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da Rocha ST, Lin SP, Youngson NA. Editorial: Legacies of epigenetic perturbations. Front Cell Dev Biol 2023; 11:1228115. [PMID: 37384254 PMCID: PMC10295125 DOI: 10.3389/fcell.2023.1228115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023] Open
Affiliation(s)
- Simão Teixeira da Rocha
- iBB–Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Shau-Ping Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Bachelor Program of Biotechnology and Food Nutrition, National Taiwan University, Taipei, Taiwan
- Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Neil A. Youngson
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW, Australia
- Centre for Reproductive Health, Department of Molecular and Translational Science, Hudson Institute of Medical Research, Monash University, Clayton, VIC, Australia
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2
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Liu P, Yang F, Zhang L, Hu Y, Chen B, Wang J, Su L, Wu M, Chen W. Emerging role of different DNA methyltransferases in the pathogenesis of cancer. Front Pharmacol 2022; 13:958146. [PMID: 36091786 PMCID: PMC9453300 DOI: 10.3389/fphar.2022.958146] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is one of the most essential epigenetic mechanisms to regulate gene expression. DNA methyltransferases (DNMTs) play a vital role in DNA methylation in the genome. In mammals, DNMTs act with some elements to regulate the dynamic DNA methylation patterns of embryonic and adult cells. Conversely, the aberrant function of DNMTs is frequently the hallmark in judging cancer, including total hypomethylation and partial hypermethylation of tumor suppressor genes (TSGs), which improve the malignancy of tumors, aggravate the ailment for patients, and significantly exacerbate the difficulty of cancer therapy. Since DNA methylation is reversible, currently, DNMTs are viewed as an important epigenetic target for drug development. However, the impression of DNMTs on cancers is still controversial, and therapeutic methods targeting DNMTs remain under exploration. This review mainly summarizes the relationship between the main DNMTs and cancers as well as regulatory mechanisms and clinical applications of DNMTs in cancer and highlights several forthcoming strategies for targeting DNMTs.
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Affiliation(s)
- Pengcheng Liu
- Department of Human Resources, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Fan Yang
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Lizhi Zhang
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Ying Hu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Bangjie Chen
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jianpeng Wang
- The First Clinical Medical College, Anhui Medical University, Hefei, China
| | - Lei Su
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Mingyue Wu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wenjian Chen
- Department of Orthopaedics, Anhui Provincial Children’s Hospital, Hefei, China
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3
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Hsu PS, Yu SH, Tsai YT, Chang JY, Tsai LK, Ye CH, Song NY, Yau LC, Lin SP. More than causing (epi)genomic instability: emerging physiological implications of transposable element modulation. J Biomed Sci 2021; 28:58. [PMID: 34364371 PMCID: PMC8349491 DOI: 10.1186/s12929-021-00754-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022] Open
Abstract
Transposable elements (TEs) initially attracted attention because they comprise a major portion of the genomic sequences in plants and animals. TEs may jump around the genome and disrupt both coding genes as well as regulatory sequences to cause disease. Host cells have therefore evolved various epigenetic and functional RNA-mediated mechanisms to mitigate the disruption of genomic integrity by TEs. TE associated sequences therefore acquire the tendencies of attracting various epigenetic modifiers to induce epigenetic alterations that may spread to the neighboring genes. In addition to posting threats for (epi)genome integrity, emerging evidence suggested the physiological importance of endogenous TEs either as cis-acting control elements for controlling gene regulation or as TE-containing functional transcripts that modulate the transcriptome of the host cells. Recent advances in long-reads sequence analysis technologies, bioinformatics and genetic editing tools have enabled the profiling, precise annotation and functional characterization of TEs despite their challenging repetitive nature. The importance of specific TEs in preimplantation embryonic development, germ cell differentiation and meiosis, cell fate determination and in driving species specific differences in mammals will be discussed.
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Affiliation(s)
- Pu-Sheng Hsu
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Shu-Han Yu
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Yi-Tzang Tsai
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Jen-Yun Chang
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Li-Kuang Tsai
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Chih-Hung Ye
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Ning-Yu Song
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA.,Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
| | - Lih-Chiao Yau
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Shau-Ping Lin
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan. .,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan. .,Center of Systems Biology, National Taiwan University, Taipei, Taiwan. .,The Research Center of Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan.
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4
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Srivastava A, Biswas S, Yadav S, Kumar S, Srivastava V, Mishra Y. Acute cadmium toxicity and post-stress recovery: Insights into coordinated and integrated response/recovery strategies of Anabaena sp. PCC 7120. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:124822. [PMID: 33858073 DOI: 10.1016/j.jhazmat.2020.124822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Cyanobacteria, the first photoautotrophs have remarkable adaptive capabilities against most abiotic stresses, including Cd. A model cyanobacterium, Anabaena sp. PCC 7120 has been commonly used to understand cyanobacterial plasticity under different environmental stresses. However, very few studies have focused on the acute Cd toxicity. In this context, Anabaena was subjected to 100 μM Cd for 48 h (acute Cd stress, ACdS) and then transferred into the fresh medium for post-stress recovery (PSR). We further investigated the dynamics of morpho-ultrastructure, physiology, cytosolic proteome, thylakoidal complexes, chelators, and transporters after ACdS, as well as during early (ER), mid (MR), and late (LR) phases of PSR. The findings revealed that ACdS induced intracellular Cd accumulation and ROS production, altered morpho-ultrastructure, reduced photosynthetic pigments, and affected the structural organization of PSII, which subsequently hindered photosynthetic efficiency. Anabaena responded to ACdS and recovered during PSR by reprogramming the expression pattern of proteins/genes involved in cellular defense and repair; CO2 access, Calvin-Benson cycle, glycolysis, and pentose phosphate pathway; protein biosynthesis, folding, and degradation; regulatory functions; PSI-based cyclic electron flow; Cd chelation; and efflux. These modulations occurred in an integrated and coordinated manner that facilitated Anabaena to detoxify Cd and repair ACdS-induced cellular damage.
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Affiliation(s)
- Akanksha Srivastava
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Subhankar Biswas
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Sandhya Yadav
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Sanjiv Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm 10691, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm 10691, Sweden
| | - Yogesh Mishra
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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5
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Differential gene expression in cisplatin-resistant and -sensitive testicular germ cell tumor cell lines. Oncotarget 2020; 11:4735-4753. [PMID: 33473258 PMCID: PMC7771712 DOI: 10.18632/oncotarget.27844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022] Open
Abstract
Testicular germ cell tumors (TGCTs) represent a well curable malignity due to their exceptional response to cisplatin (CDDP). Despite remarkable treatment results, approximately 5% of TGCT patients develop CDDP resistance and die. Exceptional curability makes TGCTs a highly valuable model system for studying the molecular mechanisms of CDDP sensitivity. Our study was aimed at revealing difference in gene expression between the CDDP-resistant and -sensitive TGCT cell lines, and hence at identifying candidate genes that could serve as potential biomarkers of CDDP response. Using gene expression array, we identified 281 genes that are differentially expressed in CDDP-resistant compared to -sensitive TGCT cell lines. The expression of 25 genes with the highest fold change was validated by RT-qPCR. Of them, DNMT3L, GAL, IGFBP2, IGFBP7, L1TD1, NANOG, NTF3, POU5F1, SOX2, WNT6, ZFP42, ID2, PCP4, SLC40A1 and TRIB3, displayed comparable expression change in gene expression array and RT-qPCR, when all CDDP-resistant TGCT cell lines were pairwise combined with all -sensitive ones. Products of the identified genes are pluripotency factors, or are involved in processes, such as cell metabolism, proliferation or migration. We propose that, after clinical validation, these genes could serve as prognostic biomarkers for early detection of CDDP response in TGCT patients.
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Sandoval JE, Reich NO. p53 and TDG are dominant in regulating the activity of the human de novo DNA methyltransferase DNMT3A on nucleosomes. J Biol Chem 2020; 296:100058. [PMID: 33172892 PMCID: PMC7948466 DOI: 10.1074/jbc.ra120.016125] [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: 09/20/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 11/07/2022] Open
Abstract
DNA methylation and histone tail modifications are interrelated mechanisms involved in a wide range of biological processes, and disruption of this crosstalk is linked to diseases such as acute myeloid leukemia. In addition, DNA methyltransferase 3A (DNMT3A) activity is modulated by several regulatory proteins, including p53 and thymine DNA glycosylase (TDG). However, the relative role of histone tails and regulatory proteins in the simultaneous coordination of DNMT3A activity remains obscure. We observed that DNMT3A binds H3 tails and p53 or TDG at distinct allosteric sites to form DNMT3A–H3 tail-p53 or –TDG multiprotein complexes. Functional characterization of DNMT3A–H3 tail-p53 or –TDG complexes on human-derived synthetic histone H3 tails, mononucleosomes, or polynucleosomes shows p53 and TDG play dominant roles in the modulation of DNMT3A activity. Intriguingly, this dominance occurs even when DNMT3A is actively methylating nucleosome substrates. The activity of histone modifiers is influenced by their ability to sense modifications on histone tails within the same nucleosome or histone tails on neighboring nucleosomes. In contrast, we show here that DNMT3A acts on DNA within a single nucleosome, on nucleosomal DNA within adjacent nucleosomes, and DNA not associated with the DNMT3A–nucleosome complex. Our findings have direct bearing on how the histone code drives changes in DNA methylation and highlight the complex interplay between histone tails, epigenetic enzymes, and modulators of enzymatic activity.
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Affiliation(s)
- Jonathan E Sandoval
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA.
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Yu YCY, Hui TZ, Kao TH, Liao HF, Yang CY, Hou CC, Hsieh HT, Chang JY, Tsai YT, Pinskaya M, Yang KC, Chen YR, Morillon A, Tsai MH, Lin SP. Transient DNMT3L Expression Reinforces Chromatin Surveillance to Halt Senescence Progression in Mouse Embryonic Fibroblast. Front Cell Dev Biol 2020; 8:103. [PMID: 32195249 PMCID: PMC7064442 DOI: 10.3389/fcell.2020.00103] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/07/2020] [Indexed: 01/10/2023] Open
Abstract
Global heterochromatin reduction, which is one of the hallmarks of senescent cells, is associated with reduced transposable element repression and increased risk of chromatin instability. To ensure genomic integrity, the irreparable cells in a population exit permanently from the cell cycle, and this process is termed "senescence." However, senescence only blocks the expansion of unwanted cells, and the aberrant chromatin of senescent cells remains unstable. Serendipitously, we found that the transient ectopic expression of a repressive epigenetic modulator, DNA methyltransferase 3-like (DNMT3L) was sufficient to delay the premature senescence progression of late-passage mouse embryonic fibroblasts (MEFs) associated with a tightened global chromatin structure. DNMT3L induces more repressive H3K9 methylation on endogenous retroviruses and downregulates the derepressed transposons in aging MEFs. In addition, we found that a pulse of ectopic DNMT3L resulted in the reestablishment of H3K27me3 on polycomb repressive complex 2 (PRC2)-target genes that were derepressed in old MEFs. We demonstrated that ectopic DNMT3L interacted with PRC2 in MEFs. Our data also suggested that ectopic DNMT3L might guide PRC2 to redress deregulated chromatin regions in cells undergoing senescence. This study might lead to an epigenetic reinforcement strategy for overcoming aging-associated epimutation and senescence.
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Affiliation(s)
- Yoyo Chih-Yun Yu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Tony Zk Hui
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Tzu-Hao Kao
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Hung-Fu Liao
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Chih-Yi Yang
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Chia-Chun Hou
- Center for Systems Biology, National Taiwan University, Taipei, Taiwan
| | - Hsin-Ting Hsieh
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Jen-Yun Chang
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Yi-Tzang Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Marina Pinskaya
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Kai-Chien Yang
- Graduate Institute and Department of Pharmacology, National Taiwan University School of Medicine, Taipei, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Shau-Ping Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.,Center for Systems Biology, National Taiwan University, Taipei, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.,Research Center for Developmental Biology and Regenerative Medicine, Taipei, Taiwan
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8
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Tzelepi V, Logotheti S, Efstathiou E, Troncoso P, Aparicio A, Sakellakis M, Hoang A, Perimenis P, Melachrinou M, Logothetis C, Zolota V. Epigenetics and prostate cancer: defining the timing of DNA methyltransferase deregulation during prostate cancer progression. Pathology 2019; 52:218-227. [PMID: 31864524 DOI: 10.1016/j.pathol.2019.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/25/2019] [Accepted: 10/08/2019] [Indexed: 01/31/2023]
Abstract
DNA methyltransferases (DNMTs) regulate gene expression by methylating cytosine residues within CpG dinucleotides. Aberrant methylation patterns have been shown in a variety of human tumours including prostate cancer. However, the expression of DNMTs in clinical samples across the spectrum of prostate cancer progression has not been studied before. Tissue microarrays were constructed from the prostatectomy specimens of 309 patients across the spectrum of prostate cancer progression: hormone-naïve low-grade prostate cancer (n=49), hormone-naïve high-grade prostate cancer (n=151), hormonally treated high-grade prostate cancer (n=65), and castrate-resistant prostate cancer (CRPC) including neuroendocrine carcinoma (n=44). Adjacent non-neoplastic parenchyma was also available in 100 patients. In 71 patients with high-grade carcinoma and lymph node metastasis, tissue from the metastasis was also available for analysis. Immunohistochemical staining was performed with antibodies against DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L. Our results showed that DNMT1 and DNMT3L were upregulated early in prostate cancer progression, whereas DNMT2 was upregulated as a response to androgen ablation. DNMT1, DNMT3A, and DNMT3B were higher in the late stages of prostate cancer progression, i.e., the emergence of castrate resistance and androgen-independent growth. Lastly, DNMT1, DNMT2, and DNMT3L were upregulated in lymph node metastases compared to primary carcinomas. Our results highlight a cascade of epigenetic events in prostate cancer progression.
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Affiliation(s)
- Vasiliki Tzelepi
- Department of Pathology, Medical School, University of Patras, Greece.
| | - Souzana Logotheti
- Department of Pathology, Medical School, University of Patras, Greece
| | - Eleni Efstathiou
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, USA
| | - Patricia Troncoso
- Department of Pathology, The University of Texas MD Anderson Cancer Center, USA
| | - Ana Aparicio
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, USA
| | - Minas Sakellakis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, USA
| | - Anh Hoang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, USA
| | - Petros Perimenis
- Department of Urology, Medical School, University of Patras, Greece
| | - Maria Melachrinou
- Department of Pathology, Medical School, University of Patras, Greece
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, USA
| | - Vasiliki Zolota
- Department of Pathology, Medical School, University of Patras, Greece
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9
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Epigenetic Regulation of p21 cip1/waf1 in Human Cancer. Cancers (Basel) 2019; 11:cancers11091343. [PMID: 31514410 PMCID: PMC6769618 DOI: 10.3390/cancers11091343] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023] Open
Abstract
p21cip1/waf1 is a central regulator of cell cycle control and survival. While mutations are rare, it is commonly dysregulated in several human cancers due to epigenetic mechanisms influencing its transcriptional control. These mechanisms include promoter hypermethylation as well as additional pathways such as histone acetylation or methylation. The epigenetic regulators include writers, such as DNA methyltransferases (DNMTs); histone acetyltransferases (HATs) and histone lysine methyltransferases; erasers, such as histone deacetylases (HDACs); histone lysine demethylases [e.g., the Lysine Demethylase (KDM) family]; DNA hydroxylases; readers, such as the methyl-CpG-binding proteins (MBPs); and bromodomain-containing proteins, including the bromo- and extraterminal domain (BET) family. We further discuss the roles that long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) play in the epigenetic control of p21cip1/waf1 expression and its function in human cancers.
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Murín R, Abdalla M, Murínová N, Hatok J, Dobrota D. The metabolism of 5-methylcytosine residues in DNA. Physiol Res 2018. [PMID: 29527909 DOI: 10.33549/physiolres.933550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The fundamental biochemical processes of 5-methylcytosine (5-mC) synthesis, maintenance, conversion and removal determine the time and spatial pattern of DNA methylation. This has a strong effect on a plethora of physiological aspects of cellular metabolism. While the presence of 5-mC within the promoter region can silence gene expression, its derivative - 5-hydroxymethylcytosine exerts an opposite effect. Dysregulations in the metabolism of 5-mC lead to an altered DNA methylation pattern which is linked with a disrupted epigenome, and are considered to play a significant part in the etiology of several human diseases. A summary of recent knowledge about the molecular processes participating in DNA methylation pattern shaping is provided here.
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Affiliation(s)
- R Murín
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
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11
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Saraswat S, Rout PK, Kharche SD, Jindal SK, Goel AK. Molecular expression of caprine estrogen receptor gene 1 in reproductive and non-reproductive tissues. Reprod Domest Anim 2016; 51:1049-1054. [DOI: 10.1111/rda.12774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/02/2016] [Indexed: 11/28/2022]
Affiliation(s)
- S Saraswat
- ICAR-Central Institute for Research on goats; Mathura India
| | - PK Rout
- ICAR-Central Institute for Research on goats; Mathura India
| | - SD Kharche
- ICAR-Central Institute for Research on goats; Mathura India
| | - SK Jindal
- ICAR-Central Institute for Research on goats; Mathura India
| | - AK Goel
- ICAR-Central Institute for Research on goats; Mathura India
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12
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Zasłona Z, Scruggs AM, Peters-Golden M, Huang SK. Protein kinase A inhibition of macrophage maturation is accompanied by an increase in DNA methylation of the colony-stimulating factor 1 receptor gene. Immunology 2016; 149:225-37. [PMID: 27353657 DOI: 10.1111/imm.12641] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/17/2016] [Accepted: 06/27/2016] [Indexed: 01/21/2023] Open
Abstract
Macrophage colony-stimulating factor 1 (CSF-1) plays a critical role in the differentiation of mononuclear phagocytes from bone marrow precursors, and maturing monocytes and macrophages exhibit increased expression of the CSF-1 receptor, CSF1R. The expression of CSF1R is tightly regulated by transcription factors and epigenetic mechanisms. We previously showed that prostaglandin E2 and subsequent activation of protein kinase A (PKA) inhibited CSF1R expression and macrophage maturation. Here, we examine the DNA methylation changes that occur at the Csf1r locus during macrophage maturation in the presence or absence of activated PKA. Murine bone marrow cells were matured to macrophages by incubating cells with CSF-1-containing conditioned medium for up to 6 days in the presence or absence of the PKA agonist 6-bnz-cAMP. DNA methylation of Csf1r promoter and enhancer regions was assayed by bisulphite pyrosequencing. DNA methylation of Csf1r decreased during normal macrophage maturation in concert with an increase in Csf1r mRNA expression. Treatment with the PKA agonist inhibited Csf1r mRNA and protein expression, and increased DNA methylation at the Csf1r promoter. This was associated with decreased binding of the transcription factor PU.1 to the Csf1r promoter. Treatment with the PKA agonist inhibited the responsiveness of macrophages to CSF-1. Levels of endogenous PKA activity decreased during normal macrophage maturation, suggesting that attenuation of this signalling pathway contributes to the increase in CSF1R expression during macrophage maturation. Together, these results demonstrate that macrophage maturation is accompanied by Csf1r hypomethylation, and illustrates for the first time the ability of PKA to increase Csf1r DNA methylation.
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Affiliation(s)
- Zbigniew Zasłona
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anne M Scruggs
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marc Peters-Golden
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Steven K Huang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
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13
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Mostowska A, Szczepańska M, Wirstlein P, Skrzypczak J, Jagodziński PP. Association between DNMT3L polymorphic variants and the risk of endometriosis-associated infertility. Mol Med Rep 2015; 13:1040-6. [PMID: 26647998 DOI: 10.3892/mmr.2015.4626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 11/06/2015] [Indexed: 11/05/2022] Open
Abstract
Endometriosis is considered to be an epigenetic disease. It has previously been reported that the DNA methyltransferase 3-like (DNMT3L) rs8129776 single nucleotide polymorphism (SNP) contributes to endometrioma. In the present study, high‑resolution melting curve analysis was used to investigate the risks associated with the DNMT3L c.910‑635A/G (rs8129776), c.832C/T (rs7354779), c.812C/T (rs113593938) and c.344+62C/T (rs2276248) SNPs on stage I‑II endometriosis‑associated infertility. Included in the present study were patients presenting with stage I‑II endometriosis‑associated infertility (n=154) and a control cohort of healthy patients with confirmed fertility (n=383). No significant association between the above‑listed DNMT3L SNPs and the development of endometriosis‑associated infertility was identified. The lowest P‑values generated from trend analysis were observed in the DNMT3L c.832C/T (rs7354779) SNP (Ptrend=0.114). Furthermore, haplotype analyses of the DNMT3L SNPs failed to reveal any risk association between the development of endometriosis‑associated infertility and the above‑listed polymorphisms, even when the SNPs were present in combinations. Finally, a meta‑analysis was performed to examine the association between the DNMT3L rs8129776 SNP and the development of endometrioma, from which no association between the two was identified. On the basis of these results, the present study has demonstrated that variations in the DNMT3L gene do not contribute to stage I-II endometriosis-associated infertility.
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Affiliation(s)
- Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poznań 60‑781, Poland
| | - Malgorzata Szczepańska
- Department of Obstetrics, Gynecology and Gynecological Oncology, Division of Reproduction, Poznań University of Medical Sciences, Poznań 60‑781, Poland
| | - Przemyslaw Wirstlein
- Department of Obstetrics, Gynecology and Gynecological Oncology, Division of Reproduction, Poznań University of Medical Sciences, Poznań 60‑781, Poland
| | - Jana Skrzypczak
- Department of Obstetrics, Gynecology and Gynecological Oncology, Division of Reproduction, Poznań University of Medical Sciences, Poznań 60‑781, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poznań 60‑781, Poland
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14
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Liao HF, Chen WSC, Chen YH, Kao TH, Tseng YT, Lee CY, Chiu YC, Lee PL, Lin QJ, Ching YH, Hata K, Cheng WTK, Tsai MH, Sasaki H, Ho HN, Wu SC, Huang YH, Yen P, Lin SP. DNMT3L promotes quiescence in postnatal spermatogonial progenitor cells. Development 2014; 141:2402-13. [PMID: 24850856 DOI: 10.1242/dev.105130] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The ability of adult stem cells to reside in a quiescent state is crucial for preventing premature exhaustion of the stem cell pool. However, the intrinsic epigenetic factors that regulate spermatogonial stem cell quiescence are largely unknown. Here, we investigate in mice how DNA methyltransferase 3-like (DNMT3L), an epigenetic regulator important for interpreting chromatin context and facilitating de novo DNA methylation, sustains the long-term male germ cell pool. We demonstrated that stem cell-enriched THY1(+) spermatogonial stem/progenitor cells (SPCs) constituted a DNMT3L-expressing population in postnatal testes. DNMT3L influenced the stability of promyelocytic leukemia zinc finger (PLZF), potentially by downregulating Cdk2/CDK2 expression, which sequestered CDK2-mediated PLZF degradation. Reduced PLZF in Dnmt3l KO THY1(+) cells released its antagonist, Sal-like protein 4A (SALL4A), which is associated with overactivated ERK and AKT signaling cascades. Furthermore, DNMT3L was required to suppress the cell proliferation-promoting factor SALL4B in THY1(+) SPCs and to prevent premature stem cell exhaustion. Our results indicate that DNMT3L is required to delicately balance the cycling and quiescence of SPCs. These findings reveal a novel role for DNMT3L in modulating postnatal SPC cell fate decisions.
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Affiliation(s)
- Hung-Fu Liao
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Wendy S C Chen
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Yu-Hsiang Chen
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Tzu-Hao Kao
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Yen-Tzu Tseng
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Chien-Yueh Lee
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Chiao Chiu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan
| | - Pei-Lung Lee
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Qian-Jia Lin
- Department of Biochemistry, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan Center for Reproductive Medicine, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
| | - Yung-Hao Ching
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien 97004, Taiwan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Okura, Setagaya, Tokyo 157-8535, Japan
| | - Winston T K Cheng
- Department of Animal Science and Biotechnology, Tunghai University, Taichung 40704, Taiwan
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Hiroyuki Sasaki
- Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Hong-Nerng Ho
- Department of Obstetrics and Gynecology, College of Medicine and the Hospital, National Taiwan University, Taipei 100, Taiwan
| | - Shinn-Chih Wu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Yen-Hua Huang
- Department of Biochemistry, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan Center for Reproductive Medicine, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
| | - Pauline Yen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shau-Ping Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan Center for Systems Biology, National Taiwan University, Taipei 106, Taiwan Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei 106, Taiwan
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15
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Abstract
Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci ("Dobzhansky-Muller incompatibilities"). The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus) provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven 'hotspots,' seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL-but not cis eQTL-were substantially lower when mapping was restricted to a 'fertile' subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is applicable in a broad range of organisms and we advocate for widespread adoption of a network-centered approach in speciation genetics.
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16
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Understanding the relationship between DNA methylation and histone lysine methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1362-72. [PMID: 24560929 PMCID: PMC4316174 DOI: 10.1016/j.bbagrm.2014.02.007] [Citation(s) in RCA: 353] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/11/2014] [Indexed: 12/19/2022]
Abstract
DNA methylation acts as an epigenetic modification in vertebrate DNA. Recently it has become clear that the DNA and histone lysine methylation systems are highly interrelated and rely mechanistically on each other for normal chromatin function in vivo. Here we examine some of the functional links between these systems, with a particular focus on several recent discoveries suggesting how lysine methylation may help to target DNA methylation during development, and vice versa. In addition, the emerging role of non-methylated DNA found in CpG islands in defining histone lysine methylation profiles at gene regulatory elements will be discussed in the context of gene regulation. This article is part of a Special Issue entitled: Methylation: A Multifaceted Modification — looking at transcription and beyond. There is an emerging realisation that DNA and histone lysine methylation in mammals are highly interrelated. Targeting of DNA methylation is mechanistically linked to H3K9 methylation. Uhrf1 acts as a link between H3K9 methylation and maintenance methylation during DNA replication. Targeting of Dnmt3a/b is influenced by H3K4 and H3K36 methylation. Non-methylated DNA at CpG islands influences histone methylation through ZF-CxxC proteins.
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17
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An alkylphenol mix promotes seminoma derived cell proliferation through an ERalpha36-mediated mechanism. PLoS One 2013; 8:e61758. [PMID: 23626723 PMCID: PMC3634018 DOI: 10.1371/journal.pone.0061758] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/11/2013] [Indexed: 11/19/2022] Open
Abstract
Long chain alkylphenols are man-made compounds still present in industrial and agricultural processes. Their main use is domestic and they are widespread in household products, cleansers and cosmetics, leading to a global environmental and human contamination. These molecules are known to exert estrogen-like activities through binding to classical estrogen receptors. In vitro, they can also interact with the G-protein coupled estrogen receptor. Testicular germ cell tumor etiology and progression are proposed to be stimulated by lifelong estrogeno-mimetic exposure. We studied the transduction signaling pathways through which an alkyphenol mixture triggers testicular cancer cell proliferation in vitro and in vivo. Proliferation assays were monitored after exposure to a realistic mixture of 4-tert-octylphenol and 4-nonylphenol of either TCam-2 seminoma derived cells, NT2/D1 embryonal carcinoma cells or testis tumor in xenografted nude mice. Specific pharmacological inhibitors and gene-silencing strategies were used in TCam-2 cells in order to demonstrate that the alkylphenol mix triggers CREB-phosphorylation through a rapid, ERα36-PI3kinase non genomic pathway. Microarray analysis of the mixture target genes revealed that this pathway can modulate the expression of the DNA-methyltransferase-3 (Dnmt3) gene family which is involved in DNA methylation control. Our results highlight a key role for ERα36 in alkylphenol non genomic signaling in testicular germ cell tumors. Hence, ERα36-dependent control of the epigenetic status opens the way for the understanding of the link between endocrine disruptor exposure and the burden of hormone sensitive cancers.
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18
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Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H. Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet 2013; 9:e1003439. [PMID: 23637617 PMCID: PMC3630097 DOI: 10.1371/journal.pgen.1003439] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 02/23/2013] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in normal mammalian development, retrotransposon silencing, and cellular reprogramming. Although methylation mainly occurs on the cytosine in a CG site, non-CG methylation is prevalent in pluripotent stem cells, brain, and oocytes. We previously identified non-CG methylation in several CG-rich regions in mouse germinal vesicle oocytes (GVOs), but the overall distribution of non-CG methylation and the enzymes responsible for this modification are unknown. Using amplification-free whole-genome bisulfite sequencing, which can be used with minute amounts of DNA, we constructed the base-resolution methylome maps of GVOs, non-growing oocytes (NGOs), and mutant GVOs lacking the DNA methyltransferase Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3L. We found that nearly two-thirds of all methylcytosines occur in a non-CG context in GVOs. The distribution of non-CG methylation closely resembled that of CG methylation throughout the genome and showed clear enrichment in gene bodies. Compared to NGOs, GVOs were over four times more methylated at non-CG sites, indicating that non-CG methylation accumulates during oocyte growth. Lack of Dnmt3a or Dnmt3L resulted in a global reduction in both CG and non-CG methylation, showing that non-CG methylation depends on the Dnmt3a-Dnmt3L complex. Dnmt3b was dispensable. Of note, lack of Dnmt1 resulted in a slight decrease in CG methylation, suggesting that this maintenance enzyme plays a role in non-dividing oocytes. Dnmt1 may act on CG sites that remain hemimethylated in the de novo methylation process. Our results provide a basis for understanding the mechanisms and significance of non-CG methylation in mammalian oocytes.
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Affiliation(s)
- Kenjiro Shirane
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hidehiro Toh
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
| | - Hisato Kobayashi
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Fumihito Miura
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hatsune Chiba
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Ito
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Kono
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- * E-mail:
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19
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Song J, Saha S, Gokulrangan G, Tesar PJ, Ewing RM. DNA and chromatin modification networks distinguish stem cell pluripotent ground states. Mol Cell Proteomics 2012; 11:1036-47. [PMID: 22822199 DOI: 10.1074/mcp.m111.011114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pluripotent stem cells are capable of differentiating into all cell types of the body and therefore hold tremendous promise for regenerative medicine. Despite their widespread use in laboratories across the world, a detailed understanding of the molecular mechanisms that regulate the pluripotent state is currently lacking. Mouse embryonic (mESC) and epiblast (mEpiSC) stem cells are two closely related classes of pluripotent stem cells, derived from distinct embryonic tissues. Although both mESC and mEpiSC are pluripotent, these cell types show important differences in their properties suggesting distinct pluripotent ground states. To understand the molecular basis of pluripotency, we analyzed the nuclear proteomes of mESCs and mEpiSCs to identify protein networks that regulate their respective pluripotent states. Our study used label-free LC-MS/MS to identify and quantify 1597 proteins in embryonic and epiblast stem cell nuclei. Immunoblotting of a selected protein subset was used to confirm that key components of chromatin regulatory networks are differentially expressed in mESCs and mEpiSCs. Specifically, we identify differential expression of DNA methylation, ATP-dependent chromatin remodeling and nucleosome remodeling networks in mESC and mEpiSC nuclei. This study is the first comparative study of protein networks in cells representing the two distinct, pluripotent states, and points to the importance of DNA and chromatin modification processes in regulating pluripotency. In addition, by integrating our data with existing pluripotency networks, we provide detailed maps of protein networks that regulate pluripotency that will further both the fundamental understanding of pluripotency as well as efforts to reliably control the differentiation of these cells into functional cell fates.
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Affiliation(s)
- Jing Song
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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