala266 of AP-1 Jun protein lacks such flexibility. Our analyses demonstrate a novel mechanism of 5mC/T recognition in a methylation-dependent, spatial and sequence-specific approach by basic leucine-zipper transcriptional factors.
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Affiliation(s)
- Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Molecular and Systems Pharmacology graduate program, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - John R Horton
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samuel H Speck
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Emory Vaccine Center, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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15
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Nasri F, Gharesi-Fard B, Namavar Jahromi B, Farazi-Fard MA, Banaei M, Davari M, Ebrahimi S, Anvar Z. Sperm DNA methylation of H19 imprinted gene and male infertility. Andrologia 2017; 49. [PMID: 28295500 DOI: 10.1111/and.12766] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 02/06/2023] Open
Abstract
Infertility affects up to 15% of reproductive-aged couples worldwide, with male factor being detected in 40%-50% of the cases. Proper sperm production is associated with the establishment of appropriate epigenetic marks in developing germ cells. Several studies have demonstrated the association between abnormal spermatogenesis and epigenetic disturbances with the major focus on DNA methylation. Imprinted genes are expressed in a parent-of-origin-specific manner, and the role of their DNA methylation in proper spermatogenesis has been documented recently. The existing evidence along with the absence of relevant data in south of Iran prompted us to study the methylation of H19 imprinted gene in spermatozoa of idiopathic infertile patients (males with abnormalities in sperm parameters) and healthy controls by Combined Bisulfite Restriction Analysis. According to our results, the lowest methylation percentage of H19 imprinted gene belongs to three cases with sperm characteristics under normal range (two cases Oligoasthenoteratozoospermia and one case Oligoteratozoospermia). However, our results show that the median of methylation percentage for H19 is not statistically significant between case and control groups. Our results and those of others introduce DNA methylation as a potential marker of fertility and should be investigated with more patients in future studies.
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Affiliation(s)
- F Nasri
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - B Gharesi-Fard
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.,Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - B Namavar Jahromi
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Obstetrics and Gynecology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - M A Farazi-Fard
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - M Banaei
- IVF Division, Ghadir-Mother and Child Hospital of Shiraz, Shiraz, Iran
| | - M Davari
- Department of Obstetrics and Gynecology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.,IVF Division, Ghadir-Mother and Child Hospital of Shiraz, Shiraz, Iran
| | - S Ebrahimi
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Z Anvar
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Obstetrics and Gynecology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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16
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Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JHA, Pourfarzad F, Kuijpers TW, Burden F, Farrow S, Downes K, Ouwehand WH, Clarke L, Datta A, Lowy E, Flicek P, Frontini M, Stunnenberg HG, Martín-Subero JI, Gut I, Heath S. Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems. Cell Rep 2016; 17:2101-2111. [PMID: 27851971 PMCID: PMC5889099 DOI: 10.1016/j.celrep.2016.10.054] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/17/2016] [Accepted: 09/12/2016] [Indexed: 01/15/2023] Open
Abstract
DNA methylation and the localization and post-translational modification of nucleosomes are interdependent factors that contribute to the generation of distinct phenotypes from genetically identical cells. With 112 whole-genome bisulfite sequencing datasets from the BLUEPRINT Epigenome Project, we analyzed the global development of DNA methylation patterns during lineage commitment and maturation of a range of immune system effector cells and the cancers that arise from them. We show clear trends in methylation patterns that are distinct in the innate and adaptive arms of the human immune system, both globally and in relation to consistently positioned nucleosomes. Most notable are a progressive loss of methylation in developing lymphocytes and the consistent occurrence of non-CG methylation in specific cell types. Cancer samples from the two lineages are further polarized, suggesting the involvement of distinct lineage-specific epigenetic mechanisms. We anticipate broad utility for this resource as a basis for further comparative epigenetic analyses.
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Affiliation(s)
- Ronald P Schuyler
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Angelika Merkel
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Emanuele Raineri
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Lucia Altucci
- Dipartimento di Biochimica Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, Vico Luigi de Crecchio 7, Napoli 80138, Italy
| | - Edo Vellenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Radboud University, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - Farzin Pourfarzad
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, the Netherlands
| | - Taco W Kuijpers
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, the Netherlands; Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; British Heart Foundation Centre of Excellence, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0QQ Cambridge, UK; Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1HH Cambridge, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, CB2 0PT Cambridge, UK; British Heart Foundation Centre of Excellence, University of Cambridge, Cambridge Biomedical Campus, Long Road, CB2 0QQ Cambridge, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Radboud University, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, the Netherlands
| | - José I Martín-Subero
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain.
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17
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Abstract
Epigenetic modifications established during gametogenesis regulate transcription and other nuclear processes in gametes, but also have influences in the zygote, embryo and postnatal life. This is best understood for DNA methylation which, established at discrete regions of the oocyte and sperm genomes, governs genomic imprinting. In this review, we describe how imprinting has informed our understanding of de novo DNA methylation mechanisms, highlight how recent genome-wide profiling studies have provided unprecedented insights into establishment of the sperm and oocyte methylomes and consider the fate and function of gametic methylation and other epigenetic modifications after fertilization.
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Affiliation(s)
- Kathleen R Stewart
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK2200 Copenhagen, Denmark
| | - Lenka Veselovska
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Laboratory of Developmental Biology & Genetics, Department of Molecular Biology, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
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18
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Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X. Distinctive Klf4 mutants determine preference for DNA methylation status. Nucleic Acids Res 2016; 44:10177-10185. [PMID: 27596594 PMCID: PMC5137437 DOI: 10.1093/nar/gkw774] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/06/2023] Open
Abstract
Reprogramming of mammalian genome methylation is critically important but poorly understood. Klf4, a transcription factor directing reprogramming, contains a DNA binding domain with three consecutive C2H2 zinc fingers. Klf4 recognizes CpG or TpG within a specific sequence. Mouse Klf4 DNA binding domain has roughly equal affinity for methylated CpG or TpG, and slightly lower affinity for unmodified CpG. The structural basis for this key preference is unclear, though the side chain of Glu446 is known to contact the methyl group of 5-methylcytosine (5mC) or thymine (5-methyluracil). We examined the role of Glu446 by mutagenesis. Substituting Glu446 with aspartate (E446D) resulted in preference for unmodified cytosine, due to decreased affinity for 5mC. In contrast, substituting Glu446 with proline (E446P) increased affinity for 5mC by two orders of magnitude. Structural analysis revealed hydrophobic interaction between the proline's aliphatic cyclic structure and the 5-methyl group of the pyrimidine (5mC or T). As in wild-type Klf4 (E446), the proline at position 446 does not interact directly with either the 5mC N4 nitrogen or the thymine O4 oxygen. In contrast, the unmethylated cytosine's exocyclic N4 amino group (NH2) and its ring carbon C5 atom hydrogen bond directly with the aspartate carboxylate of the E446D variant. Both of these interactions would provide a preference for cytosine over thymine, and the latter one could explain the E446D preference for unmethylated cytosine. Finally, we evaluated the ability of these Klf4 mutants to regulate transcription of methylated and unmethylated promoters in a luciferase reporter assay.
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Affiliation(s)
| | - Dongxue Wang
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Alyse N Steves
- Genetics and Molecular Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology & Immunology and Program in Bioinformatics, The University of Toledo College of Medicine & Life Sciences, Toledo, Ohio 43614, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA .,Genetics and Molecular Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
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19
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Cui X, Jing X, Wu X, Yan M, Li Q, Shen Y, Wang Z. DNA methylation in spermatogenesis and male infertility. Exp Ther Med 2016; 12:1973-1979. [PMID: 27698683 DOI: 10.3892/etm.2016.3569] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/06/2016] [Indexed: 12/12/2022] Open
Abstract
Infertility is a significant problem for human reproduction, with males and females equally affected. However, the molecular mechanisms underlying male infertility remain unclear. Spermatogenesis is a highly complex process involving mitotic cell division, meiosis cell division and spermiogenesis; during this period, unique and extensive chromatin and epigenetic modifications occur to bring about specific epigenetic profiles in spermatozoa. It has recently been suggested that the dysregulation of epigenetic modifications, in particular the methylation of sperm genomic DNA, may serve an important role in the development of numerous diseases. The present study is a comprehensive review on the topic of male infertility, aiming to elucidate the association between sperm genomic DNA methylation and poor semen quality in male infertility. In addition, the current status of the genetic and epigenetic determinants of spermatogenesis in humans is discussed.
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Affiliation(s)
- Xiangrong Cui
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China; Division of Clinical Microbiology The Center Hospital of Linfen, Linfen, Shanxi 041000, P.R. China
| | - Xuan Jing
- Clinical Laboratory, Shanxi Province People's Hospital, Taiyuan, Shanxi 030001, P.R. China
| | - Xueqing Wu
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China
| | - Meiqin Yan
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China
| | - Qiang Li
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China
| | - Yan Shen
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China
| | - Zhenqiang Wang
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China
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20
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Patel A, Hashimoto H, Zhang X, Cheng X. Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins. Methods Enzymol 2016; 573:387-401. [PMID: 27372763 DOI: 10.1016/bs.mie.2016.01.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Much is known about vertebrate DNA methylation and oxidation; however, much less is known about how modified cytosine residues within particular sequences are recognized. Among the known methylated DNA-binding domains, the Cys2-His2 zinc finger (ZnF) protein superfamily is the largest with hundreds of members, each containing tandem ZnFs ranging from 3 to >30 fingers. We have begun to biochemically and structurally characterize these ZnFs not only on their sequence specificity but also on their sensitivity to various DNA modifications. Rather than following published methods of refolding insoluble ZnF arrays, we have expressed and purified soluble forms of ZnFs, ranging in size from a tandem array of two to six ZnFs, from seven different proteins. We also describe a fluorescence polarization assay to measure ZnFs affinity with oligonucleotides containing various modifications and our approaches for cocrystallization of ZnFs with oligonucleotides.
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Affiliation(s)
- A Patel
- Emory University School of Medicine, Atlanta, GA, United States
| | - H Hashimoto
- Emory University School of Medicine, Atlanta, GA, United States
| | - X Zhang
- Emory University School of Medicine, Atlanta, GA, United States.
| | - X Cheng
- Emory University School of Medicine, Atlanta, GA, United States.
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21
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Dan J, Chen T. Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:123-150. [PMID: 27826837 DOI: 10.1007/978-3-319-43624-1_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cytosine methylation at the C5-position, generating 5-methylcytosine (5mC), is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80 %) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation levels and patterns are associated with various human diseases, including cancer and developmental disorders. DNA methylation is mediated by three active DNA methyltransferases (Dnmts), namely, Dnmt1, Dnmt3a, and Dnmt3b, in mammals. Over the last two decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and X-chromosome inactivation.
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Affiliation(s)
- Jiameng Dan
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Graduate School of Biomedical Sciences at Houston, Houston, TX, 77030, USA.
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22
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Lister R, Mukamel EA. Turning over DNA methylation in the mind. Front Neurosci 2015; 9:252. [PMID: 26283895 PMCID: PMC4519686 DOI: 10.3389/fnins.2015.00252] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/06/2015] [Indexed: 01/22/2023] Open
Abstract
Cytosine DNA methylation is a stable epigenetic modification with established roles in regulating transcription, imprinting, female X-chromosome inactivation, and silencing of transposons. Dynamic gain or loss of DNA methylation reshapes the genomic landscape of cells during early differentiation, and in post-mitotic mammalian brain cells these changes continue to accumulate throughout the phases of cortical maturation in childhood and adolescence. There is also evidence for dynamic changes in the methylation status of specific genomic loci during the encoding of new memories, and these epigenome dynamics could play a causal role in memory formation. However, the mechanisms that may dynamically regulate DNA methylation in neurons during memory formation and expression, and the function of such epigenomic changes in this context, are unclear. Here we discuss the possible roles of DNA methylation in encoding and retrieval of memory.
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Affiliation(s)
- Ryan Lister
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia Perth, WA, Australia ; The Harry Perkins Institute of Medical Research Perth, WA, Australia
| | - Eran A Mukamel
- Department of Cognitive Science, University of California San Diego La Jolla, CA, USA
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23
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Liao HF, Mo CF, Wu SC, Cheng DH, Yu CY, Chang KW, Kao TH, Lu CW, Pinskaya M, Morillon A, Lin SS, Cheng WTK, Bourc'his D, Bestor T, Sung LY, Lin SP. Dnmt3l-knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency. Reproduction 2015; 150:245-56. [PMID: 26159833 DOI: 10.1530/rep-15-0031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 07/09/2015] [Indexed: 12/18/2022]
Abstract
Nuclear transfer (NT) is a technique used to investigate the development and reprogramming potential of a single cell. DNA methyltransferase-3-like, which has been characterized as a repressive transcriptional regulator, is expressed in naturally fertilized egg and morula/blastocyst at pre-implantation stages. In this study, we demonstrate that the use of Dnmt3l-knockout (Dnmt3l-KO) donor cells in combination with Trichostatin A treatment improved the developmental efficiency and quality of the cloned embryos. Compared with the WT group, Dnmt3l-KO donor cell-derived cloned embryos exhibited increased cell numbers as well as restricted OCT4 expression in the inner cell mass (ICM) and silencing of transposable elements at the blastocyst stage. In addition, our results indicate that zygotic Dnmt3l is dispensable for cloned embryo development at pre-implantation stages. In Dnmt3l-KO mouse embryonic fibroblasts, we observed reduced nuclear localization of HDAC1, increased levels of the active histone mark H3K27ac and decreased accumulation of the repressive histone marks H3K27me3 and H3K9me3, suggesting that Dnmt3l-KO donor cells may offer a more permissive epigenetic state that is beneficial for NT reprogramming.
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Affiliation(s)
- Hung-Fu Liao
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Chu-Fan Mo
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Shinn-Chih Wu
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Dai-Han Cheng
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Chih-Yun Yu
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Kai-Wei Chang
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Tzu-Hao Kao
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Chia-Wei Lu
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Marina Pinskaya
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Antonin Morillon
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Shih-Shun Lin
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, T
| | - Winston T K Cheng
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Déborah Bourc'his
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Timothy Bestor
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Li-Ying Sung
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Shau-Ping Lin
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, T
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24
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Abstract
DNA methylation is a chemical modification that occurs predominantly on CG dinucleotides in mammalian genomes. However, recent studies have revealed that non-CG methylation (mCH) is abundant and nonrandomly distributed in the genomes of pluripotent cells and brain cells, and is present at lower levels in many other human cells and tissues. Surprisingly, mCH in pluripotent cells is distinct from that in brain cells in terms of sequence specificity and association with transcription, indicating the existence of different mCH pathways. In addition, several recent studies have begun to reveal the biological significance of mCH in diverse cellular processes. In reprogrammed somatic cells, mCH marks megabase-scale regions that have failed to revert to the pluripotent epigenetic state. In myocytes, promoter mCH accumulation is associated with the transcriptional response to environmental factors. In brain cells, mCH accumulates during the establishment of neural circuits and is associated with Rett syndrome. In this review, we summarize the current understanding of mCH and its possible functional consequences in different biological contexts.
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Affiliation(s)
- Yupeng He
- Bioinformatics Program, University of California, San Diego, La Jolla, California 92093
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25
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Robbez-Masson L, Rowe HM. Retrotransposons shape species-specific embryonic stem cell gene expression. Retrovirology 2015; 12:45. [PMID: 26021318 PMCID: PMC4448215 DOI: 10.1186/s12977-015-0173-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/07/2015] [Indexed: 01/20/2023] Open
Abstract
Over half of our genome is composed of retrotransposons, which are mobile elements that can readily amplify their copy number by replicating through an RNA intermediate. Most of these elements are no longer mobile but still contain regulatory sequences that can serve as promoters, enhancers or repressors for cellular genes. Despite dominating our genetic content, little is known about the precise functions of retrotransposons, which include both endogenous retroviruses (ERVs) and non-LTR elements like long interspersed nuclear element 1 (LINE-1). However, a few recent cutting-edge publications have illustrated how retrotransposons shape species-specific stem cell gene expression by two opposing mechanisms, involving their recruitment of stem cell-enriched transcription factors (TFs): firstly, they can activate expression of genes linked to naïve pluripotency, and secondly, they can induce repression of proximal genes. The paradox that different retrotransposons are active or silent in embryonic stem cells (ESCs) can be explained by differences between retrotransposon families, between individual copies within the same family, and between subpopulations of ESCs. Since they have coevolved with their host genomes, some of them have been co-opted to perform species-specific beneficial functions, while others have been implicated in genetic disease. In this review, we will discuss retrotransposon functions in ESCs, focusing on recent mechanistic advances of how HERV-H has been adopted to preserve human naïve pluripotency and how particular LINE-1, SVA and ERV family members recruit species-specific transcriptional repressors. This review highlights the fine balance between activation and repression of retrotransposons that exists to harness their ability to drive evolution, while minimizing the risk they pose to genome integrity.
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Affiliation(s)
- Luisa Robbez-Masson
- Division of Infection and Immunity, Medical Research Council Centre for Medical Molecular Virology, University College London, 90 Gower Street, London, WC1E 6BT, UK.
| | - Helen M Rowe
- Division of Infection and Immunity, Medical Research Council Centre for Medical Molecular Virology, University College London, 90 Gower Street, London, WC1E 6BT, UK.
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