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Habano W, Miura T, Terashima J, Ozawa S. Aryl hydrocarbon receptor as a DNA methylation reader in the stress response pathway. Toxicology 2022; 470:153154. [PMID: 35301058 DOI: 10.1016/j.tox.2022.153154] [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: 10/05/2021] [Revised: 01/31/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
The aryl hydrocarbon receptor (AhR) mediates various cellular responses upon exposure to exogenous and endogenous stress factors. In these responses, AhR plays a dual role as a stress sensor for detecting various AhR ligands and as a transcription factor that upregulates the expression of downstream effector genes, such as those encoding drug-metabolizing enzymes. As a transcription factor, it selectively binds to the unmethylated form of a specific sequence called the xenobiotic responsive element (XRE). We suggest that AhR is a novel DNA methylation reader, unlike classical methylation readers, such as methyl-CpG-binding protein 2, which binds to methylated sequences. Under physiological conditions of continuous exposure to endogenous AhR ligands, such as kynurenine, methylation states of the individual target XREs must be strictly regulated to select and coordinate the expression of downstream genes responsible for maintaining homeostasis in the body. In contrast, long-term exposure to AhR ligands frequently leads to changes in the methylation patterns around the XRE sequence. These data indicate that AhR may contribute to the adaptive cellular response to various stresses by modulating DNA methylation. Thus, the DNA methylation profile of AhR target genes should be dynamically controlled through a balance between robustness and flexibility under both physiological and stress conditions. AhR is a pivotal player in the regulation of stress response as it shows versatility by functioning as a stress sensor, methylation reader, and putative methylation modulator.
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Affiliation(s)
- Wataru Habano
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan.
| | - Toshitaka Miura
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
| | - Jun Terashima
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
| | - Shogo Ozawa
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
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102
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Shyamala N, Kongettira CL, Puranam K, Kupsal K, Kummari R, Padala C, Hanumanth SR. In silico identification of single nucleotide variations at CpG sites regulating CpG island existence and size. Sci Rep 2022; 12:3574. [PMID: 35246549 PMCID: PMC8897451 DOI: 10.1038/s41598-022-05198-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/03/2022] [Indexed: 12/20/2022] Open
Abstract
Genetic and epigenetic modifications of genes involved in the key regulatory pathways play a significant role in the pathophysiology and progression of multifactorial diseases. The present study is an attempt to identify single nucleotide variations (SNVs) at CpG sites of promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes influencing CpG island (CGI) existence and size associated with the pathophysiology of Diabetes mellitus, Coronary artery disease and Cancers. Promoter sequences located between -2000 to + 2000 bp were retrieved from the EPDnew database and predicted the CpG island using MethPrimer. Further, SNVs at CpG sites were accessed from NCBI, Ensembl while transcription factor (TF) binding sites were accessed using AliBaba2.1. CGI existence and size were determined for each SNV at CpG site with respect to wild type and variant allele by MethPrimer. A total of 200 SNVs at CpG sites were analyzed from the promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes. Of these, only 17 (8.5%) SNVs were found to influence the loss of CGI while 70 (35%) SNVs were found to reduce the size of CGI. It has also been found that 59% (10) of CGI abolishing SNVs are showing differences in binding of TFs. The findings of the study suggest that the candidate SNVs at CpG sites regulating CGI existence and size might influence the DNA methylation status and expression of genes involved in molecular pathways associated with several diseases. The insights of the present study may pave the way for new experimental studies to undertake challenges in DNA methylation, gene expression and protein assays.
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Affiliation(s)
- Nivas Shyamala
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Chaitra Lava Kongettira
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Kaushik Puranam
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Keerthi Kupsal
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Ramanjaneyulu Kummari
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Chiranjeevi Padala
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana State, India
| | - Surekha Rani Hanumanth
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India.
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103
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Lai FL, Gao F. GC-Profile 2.0: an extended web server for the prediction and visualization of CpG islands. Bioinformatics 2022; 38:1738-1740. [PMID: 34954794 DOI: 10.1093/bioinformatics/btab864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/19/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY Due to the spontaneous deamination of 5'-methylcytosine into thymine, the number of CpG dinucleotides is less than expected in vertebrate genomes. Exceptionally, there are a large number of CpG dinucleotides clustered at certain genomic loci, known as CpG islands (CGIs), where CpG dinucleotides are free from methylation. Identification of CGIs is of great significance in the field of genomics and epigenetics because they can serve as important gene markers or regulatory elements. Here, GC-Profile 2.0 has been presented as a newly extended application for CGIs detection and visualization. Based on a benchmark test of assembled sequences, GC-Profile 2.0 has shown better overall performance compared with other four popular methods. In addition, cumulative CpG profile, a visualization tool of CpG content variation, is also proposed to intuitively display the change trend of CpG content. AVAILABILITY AND IMPLEMENTATION GC-Profile 2.0 is freely available at http://tubic.org/GC-Profile2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Fei-Liao Lai
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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104
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Tan L, Fu L, Zheng L, Fan W, Tan H, Tao Z, Xu Y. TET2 Regulates 5-Hydroxymethylcytosine Signature and CD4 + T-Cell Balance in Allergic Rhinitis. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2022; 14:254-272. [PMID: 35255541 PMCID: PMC8914607 DOI: 10.4168/aair.2022.14.2.254] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/03/2022] [Accepted: 01/16/2022] [Indexed: 11/23/2022]
Abstract
Purpose Previous studies have shown the role of ten-eleven translocation 2 (TET2) in CD4+ T cells. However, its function in CD4+ T cells under allergic inflammation is unclear. We aimed to investigate the epigenomic distribution of DNA 5-hydroxymethylcytosine (5hmC) and the role of TET2 in CD4+ T cells of allergic rhinitis (AR). Methods The hMeDIP-seq was performed to identify sequences with 5hmC deposition in CD4+ T cells of AR patients. Tet2-deficient or wild type mice were stimulated with ovalbumin (OVA) to develop an AR mouse model. The histopathology in nasal mucosae, Th1/Th2/Treg/Th17 cell percentage, concentrations of Th-related cytokines, expression of Tet and differential hydroxymethylated genes (DhMG), and the global deposition of 5hmC in sorted CD4+ T cells were detected. Results Epigenome-wide 5hmC landscape and DhMG in the CD4+ T cells of AR patients were identified. Tet2 depletion did not led to spontaneous inflammation. However, under the stimulation of allergen, OVA, loss of Tet2 resulted in the exacerbation of allergic inflammation, which was characterized by severer allergic symptoms, more inflammatory cells infiltrating the nasal lamina propria, sharper imbalances between Th1/Th2 and Treg/Th17 cells, and excessive secretion of OVA-specific IgE and Th2-related cytokines. Moreover, altered mRNA production of several DhMG and sharp decrease in 5hmC deposition were also observed in Tet2-deficient OVA-exposed mice. Conclusions TET2 may regulate DNA 5hmC, DhMG expressions, and CD4+ T cell balance in AR.
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Affiliation(s)
- Lu Tan
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lisheng Fu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Li Zheng
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenjun Fan
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hanyu Tan
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zezhang Tao
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yu Xu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.
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105
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Schaefer EJ, Wang HC, Karp HQ, Meyer CA, Cejas P, Gearhart MD, Adelman ER, Fares I, Apffel A, Lim K, Xie Y, Gibson CJ, Schenone M, Murdock HM, Wang ES, Gondek LP, Carroll MP, Vedula RS, Winer ES, Garcia JS, Stone RM, Luskin MR, Carr SA, Long HW, Bardwell VJ, Figueroa ME, Lindsley RC. BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes. Blood Cancer Discov 2022; 3:116-135. [PMID: 35015684 PMCID: PMC9414116 DOI: 10.1158/2643-3230.bcd-21-0115] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/06/2021] [Accepted: 12/10/2021] [Indexed: 02/02/2023] Open
Abstract
Polycomb repressive epigenetic complexes are recurrently dysregulated in cancer. Unlike polycomb repressive complex 2 (PRC2), the role of PRC1 in oncogenesis and therapy resistance is not well-defined. Here, we demonstrate that highly recurrent mutations of the PRC1 subunits BCOR and BCORL1 in leukemia disrupt assembly of a noncanonical PRC1.1 complex, thereby selectively unlinking the RING-PCGF enzymatic core from the chromatin-targeting auxiliary subcomplex. As a result, BCOR-mutated PRC1.1 is localized to chromatin but lacks repressive activity, leading to epigenetic reprogramming and transcriptional activation at target loci. We define a set of functional targets that drive aberrant oncogenic signaling programs in PRC1.1-mutated cells and primary patient samples. Activation of these PRC1.1 targets in BCOR-mutated cells confers acquired resistance to treatment while sensitizing to targeted kinase inhibition. Our study thus reveals a novel epigenetic mechanism that explains PRC1.1 tumor-suppressive activity and identifies a therapeutic strategy in PRC1.1-mutated cancer. SIGNIFICANCE We demonstrate that BCOR and BCORL1 mutations in leukemia unlink PRC1.1 repressive function from target genes, resulting in epigenetic reprogramming and activation of aberrant cell signaling programs that mediate treatment resistance. Our study provides mechanistic insights into the pathogenesis of PRC1.1-mutated leukemia that inform novel therapeutic approaches. This article is highlighted in the In This Issue feature, p. 85.
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Affiliation(s)
- Eva J. Schaefer
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Helen C. Wang
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hannah Q. Karp
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Clifford A. Meyer
- Department of Data Science, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Micah D. Gearhart
- Developmental Biology Center, Masonic Cancer Center, and Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Emmalee R. Adelman
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida.,Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida
| | - Iman Fares
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Annie Apffel
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Christopher J. Gibson
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Monica Schenone
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - H. Moses Murdock
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eunice S. Wang
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Lukasz P. Gondek
- Division of Molecular Pathology, Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Martin P. Carroll
- Department of Medicine, Perelman Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rahul S. Vedula
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eric S. Winer
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacqueline S. Garcia
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Richard M. Stone
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marlise R. Luskin
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Steven A. Carr
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Henry W. Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vivian J. Bardwell
- Developmental Biology Center, Masonic Cancer Center, and Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Maria E. Figueroa
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida
| | - R. Coleman Lindsley
- Department of Medical Oncology, Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, Massachusetts.,Corresponding Author: R. Coleman Lindsley, Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215. Phone: 617-632-6649; E-mail:
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106
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Cain JA, Montibus B, Oakey RJ. Intragenic CpG Islands and Their Impact on Gene Regulation. Front Cell Dev Biol 2022; 10:832348. [PMID: 35223855 PMCID: PMC8873577 DOI: 10.3389/fcell.2022.832348] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
Abstract
The mammalian genome is depleted in CG dinucleotides, except at protected regions where they cluster as CpG islands (CGIs). CGIs are gene regulatory hubs and serve as transcription initiation sites and are as expected, associated with gene promoters. Advances in genomic annotations demonstrate that a quarter of CGIs are found within genes. Such intragenic regions are repressive environments, so it is surprising that CGIs reside here and even more surprising that some resist repression and are transcriptionally active within a gene. Hence, intragenic CGI positioning within genes is not arbitrary and is instead, selected for. As a wealth of recent studies demonstrate, intragenic CGIs are embedded within genes and consequently, influence ‘host’ gene mRNA isoform length and expand transcriptome diversity.
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107
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Laser Capture Microdissection in the Spatial Analysis of Epigenetic Modifications in Skin: A Comprehensive Review. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4127238. [PMID: 35186184 PMCID: PMC8850045 DOI: 10.1155/2022/4127238] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/29/2021] [Accepted: 12/24/2021] [Indexed: 12/15/2022]
Abstract
Each cell in the body contains an intricate regulation for the expression of its relevant DNA. While every cell in a multicellular organism contains identical DNA, each tissue-specific cell expresses a different set of active genes. This organizational property exists in a paradigm that is largely controlled by forces external to the DNA sequence via epigenetic regulation. DNA methylation and chromatin modifications represent some of the classical epigenetic modifications that control gene expression. Complex tissues like skin consist of heterogeneous cell types that are spatially distributed and mixed. Furthermore, each individual skin cell has a unique response to physiological and pathological cues. As such, it is difficult to classify skin tissue as homogenous across all cell types and across different environmental exposures. Therefore, it would be prudent to isolate targeted tissue elements prior to any molecular analysis to avoid a possibility of confounding the sample with unwanted cell types. Laser capture microdissection (LCM) is a powerful technique used to isolate a targeted cell group with extreme microscopic precision. LCM presents itself as a solution to tackling the problem of tissue heterogeneity in molecular analysis. This review will cover an overview of LCM technology, the principals surrounding its application, and benefits of its application to the newly defined field of epigenomics, in particular of cutaneous pathology. This presents a comprehensive review about LCM and its use in the spatial analysis of skin epigenetics. Within the realm of skin pathology, this ability to isolate tissues under specific environmental stresses, such as oxidative stress, allows a far more focused investigation.
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Kato K, Okamura K, Hiki K, Kintsu H, Nohara K, Yamagishi T, Nakajima N, Watanabe H, Yamamoto H. Potential differences in chitin synthesis ability cause different sensitivities to diflubenzuron among three strains of Daphnia magna. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 243:106071. [PMID: 34995867 DOI: 10.1016/j.aquatox.2021.106071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/24/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
Ecotoxicity testing of crustaceans using Daphnia magna has been implemented in the chemical management systems of various countries. While the chemical sensitivity of D. magna varies depending on genetically different clonal lineages, the strain used in ecotoxicity tests, including the acute immobilization test (OECD TG202), has not been specified. We hypothesized that comprehensive gene expression profiles could provide useful information on phenotypic differences among strains, including chemical sensitivity. To test this hypothesis, we performed mRNA sequencing on three different strains (NIES, England, and Clone 5) of D. magna under culture conditions. The resulting expression profile of the NIES strain was clearly different compared to the profiles of the other two strains. Gene ontology (GO) enrichment analysis suggested that chitin metabolism was significantly enriched in the NIES strain compared to that in the England strain. Consistent with the GO analysis, evidence of high levels of chitin metabolism in the NIES strain were observed across multiple levels of biological organization, such as expression of chitin synthase genes, chitin content, and chitinase activity, which suggested that the different strains would exhibit different sensitivities to chemicals used to inhibit chitin synthesis. We found that among all strains, the NIES strain was more tolerant to diflubenzuron, a chitin synthesis inhibitor, with a 14-fold difference in the 48 h-EC50 value for the acute immobilization test compared to the England strain. The present study demonstrates that the differences among strains in chitin metabolism may lead to sensitivity difference to diflubenzuron, and serves as a case study of the usefulness of comprehensive gene expression profiles in finding sensitivity differences.
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Affiliation(s)
- Kota Kato
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8563, Japan; Health and Environmental Risk Division, National Institute for Environmental Studies (NIES), 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Kazuyuki Okamura
- Health and Environmental Risk Division, National Institute for Environmental Studies (NIES), 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Kyoshiro Hiki
- Health and Environmental Risk Division, National Institute for Environmental Studies (NIES), 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Hiroyuki Kintsu
- Health and Environmental Risk Division, National Institute for Environmental Studies (NIES), 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Keiko Nohara
- Health and Environmental Risk Division, National Institute for Environmental Studies (NIES), 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Takahiro Yamagishi
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8563, Japan; Health and Environmental Risk Division, National Institute for Environmental Studies (NIES), 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies (NIES), 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Haruna Watanabe
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8563, Japan; Health and Environmental Risk Division, National Institute for Environmental Studies (NIES), 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Hiroshi Yamamoto
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8563, Japan; Health and Environmental Risk Division, National Institute for Environmental Studies (NIES), 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan.
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109
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Hindle A, Bose C, Lee J, Palade PT, Peterson CJ, Reddy PH, Awasthi S, Singh SP. Rlip Depletion Alters Oncogene Transcription at Multiple Distinct Regulatory Levels. Cancers (Basel) 2022; 14:cancers14030527. [PMID: 35158795 PMCID: PMC8833773 DOI: 10.3390/cancers14030527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/07/2022] [Accepted: 01/15/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Rlip76 is a multifunctional membrane protein that facilitates cancer growth, and its depletion kills cancer cells. We recently found that Rlip depletion also results in broad changes to oncogene and tumor suppressor transcription. The present studies were designed to decipher the unknown downstream signaling pathways and transcriptional regulatory mechanisms driving the effect. Building on prior findings that Rlip depletion induces broad methylomic changes, we found using bioluminescence reporter assays that depletion of Rlip also exerts transcriptional control over several cancer genes through methylation-independent changes in transcription factor-mediated activation of their promoter regions and through additional as yet unidentified mechanisms. These findings have important implications for Rlip-targeted cancer therapy. Abstract Rlip76 (Rlip) is a multifunctional membrane protein that facilitates the high metabolic rates of cancer cells through the efflux of toxic metabolites and other functions. Rlip inhibition or depletion results in broad-spectrum anti-cancer effects in vitro and in vivo. Rlip depletion effectively suppresses malignancy and causes global reversion of characteristic CpG island methylomic and transcriptomic aberrations in the p53-null mouse model of spontaneous carcinogenesis through incompletely defined signaling and transcriptomic mechanisms. The methylome and transcriptome are normally regulated by the concerted actions of several mechanisms that include chromatin remodeling, promoter methylation, transcription factor interactions, and miRNAs. The present studies investigated the interaction of Rlip depletion or inhibition with the promoter methylation and transcription of selected cancer-related genes identified as being affected by Rlip depletion in our previous studies. We constructed novel promoter CpG island/luciferase reporter plasmids that respond only to CpG methylation and transcription factors. We found that Rlip depletion regulated expression by a transcription factor-based mechanism that functioned independently of promoter CpG methylation, lipid peroxidation, and p53 status.
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Affiliation(s)
- Ashly Hindle
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
| | - Chhanda Bose
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
| | - Jihyun Lee
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
- Division of Hematology & Oncology, Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Philip T. Palade
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Christopher J. Peterson
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
| | - P. Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Speech, Language and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Sanjay Awasthi
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
- Division of Hematology & Oncology, Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- UMC Cancer Center, UMC Health System, Lubbock, TX 79415, USA
- Correspondence: (S.A.); (S.P.S.); Tel.: +1-806-743-3543 (S.A.); +1-806-743-1540 (S.P.S.)
| | - Sharda P. Singh
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (A.H.); (C.B.); (J.L.); (C.J.P.); (P.H.R.)
- Division of Hematology & Oncology, Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: (S.A.); (S.P.S.); Tel.: +1-806-743-3543 (S.A.); +1-806-743-1540 (S.P.S.)
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110
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Tang SY, Zhou PJ, Meng Y, Zeng FR, Deng GT. Gastric cancer: An epigenetic view. World J Gastrointest Oncol 2022; 14:90-109. [PMID: 35116105 PMCID: PMC8790429 DOI: 10.4251/wjgo.v14.i1.90] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/17/2021] [Accepted: 12/23/2021] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) poses a serious threat worldwide with unfavorable prognosis mainly due to late diagnosis and limited therapies. Therefore, precise molecular classification and search for potential targets are required for diagnosis and treatment, as GC is complicated and heterogeneous in nature. Accumulating evidence indicates that epigenetics plays a vital role in gastric carcinogenesis and progression, including histone modifications, DNA methylation and non-coding RNAs. Epigenetic biomarkers and drugs are currently under intensive evaluations to ensure efficient clinical utility in GC. In this review, key epigenetic alterations and related functions and mechanisms are summarized in GC. We focus on integration of existing epigenetic findings in GC for the bench-to-bedside translation of some pivotal epigenetic alterations into clinical practice and also describe the vacant field waiting for investigation.
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Affiliation(s)
- Si-Yuan Tang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Pei-Jun Zhou
- Cancer Research Institute, School of Basic Medicine Science, Central South University, School of Basic Medicine Science, Central South University 410008, Hunan Province, China
| | - Yu Meng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Fu-Rong Zeng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Guang-Tong Deng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
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111
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Tang F, Lu Z, Lei H, Lai Y, Lu Z, Li Z, Tang Z, Zhang J, He Z. DNA Methylation Data-Based Classification and Identification of Prognostic Signature of Children With Wilms Tumor. Front Cell Dev Biol 2022; 9:683242. [PMID: 35004665 PMCID: PMC8740190 DOI: 10.3389/fcell.2021.683242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/02/2021] [Indexed: 11/29/2022] Open
Abstract
Background: As an epigenetic alteration, DNA methylation plays an important role in early Wilms tumorigenesis and is possibly used as marker to improve the diagnosis and classification of tumor heterogeneity. Methods: Methylation data, RNA-sequencing (RNA-seq) data, and corresponding clinical information were downloaded from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. The prognostic values of DNA methylation subtypes in Wilms tumor were identified. Results: Four prognostic subtypes of Wilms tumor patients were identified by consensus cluster analysis performed on 312 independent prognostic CpG sites. Cluster one showed the best prognosis, whereas Cluster two represented the worst prognosis. Unique CpG sites identified in Cluster one that were not identified in other subtypes were assessed to construct a prognostic signature. The prognostic methylation risk score was closely related to prognosis, and the area under the curve (AUC) was 0.802. Furthermore, the risk score based on prognostic signature was identified as an independent prognostic factor for Wilms tumor in univariate and multivariate Cox regression analyses. Finally, the abundance of B cell infiltration was higher in the low-risk group than in the high-risk group, based on the methylation data. Conclusion: Collectively, we divided Wilms tumor cases into four prognostic subtypes, which could efficiently identify high-risk Wilms tumor patients. Prognostic methylation risk scores that were significantly associated with the adverse clinical outcomes were established, and this prognostic signature was able to predict the prognosis of Wilms tumor in children, which may be useful in guiding clinicians in therapeutic decision-making. Further independent studies are needed to validate and advance this hypothesis.
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Affiliation(s)
- Fucai Tang
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Zeguang Lu
- The Second Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Hanqi Lei
- Department of Urology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China.,Department of Urology, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yongchang Lai
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Zechao Lu
- The First Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Zhibiao Li
- The Third Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Zhicheng Tang
- The Third Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Jiahao Zhang
- The Sixth Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Zhaohui He
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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112
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Skorupski J. Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications. Genes (Basel) 2022; 13:genes13010125. [PMID: 35052465 PMCID: PMC8774856 DOI: 10.3390/genes13010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023] Open
Abstract
In this paper, a complete mitochondrial genome of the critically endangered European mink Mustela lutreola L., 1761 is reported. The mitogenome was 16,504 bp in length and encoded the typical 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and harboured a putative control region. The A+T content of the entire genome was 60.06% (A > T > C > G), and the AT-skew and GC-skew were 0.093 and −0.308, respectively. The encoding-strand identity of genes and their order were consistent with a collinear gene order characteristic for vertebrate mitogenomes. The start codons of all protein-coding genes were the typical ATN. In eight cases, they were ended by complete stop codons, while five had incomplete termination codons (TA or T). All tRNAs had a typical cloverleaf secondary structure, except tRNASer(AGC) and tRNALys, which lacked the DHU stem and had reduced DHU loop, respectively. Both rRNAs were capable of folding into complex secondary structures, containing unmatched base pairs. Eighty-one single nucleotide variants (substitutions and indels) were identified. Comparative interspecies analyses confirmed the close phylogenetic relationship of the European mink to the so-called ferret group, clustering the European polecat, the steppe polecat and the black-footed ferret. The obtained results are expected to provide useful molecular data, informing and supporting effective conservation measures to save M. lutreola.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-91-444-16-85
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
- The European Mink Centre, 71-415 Szczecin, Poland
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113
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Krishnan M, Senagolage MD, Baeten JT, Wolfgeher DJ, Khan S, Kron SJ, McNerney ME. Genomic studies controvert the existence of the CUX1 p75 isoform. Sci Rep 2022; 12:151. [PMID: 34997000 PMCID: PMC8741762 DOI: 10.1038/s41598-021-03930-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 12/13/2021] [Indexed: 01/19/2023] Open
Abstract
CUX1, encoding a homeodomain-containing transcription factor, is recurrently deleted or mutated in multiple tumor types. In myeloid neoplasms, CUX1 deletion or mutation carries a poor prognosis. We have previously established that CUX1 functions as a tumor suppressor in hematopoietic cells across multiple organisms. Others, however, have described oncogenic functions of CUX1 in solid tumors, often attributed to truncated CUX1 isoforms, p75 and p110, generated by an alternative transcriptional start site or post-translational cleavage, respectively. Given the clinical relevance, it is imperative to clarify these discrepant activities. Herein, we sought to determine the CUX1 isoforms expressed in hematopoietic cells and find that they express the full-length p200 isoform. Through the course of this analysis, we found no evidence of the p75 alternative transcript in any cell type examined. Using an array of orthogonal approaches, including biochemistry, proteomics, CRISPR/Cas9 genomic editing, and analysis of functional genomics datasets across a spectrum of normal and malignant tissue types, we found no data to support the existence of the CUX1 p75 isoform as previously described. Based on these results, prior studies of p75 require reevaluation, including the interpretation of oncogenic roles attributed to CUX1.
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Affiliation(s)
- Manisha Krishnan
- Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA.,Department of Pathology, The University of Chicago, Chicago, IL, USA
| | | | - Jeremy T Baeten
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Donald J Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Saira Khan
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Stephen J Kron
- Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA.,Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA.,The University of Chicago Medicine Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA
| | - Megan E McNerney
- Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA. .,Department of Pathology, The University of Chicago, Chicago, IL, USA. .,Department of Pediatrics, The University of Chicago, Chicago, IL, USA. .,The University of Chicago Medicine Comprehensive Cancer Center, University of Chicago, Chicago, IL, USA.
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114
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Fanis P, Morrou M, Tomazou M, Michailidou K, Spyrou GM, Toumba M, Skordis N, Neocleous V, Phylactou LA. Methylation status of hypothalamic Mkrn3 promoter across puberty. Front Endocrinol (Lausanne) 2022; 13:1075341. [PMID: 36714607 PMCID: PMC9880154 DOI: 10.3389/fendo.2022.1075341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
Makorin RING finger protein 3 (MKRN3) is an important factor located on chromosome 15 in the imprinting region associated with Prader-Willi syndrome. Imprinted MKRN3 is expressed in hypothalamic regions essential for the onset of puberty and mutations in the gene have been found in patients with central precocious puberty. The pubertal process is largely controlled by epigenetic mechanisms that include, among other things, DNA methylation at CpG dinucleotides of puberty-related genes. In the present study, we investigated the methylation status of the Mkrn3 promoter in the hypothalamus of the female mouse before, during and after puberty. Initially, we mapped the 32 CpG dinucleotides in the promoter, the 5'UTR and the first 50 nucleotides of the coding region of the Mkrn3 gene. Moreover, we identified a short CpG island region (CpG islet) located within the promoter. Methylation analysis using bisulfite sequencing revealed that CpG dinucleotides were methylated regardless of developmental stage, with the lowest levels of methylation being found within the CpG islet region. In addition, the CpG islet region showed significantly lower methylation levels at the pre-pubertal stage when compared with the pubertal or post-pubertal stage. Finally, in silico analysis of transcription factor binding sites on the Mkrn3 CpG islet identified the recruitment of 29 transcriptional regulators of which 14 were transcriptional repressors. Our findings demonstrate the characterization and differential methylation of the CpG dinucleotides located in the Mkrn3 promoter that could influence the transcriptional activity in pre-pubertal compared to pubertal or post-pubertal period. Further studies are needed to clarify the possible mechanisms and effects of differential methylation of the Mkrn3 promoter.
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Affiliation(s)
- Pavlos Fanis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Maria Morrou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios Tomazou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M. Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Meropi Toumba
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Child Endocrine Care, Department of Pediatrics, Aretaeio Hospital, Nicosia, Cyprus
| | - Nicos Skordis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Division of Pediatric Endocrinology, Paedi Center for Specialized Pediatrics, Nicosia, Cyprus
- Medical School, University of Nicosia, Nicosia, Cyprus
| | - Vassos Neocleous
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Leonidas A. Phylactou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- *Correspondence: Leonidas A. Phylactou,
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115
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Mancia A. Genome-Wide DNA Methylation Protocol for Epigenetics Studies. Methods Mol Biol 2022; 2498:19-41. [PMID: 35727538 DOI: 10.1007/978-1-0716-2313-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Epigenetic modification are heritable changes in gene expression not encoded by the DNA sequence therefore playing a significant role in a broad range of biological processes and diseases.A key player of the epigenetic modifications is the DNA methylation, a process involving the covalent transfer of a methyl group to the C-5 position of the cytosine ring of DNA forming 5-methylcytosine (5mC), catalyzed by DNA methyltransferases. Altering the structure of the chromatin, DNA methylation has the potential to down-regulate gene expression.The here presented protocol shows a method to obtain DNA samples ready for NGS sequencing for genome-wide methylation analysis.
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Affiliation(s)
- Annalaura Mancia
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy.
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116
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St Germain C, Zhao H, Sinha V, Sanz LA, Chédin F, Barlow J. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2051-2073. [PMID: 35100392 PMCID: PMC8887484 DOI: 10.1093/nar/gkac035] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 01/05/2022] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
Conflicts between transcription and replication machinery are a potent source of replication stress and genome instability; however, no technique currently exists to identify endogenous genomic locations prone to transcription–replication interactions. Here, we report a novel method to identify genomic loci prone to transcription–replication interactions termed transcription–replication immunoprecipitation on nascent DNA sequencing, TRIPn-Seq. TRIPn-Seq employs the sequential immunoprecipitation of RNA polymerase 2 phosphorylated at serine 5 (RNAP2s5) followed by enrichment of nascent DNA previously labeled with bromodeoxyuridine. Using TRIPn-Seq, we mapped 1009 unique transcription–replication interactions (TRIs) in mouse primary B cells characterized by a bimodal pattern of RNAP2s5, bidirectional transcription, an enrichment of RNA:DNA hybrids, and a high probability of forming G-quadruplexes. TRIs are highly enriched at transcription start sites and map to early replicating regions. TRIs exhibit enhanced Replication Protein A association and TRI-associated genes exhibit higher replication fork termination than control transcription start sites, two marks of replication stress. TRIs colocalize with double-strand DNA breaks, are enriched for deletions, and accumulate mutations in tumors. We propose that replication stress at TRIs induces mutations potentially contributing to age-related disease, as well as tumor formation and development.
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Affiliation(s)
- Commodore P St Germain
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
- School of Mathematics and Science, Solano Community College, 4000 Suisun Valley Road, Fairfield, CA 94534, USA
| | - Hongchang Zhao
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Vrishti Sinha
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jacqueline H Barlow
- To whom correspondence should be addressed. Tel: +1 530 752 9529; Fax: +1 530 752 9014;
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117
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DNA Methyltransferases and DNA Damage. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:349-361. [DOI: 10.1007/978-3-031-11454-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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118
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The Role of DNA Methylation and DNA Methyltransferases in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:317-348. [DOI: 10.1007/978-3-031-11454-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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119
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Lee JY, Davis I, Youth EHH, Kim J, Churchill G, Godwin J, Korstanje R, Beck S. Misexpression of genes lacking CpG islands drives degenerative changes during aging. SCIENCE ADVANCES 2021; 7:eabj9111. [PMID: 34910517 PMCID: PMC8673774 DOI: 10.1126/sciadv.abj9111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/26/2021] [Indexed: 05/14/2023]
Abstract
Cellular aging is characterized by disruption of the nuclear lamina and its associated heterochromatin. How these structural changes within the nucleus contribute to age-related degeneration of the organism is unclear. Genes lacking CpG islands (CGI− genes) generally associate with heterochromatin when they are inactive. Here, we show that the expression of these genes is globally activated in aged cells and tissues. This CGI− gene misexpression is a common feature of normal and pathological aging in mice and humans. We report evidence that CGI− gene up-regulation is directly responsible for age-related physiological deterioration, notably for increased secretion of inflammatory mediators.
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Affiliation(s)
- Jun-Yeong Lee
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Ian Davis
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Elliot H. H. Youth
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
- Brown University, Providence, RI 02912, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - James Godwin
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | - Samuel Beck
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
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Pires VS, de O. Ganzella FA, Minozzo GA, Dias de Castro LL, Moncada AD, Klassen G, Ramos EA, Molento MB. Epigenetic regulation of SLC11a1 gene in horses infected with cyathostomins. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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121
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Sex-specific chromatin remodelling safeguards transcription in germ cells. Nature 2021; 600:737-742. [PMID: 34880491 DOI: 10.1038/s41586-021-04208-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 11/01/2021] [Indexed: 11/08/2022]
Abstract
Stability of the epigenetic landscape underpins maintenance of the cell-type-specific transcriptional profile. As one of the main repressive epigenetic systems, DNA methylation has been shown to be important for long-term gene silencing; its loss leads to ectopic and aberrant transcription in differentiated cells and cancer1. The developing mouse germ line endures global changes in DNA methylation in the absence of widespread transcriptional activation. Here, using an ultra-low-input native chromatin immunoprecipitation approach, we show that following DNA demethylation the gonadal primordial germ cells undergo remodelling of repressive histone modifications, resulting in a sex-specific signature in mice. We further demonstrate that Polycomb has a central role in transcriptional control in the newly hypomethylated germline genome as the genetic loss of Ezh2 leads to aberrant transcriptional activation, retrotransposon derepression and dramatic loss of developing female germ cells. This sex-specific effect of Ezh2 deletion is explained by the distinct landscape of repressive modifications observed in male and female germ cells. Overall, our study provides insight into the dynamic interplay between repressive chromatin modifications in the context of a developmental reprogramming system.
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122
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Li L, Wang T, Chen S, Yue Y, Xu Z, Yuan Y. DNA methylations of brain-derived neurotrophic factor exon VI are associated with major depressive disorder and antidepressant-induced remission in females. J Affect Disord 2021; 295:101-107. [PMID: 34418778 DOI: 10.1016/j.jad.2021.08.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Brain-derived neurotrophic factor (BDNF) has been suggested to play important roles in major depressive disorder (MDD) and antidepressant treatment. The main purpose of this study was to evaluate the association of DNA methylation changes in the BDNF gene with MDD and antidepressant treatment. METHODS A total of 291 MDD patients and 100 healthy controls were included and followed up for 6 weeks. The Hamilton Depression Rating Scale-17 (HDRS-17) was used to measure treatment improvement. The life events scales (LES) and childhood trauma questionnaire (CTQ) were used to rate recent and early life stress. DNA methylation levels of CpG sites in the BDNF gene were measured. RESULTS Two CpG sites in BDNF exon VI (BDNF133 and BDNF134) were demonstrated to have significantly higher methylation in MDD patients than in controls (both FDR-adjusted P = 0.001). A logistics regression model indicated that the interaction between the hypermethylation of BDNF133 and negative subscore of LES was associated to MDD (OR=0.0075, P<0.001). Methylation of BDNF140 at baseline was significantly elevated in remitters (FDR-adjusted P = 0.046) at week 6. In subgroup analyses, these findings could be replicated in females, but not in males. LIMITATIONS The methylation status of BDNF after 6 weeks of antidepressant treatment was not measured and the DNA methylation were detected in peripheral blood cells. CONCLUSIONS These findings highlight gender-specific alteration of methylation at several CpG sites in BDNF exon VI as a promising candidate indicator of MDD and antidepressant-induced remission.
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Affiliation(s)
- Lei Li
- Institute of Psychosomatics, School of Medicine, Southeast University, Nanjing, 210023, China; Department of Psychosomatics and Psychiatry, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China; Department of Sleep Medicine, The Fourth People's Hospital of Lianyungang, Lianyungang, 222000, China
| | - Tianyu Wang
- Institute of Psychosomatics, School of Medicine, Southeast University, Nanjing, 210023, China; Department of Psychosomatics and Psychiatry, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China
| | - Suzhen Chen
- Institute of Psychosomatics, School of Medicine, Southeast University, Nanjing, 210023, China; Department of Psychosomatics and Psychiatry, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China
| | - Yingying Yue
- Institute of Psychosomatics, School of Medicine, Southeast University, Nanjing, 210023, China; Department of Psychosomatics and Psychiatry, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China
| | - Zhi Xu
- Institute of Psychosomatics, School of Medicine, Southeast University, Nanjing, 210023, China; Department of Psychosomatics and Psychiatry, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China.
| | - Yonggui Yuan
- Institute of Psychosomatics, School of Medicine, Southeast University, Nanjing, 210023, China; Department of Psychosomatics and Psychiatry, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, China; Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast university, Nanjing, 210009, China.
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123
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Mavaie P, Holder L, Beck D, Skinner MK. Predicting environmentally responsive transgenerational differential DNA methylated regions (epimutations) in the genome using a hybrid deep-machine learning approach. BMC Bioinformatics 2021; 22:575. [PMID: 34847877 PMCID: PMC8630850 DOI: 10.1186/s12859-021-04491-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/18/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Deep learning is an active bioinformatics artificial intelligence field that is useful in solving many biological problems, including predicting altered epigenetics such as DNA methylation regions. Deep learning (DL) can learn an informative representation that addresses the need for defining relevant features. However, deep learning models are computationally expensive, and they require large training datasets to achieve good classification performance. RESULTS One approach to addressing these challenges is to use a less complex deep learning network for feature selection and Machine Learning (ML) for classification. In the current study, we introduce a hybrid DL-ML approach that uses a deep neural network for extracting molecular features and a non-DL classifier to predict environmentally responsive transgenerational differential DNA methylated regions (DMRs), termed epimutations, based on the extracted DL-based features. Various environmental toxicant induced epigenetic transgenerational inheritance sperm epimutations were used to train the model on the rat genome DNA sequence and use the model to predict transgenerational DMRs (epimutations) across the entire genome. CONCLUSION The approach was also used to predict potential DMRs in the human genome. Experimental results show that the hybrid DL-ML approach outperforms deep learning and traditional machine learning methods.
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Affiliation(s)
- Pegah Mavaie
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, 99164-2752, USA
| | - Lawrence Holder
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, 99164-2752, USA.
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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Marion MC, Ramos PS, Bachali P, Labonte AC, Zimmerman KD, Ainsworth HC, Heuer SE, Robl RD, Catalina MD, Kelly JA, Howard TD, Lipsky PE, Grammer AC, Langefeld CD. Nucleic Acid-Sensing and Interferon-Inducible Pathways Show Differential Methylation in MZ Twins Discordant for Lupus and Overexpression in Independent Lupus Samples: Implications for Pathogenic Mechanism and Drug Targeting. Genes (Basel) 2021; 12:genes12121898. [PMID: 34946847 PMCID: PMC8701117 DOI: 10.3390/genes12121898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/27/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic, multisystem, autoimmune inflammatory disease with genomic and non-genomic contributions to risk. We hypothesize that epigenetic factors are a significant contributor to SLE risk and may be informative for identifying pathogenic mechanisms and therapeutic targets. To test this hypothesis while controlling for genetic background, we performed an epigenome-wide analysis of DNA methylation in genomic DNA from whole blood in three pairs of female monozygotic (MZ) twins of European ancestry, discordant for SLE. Results were replicated on the same array in four cell types from a set of four Danish female MZ twin pairs discordant for SLE. Genes implicated by the epigenetic analyses were then evaluated in 10 independent SLE gene expression datasets from the Gene Expression Omnibus (GEO). There were 59 differentially methylated loci between unaffected and affected MZ twins in whole blood, including 11 novel loci. All but two of these loci were hypomethylated in the SLE twins relative to the unaffected twins. The genes harboring these hypomethylated loci exhibited increased expression in multiple independent datasets of SLE patients. This pattern was largely consistent regardless of disease activity, cell type, or renal tissue type. The genes proximal to CpGs exhibiting differential methylation (DM) in the SLE-discordant MZ twins and exhibiting differential expression (DE) in independent SLE GEO cohorts (DM-DE genes) clustered into two pathways: the nucleic acid-sensing pathway and the type I interferon pathway. The DM-DE genes were also informatically queried for potential gene–drug interactions, yielding a list of 41 drugs including a known SLE therapy. The DM-DE genes delineate two important biologic pathways that are not only reflective of the heterogeneity of SLE but may also correlate with distinct IFN responses that depend on the source, type, and location of nucleic acid molecules and the activated receptors in individual patients. Cell- and tissue-specific analyses will be critical to the understanding of genetic factors dysregulating the nucleic acid-sensing and IFN pathways and whether these factors could be appropriate targets for therapeutic intervention.
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Affiliation(s)
- Miranda C. Marion
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Paula S. Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Prathyusha Bachali
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Adam C. Labonte
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Kip D. Zimmerman
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Hannah C. Ainsworth
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Sarah E. Heuer
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
- The Jackson Laboratory, Tufts Graduate School of Biomedical Sciences, Bar Harbor, ME 04609, USA
| | - Robert D. Robl
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Michelle D. Catalina
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
| | - Timothy D. Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Peter E. Lipsky
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Amrie C. Grammer
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
- Correspondence:
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Matsumoto S, Tateishi-Karimata H, Ohyama T, Sugimoto N. Effect of DNA modifications on the transition between canonical and non-canonical DNA structures in CpG islands during senescence. RSC Adv 2021; 11:37205-37217. [PMID: 35496393 PMCID: PMC9043837 DOI: 10.1039/d1ra07201c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/08/2021] [Indexed: 12/22/2022] Open
Abstract
Patterns and levels of DNA modifications play important roles in senescence. Two major epigenetic modifications of DNA, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), target CpG sites. Importantly, CpG concentrated regions, known as CpG islands, contain GC-rich sequences, which have the potential to fold into non-canonical DNA structures such as i-motifs and G-quadruplexes. In this study, we investigated the effect of 5mC and 5hmC modifications on the transition between a duplex, and i-motif and G-quadruplexes. To examine the transition, we firstly investigated the stability and structure of the i-motif and G-quadruplexes, considering the molecular environment in senescent cells. Analyses of their stability showed that the modifications did not drastically affect the stability. However, noteworthily, the modification can weaken the (de)stabilisation effect on G-quadruplexes caused by cosolute(s) and cations. Circular dichroism analyses indicated that the surrounding environments, including the molecular crowding and the type of cations such as K+ and Na+, regulate the topology of G-quadruplexes, while neither 5mC nor 5hmC had a drastic effect. On the other hand, the modifications changed the transition between duplexes and quadruplexes. Unmodified DNA preferred to fold into quadruplexes, whereas DNA with 5mC and 5hmC preferred to fold into duplexes in the absence of PEG200; on the other hand, DNA with or without modifications tended to fold into i-motifs under crowded conditions. Furthermore, an investigation of quadruplexes forming sequences in CpG islands, which are hyper- or hypomethylated during senescence, followed by gene ontology enrichment analysis for each gene group classified by the presence of quadruplexes, showed a difference in function between genes with and without quadruplexes in the CpG region. These results indicate that it is important to consider the effects of patterns and levels of DNA modifications on the transition between canonical and non-canonical DNA structures to understand gene regulation by epigenetic modification during senescence. The modification of DNA can regulate the transition between a duplex and quadruplexes during senescence responding to surrounding environments.![]()
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Affiliation(s)
- Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan
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126
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Benner P, Vingron M. Quantifying the tissue-specific regulatory information within enhancer DNA sequences. NAR Genom Bioinform 2021; 3:lqab095. [PMID: 34729474 PMCID: PMC8557370 DOI: 10.1093/nargab/lqab095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/04/2022] Open
Abstract
Recent efforts to measure epigenetic marks across a wide variety of different cell types and tissues provide insights into the cell type-specific regulatory landscape. We use these data to study whether there exists a correlate of epigenetic signals in the DNA sequence of enhancers and explore with computational methods to what degree such sequence patterns can be used to predict cell type-specific regulatory activity. By constructing classifiers that predict in which tissues enhancers are active, we are able to identify sequence features that might be recognized by the cell in order to regulate gene expression. While classification performances vary greatly between tissues, we show examples where our classifiers correctly predict tissue-specific regulation from sequence alone. We also show that many of the informative patterns indeed harbor transcription factor footprints.
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Affiliation(s)
- Philipp Benner
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
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127
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Chequin A, Costa LE, de Campos FF, Moncada ADB, de Lima LTF, Sledz LR, Picheth GF, Adami ER, Acco A, Gonçalves MB, Manica GCM, Valdameri G, de Noronha L, Telles JEQ, Jandrey EHF, Costa ET, Costa FF, de Souza EM, Ramos EAS, Klassen G. Antitumoral activity of liraglutide, a new DNMT inhibitor in breast cancer cells in vitro and in vivo. Chem Biol Interact 2021; 349:109641. [PMID: 34534549 DOI: 10.1016/j.cbi.2021.109641] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/17/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
Breast cancer (BC) is the most frequently diagnosed female cancer and second leading cause of death. Despite the discovery of many antineoplastic drugs for BC, the current therapy is not totally efficient. In this study, we investigated the potential of repurposing the well-known diabetes type II drug liraglutide to modulate epigenetic modifications in BC cells lines in vitro and in vivo via Ehrlich mice tumors models. The in vitro results revealed a significant reduction on cell viability, migration, DNMT activity and displayed lower levels of global DNA methylation in BC cell lines after liraglutide treatment. The interaction between liraglutide and the DNMT enzymes resulted in a decrease profile of DNA methylation for the CDH1, ESR1 and ADAM33 gene promoter regions and, consequently, increased their gene and protein expression levels. To elucidate the possible interaction between liraglutide and the DNMT1 protein, we performed an in silico study that indicates liraglutide binding in the catalytic cleft via hydrogen bonds and salt bridges with the interdomain contacts and disturbs the overall enzyme conformation. The in vivo study was also able to reveal that liraglutide and the combined treatment of liraglutide and paclitaxel or methotrexate were effective in reducing tumor growth. Moreover, the modulation of CDH1 and ADAM33 mouse gene expression by DNA demethylation suggests a role for liraglutide in DNMT activity in vivo. Altogether, these results indicate that liraglutide may be further analysed as a new adjuvant treatment for BC.
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Affiliation(s)
- Andressa Chequin
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Luiz E Costa
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Felipe F de Campos
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Angie D B Moncada
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Lucas T F de Lima
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Lucas R Sledz
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Guilherme F Picheth
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Eliana R Adami
- Department of Pharmacology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Alexandra Acco
- Department of Pharmacology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Marcos B Gonçalves
- Department of Physics, Federal Technological University of Paraná, Curitiba, Parana, Brazil
| | - Graciele C M Manica
- Department of Clinical Analysis, Federal University of Paraná, Curitiba, PR, Brazil
| | - Gláucio Valdameri
- Department of Clinical Analysis, Federal University of Paraná, Curitiba, PR, Brazil
| | - Lucia de Noronha
- Department of Clinical Pathology, Pontifical Catholic University of Paraná, Curitiba, PR, Brazil
| | - José E Q Telles
- Department of Medical Pathology, Federal University of Paraná, Brazil
| | - Elisa H F Jandrey
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Erico T Costa
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | | | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Edneia A S Ramos
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Giseli Klassen
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil.
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128
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Costello KR, Leung A, Trac C, Lee M, Basam M, Pospisilik JA, Schones DE. Sequence features of retrotransposons allow for epigenetic variability. eLife 2021; 10:71104. [PMID: 34668484 PMCID: PMC8555987 DOI: 10.7554/elife.71104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that make up a large fraction of mammalian genomes. While select TEs have been co-opted in host genomes to have function, the majority of these elements are epigenetically silenced by DNA methylation in somatic cells. However, some TEs in mice, including the Intracisternal A-particle (IAP) subfamily of retrotransposons, have been shown to display interindividual variation in DNA methylation. Recent work has revealed that IAP sequence differences and strain-specific KRAB zinc finger proteins (KZFPs) may influence the methylation state of these IAPs. However, the mechanisms underlying the establishment and maintenance of interindividual variability in DNA methylation still remain unclear. Here, we report that sequence content and genomic context influence the likelihood that IAPs become variably methylated. IAPs that differ from consensus IAP sequences have altered KZFP recruitment that can lead to decreased KAP1 recruitment when in proximity of constitutively expressed genes. These variably methylated loci have a high CpG density, similar to CpG islands, and can be bound by ZF-CxxC proteins, providing a potential mechanism to maintain this permissive chromatin environment and protect from DNA methylation. These observations indicate that variably methylated IAPs escape silencing through both attenuation of KZFP binding and recognition by ZF-CxxC proteins to maintain a hypomethylated state.
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Affiliation(s)
- Kevin R Costello
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, United States
| | - Amy Leung
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States
| | - Candi Trac
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States
| | - Michael Lee
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, United States
| | - Mudaser Basam
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States
| | | | - Dustin E Schones
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, Duarte, United States.,Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, United States
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129
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Changes in PGC-1α-Dependent Mitochondrial Biogenesis Are Associated with Inflexible Hepatic Energy Metabolism in the Offspring Born to Dexamethasone-Treated Mothers. LIVERS 2021. [DOI: 10.3390/livers1040016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In the present study we investigated the participation of hepatic peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1α) in the metabolic programming of newborn rats exposed in utero to dexamethasone (DEX). On the 21st day of life, fasted offspring born to DEX-treated mothers displayed increased conversion of pyruvate into glucose with simultaneous upregulation of PEPCK (phosphoenolpyruvate carboxykinase) and G6Pase (glucose-6-phosphatase). Increased oxidative phosphorylation, higher ATP/ADP ratio and mitochondrial biogenesis and lower pyruvate levels were also found in the progeny of DEX-treated mothers. On the other hand, the 21-day-old progeny of DEX-treated mothers had increased hepatic triglycerides (TAG) and lower CPT-1 activity when subjected to short-term fasting. At the mechanistic level, rats exposed in utero to DEX exhibited increased hepatic PGC-1α protein content with lower miR-29a-c expression. Increased PGC-1α content was concurrent with increased association to HNF-4α and NRF1 and reduced PPARα expression. The data presented herein reveal that changes in the transcription machinery in neonatal liver of rats born to DEX-treated mothers leads to an inflexible metabolic response to fasting. Such programming is hallmarked by increased oxidative phosphorylation of pyruvate with impaired FFA oxidation and hepatic TAG accumulation.
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130
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Chandra K, Banerjee A, Das M. Epigenetic and transcriptional regulation of GnRH gene under altered metabolism and ageing. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00374-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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131
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Araki R, Nishida S, Nakajima Y, Iwakumo A, Tachioka H, Kita A, Yabe T. Low folate induces abnormal neuronal maturation and DNA hypomethylation of neuronal differentiation-related genes in cultured mouse neural stem and progenitor cells. Heliyon 2021; 7:e08071. [PMID: 34622073 PMCID: PMC8479244 DOI: 10.1016/j.heliyon.2021.e08071] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 02/05/2021] [Accepted: 09/22/2021] [Indexed: 11/28/2022] Open
Abstract
Folate deficiency in a fetus is well known to cause neurodevelopment defects and development disorders. A low level of folate is also thought to be a risk for depression in adults. We have previously shown that post-weaning low folate induces neuronal immaturity in the dentate gyrus in mice, which suggests that low folate causes neuropsychological disorders via inhibition of neuronal maturation. In this study, we examined the effects of low folate on expression and epigenetic modification of genes involved in neuronal differentiation and maturation in primary mouse neural stem/progenitor cells (NSPCs) in vitro. An increase in Nestin (NSPC marker)-positive cells was observed in cells differentiated in a low folate medium for 3 days. An increase in βIII-tubulin (Tuj1: immature neuron marker)-positive cells and a decrease in microtubule-associated protein 2 (MAP2: mature neuron marker)-positive cells were observed in cells differentiated in a low folate medium for 7 days. In these cells, mRNA levels for genes involved in neuronal differentiation and maturation were altered. Hypomethylation of DNA, but not of histone proteins, was also observed at some promoters of these neuronal genes. The level of S-adenosylmethionine (SAM), a methyl donor, was decreased in these cells. The abnormalities in neural maturation and changes in gene expression in culture under low folate conditions were partially normalized by addition of SAM (5 μM). Based on these results, decreased SAM may induce DNA hypomethylation at genes involved in neuronal differentiation and maturation under low folate conditions, and this hypomethylation may be associated with low folate-induced neuronal immaturity.
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Affiliation(s)
- Ryota Araki
- Laboratory of Functional Biomolecules and Chemical Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Shoji Nishida
- Laboratory of Functional Biomolecules and Chemical Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Yuki Nakajima
- Laboratory of Functional Biomolecules and Chemical Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Arimi Iwakumo
- Laboratory of Functional Biomolecules and Chemical Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Hayato Tachioka
- Laboratory of Functional Biomolecules and Chemical Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Ayami Kita
- Laboratory of Functional Biomolecules and Chemical Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Takeshi Yabe
- Laboratory of Functional Biomolecules and Chemical Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
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Wruck W, Graffmann N, Spitzhorn LS, Adjaye J. Human Induced Pluripotent Stem Cell-Derived Mesenchymal Stem Cells Acquire Rejuvenation and Reduced Heterogeneity. Front Cell Dev Biol 2021; 9:717772. [PMID: 34604216 PMCID: PMC8481886 DOI: 10.3389/fcell.2021.717772] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/17/2021] [Indexed: 12/20/2022] Open
Abstract
Despite the uniform selection criteria for the isolation of human mesenchymal stem cells (MSCs), considerable heterogeneity exists which reflects the distinct tissue origins and differences between individuals with respect to their genetic background and age. This heterogeneity is manifested by the variabilities seen in the transcriptomes, proteomes, secretomes, and epigenomes of tissue-specific MSCs. Here, we review literature on different aspects of MSC heterogeneity including the role of epigenetics and the impact of MSC heterogeneity on therapies. We then combine this with a meta-analysis of transcriptome data from distinct MSC subpopulations derived from bone marrow, adipose tissue, cruciate, tonsil, kidney, umbilical cord, fetus, and induced pluripotent stem cells derived MSCs (iMSCs). Beyond that, we investigate transcriptome differences between tissue-specific MSCs and pluripotent stem cells. Our meta-analysis of numerous MSC-related data sets revealed markers and associated biological processes characterizing the heterogeneity and the common features of MSCs from various tissues. We found that this heterogeneity is mainly related to the origin of the MSCs and infer that microenvironment and epigenetics are key drivers. The epigenomes of MSCs alter with age and this has a profound impact on their differentiation capabilities. Epigenetic modifications of MSCs are propagated during cell divisions and manifest in differentiated cells, thus contributing to diseased or healthy phenotypes of the respective tissue. An approach used to reduce heterogeneity caused by age- and tissue-related epigenetic and microenvironmental patterns is the iMSC concept: iMSCs are MSCs generated from induced pluripotent stem cells (iPSCs). During iMSC generation epigenetic and chromatin remodeling result in a gene expression pattern associated with rejuvenation thus allowing to overcome age-related shortcomings (e.g., limited differentiation and proliferation capacity). The importance of the iMSC concept is underlined by multiple clinical trials. In conclusion, we propose the use of rejuvenated iMSCs to bypass tissue- and age-related heterogeneity which are associated with native MSCs.
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Affiliation(s)
- Wasco Wruck
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nina Graffmann
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lucas-Sebastian Spitzhorn
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - James Adjaye
- Medical Faculty, Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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133
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Yamazaki J, Toyomaki H, Nakayama SMM, Yabe J, Muzandu K, Jelinek J, Yokoyama S, Ikenaka Y, Takiguchi M, Ishizuka M. Genome-wide DNA methylation analysis of dogs with high lead exposure living near a lead mining area in Kabwe, Zambia. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117229. [PMID: 33975213 DOI: 10.1016/j.envpol.2021.117229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Lead (Pb) is a heavy metal that has been proven to be toxic to both animals and humans. Genom-wide DNA methylation in domestic dogs exposed to high levels of Pb in Kabwe, Zambia was analyzed in this study. Using next-generation sequencing on samples from 20 domestic dogs (mean blood Pb concentration: 43.6 μg/dL and 7.2 μg/dL in the high and low exposure groups), a digital restriction enzyme analysis of methylation was performed to identify the genomic locations of differentially methylated CpG sites. A validation study on an additional 20 dogs followed (blood Pb concentration: 4.9-29.7 μg/dL). The cluster analysis resolved two broad clusters indicating high and low Pb exposure. The study identified 827 (1.2%) CpG sites with differences in methylation (101 CpG sites were hypermethylated in the low exposure group and 726 were hypermethylated in the high exposure group). The sites corresponded to 26 genes with differentially methylated CpG sites at their promoter regions, including the NGF gene. The methylation of four CpG sites was validated using bisulfite pyrosequencing. The results indicate that aberrant hypermethylation is prevalent in dogs exposed to Pb. The altered DNA methylation of the genes identified in this study contributes to a greater understanding of the epigenetic changes caused by Pb exposure and highlights novel biomarker discoveries across species.
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Affiliation(s)
- Jumpei Yamazaki
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan; One Health Research Center, Hokkaido University, Japan
| | - Haruya Toyomaki
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Japan
| | - Shouta M M Nakayama
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Japan.
| | - John Yabe
- School of Veterinary Medicine, The University of Zambia, P.O. Box 32379, Lusaka, Zambia; Dept of Pathobiology, Faculty of Agriculture & Natural Resources, School of Veterinary Medicine, University of Namibia, Windhoek, Namibia
| | - Kaampwe Muzandu
- School of Veterinary Medicine, The University of Zambia, P.O. Box 32379, Lusaka, Zambia
| | | | - Shoko Yokoyama
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan
| | - Yoshinori Ikenaka
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan; Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Japan; One Health Research Center, Hokkaido University, Japan; Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Mitsuyoshi Takiguchi
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan
| | - Mayumi Ishizuka
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Japan
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134
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Yamazaki J, Jelinek J, Yokoyama S, Takiguchi M. Genome-wide DNA methylation profile in feline haematological tumours: A preliminary study. Res Vet Sci 2021; 140:221-228. [PMID: 34534903 DOI: 10.1016/j.rvsc.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 08/18/2021] [Accepted: 09/06/2021] [Indexed: 01/17/2023]
Abstract
Although DNA methylation has been analysed in few studies for a limited number of loci in cats with diseases, genome-wide profile of DNA methylation has never been addressed. The hypothesis for this study is that next-generation sequencing with sequential digestion of genomic DNA with SmaI and XmaI enzymes could provide highly quantitative information on methylation levels in cats. Using blood from four healthy control cats and two disease cats as well as three feline lymphoma/leukemia cell lines, approximately 74-94 thousand CpG sites across the cat genome could be analysed. CpG sites in CpG island (CGI) were broadly either methylated or unmethylated in normal blood, while CpG sites in non-CpG islands (NCGI) are largely methylated. Lymphoma cell lines showed thousands of CpG sites with gain of methylation at normally unmethylated CGI sites and loss of methylation at normally methylated NCGI sites. Hypermethylated CpG sites located at promoter regions included genes annotated with 'developmental process' and 'anatomical structure morphogenesis' such as HOXD10. This highly quantitative method would be suitable for studies of DNA methylation changes not only in cancer but also in other common diseases in cats.
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Affiliation(s)
- Jumpei Yamazaki
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan; One Health Research Center, Hokkaido University, Japan; Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan.
| | | | - Shoko Yokoyama
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan; One Health Research Center, Hokkaido University, Japan; Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | - Mitsuyoshi Takiguchi
- Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan
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135
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Shi J, Xu J, Chen YE, Li JS, Cui Y, Shen L, Li JJ, Li W. The concurrence of DNA methylation and demethylation is associated with transcription regulation. Nat Commun 2021; 12:5285. [PMID: 34489442 PMCID: PMC8421433 DOI: 10.1038/s41467-021-25521-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
The mammalian DNA methylome is formed by two antagonizing processes, methylation by DNA methyltransferases (DNMT) and demethylation by ten-eleven translocation (TET) dioxygenases. Although the dynamics of either methylation or demethylation have been intensively studied in the past decade, the direct effects of their interaction on gene expression remain elusive. Here, we quantify the concurrence of DNA methylation and demethylation by the percentage of unmethylated CpGs within a partially methylated read from bisulfite sequencing. After verifying ‘methylation concurrence’ by its strong association with the co-localization of DNMT and TET enzymes, we observe that methylation concurrence is strongly correlated with gene expression. Notably, elevated methylation concurrence in tumors is associated with the repression of 40~60% of tumor suppressor genes, which cannot be explained by promoter hypermethylation alone. Furthermore, methylation concurrence can be used to stratify large undermethylated regions with negligible differences in average methylation into two subgroups with distinct chromatin accessibility and gene regulation patterns. Together, methylation concurrence represents a unique methylation metric important for transcription regulation and is distinct from conventional metrics, such as average methylation and methylation variation. The global pattern of the mammalian methylome is formed by changes in methylation and demethylation. Here the authors describe a metric methylation concurrence that measures the ratio of unmethylated CpGs inside the partially methylated reads and show that methylation concurrence is associated with epigenetically regulated tumour suppressor genes.
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Affiliation(s)
- Jiejun Shi
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Jianfeng Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yiling Elaine Chen
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Jason Sheng Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Lanlan Shen
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA.
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136
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Qi Z, Li J, Li M, Du X, Zhang L, Wang S, Xu B, Liu W, Xu Z, Deng Y. The Essential Role of Epigenetic Modifications in Neurodegenerative Diseases with Dyskinesia. Cell Mol Neurobiol 2021; 42:2459-2472. [PMID: 34383231 DOI: 10.1007/s10571-021-01133-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/18/2021] [Indexed: 12/20/2022]
Abstract
Epigenetics play an essential role in the occurrence and improvement of many diseases. Evidence shows that epigenetic modifications are crucial to the regulation of gene expression. DNA methylation is closely linked to embryonic development in mammalian. In recent years, epigenetic drugs have shown unexpected therapeutic effects on neurological diseases, leading to the study of the epigenetic mechanism in neurodegenerative diseases. Unlike genetics, epigenetics modify the genome without changing the DNA sequence. Research shows that epigenetics is involved in all aspects of neurodegenerative diseases. The study of epigenetic will provide valuable insights into the molecular mechanism of neurodegenerative diseases, which may lead to new treatments and diagnoses. This article reviews the role of epigenetic modifications neurodegenerative diseases with dyskinesia, and discusses the therapeutic potential of epigenetic drugs in neurodegenerative diseases.
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Affiliation(s)
- Zhipeng Qi
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Jiashuo Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Minghui Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Xianchao Du
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Lei Zhang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Shuang Wang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Bin Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Wei Liu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Zhaofa Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Yu Deng
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China.
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137
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Mosella MS, Sabedot TS, Silva TC, Malta TM, Dezem FS, Asmaro KP, Wells M, Mukherjee A, Poisson LM, Snyder J, deCarvalho AC, Walbert T, Aho T, Kalkanis S, Elias PC, Antonini SR, Rock J, Noushmehr H, Castro M, Castro AV. DNA methylation-based signatures classify sporadic pituitary tumors according to clinicopathological features. Neuro Oncol 2021; 23:1292-1303. [PMID: 33631002 DOI: 10.1093/neuonc/noab044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Distinct genome-wide methylation patterns cluster pituitary neuroendocrine tumors (PitNETs) into molecular groups associated with specific clinicopathological features. Here we aim to identify, characterize, and validate methylation signatures that objectively classify PitNET into clinicopathological groups. METHODS Combining in-house and publicly available data, we conducted an analysis of the methylome profile of a comprehensive cohort of 177 tumors (Panpit cohort) and 20 nontumor specimens from the pituitary gland. We also retrieved methylome data from an independent PitNET cohort (N = 86) to validate our findings. RESULTS We identified three methylation clusters associated with adenohypophyseal cell lineages and functional status using an unsupervised approach. Differentially methylated probes (DMP) significantly distinguished the Panpit clusters and accurately assigned the samples of the validation cohort to their corresponding lineage and functional subtypes memberships. The DMPs were annotated in regulatory regions enriched with enhancer elements, associated with pathways and genes involved in pituitary cell identity, function, tumorigenesis, and invasiveness. Some DMPs correlated with genes with prognostic and therapeutic values in other intra- or extracranial tumors. CONCLUSIONS We identified and validated methylation signatures, mainly annotated in enhancer regions that distinguished PitNETs by distinct adenohypophyseal cell lineages and functional status. These signatures provide the groundwork to develop an unbiased approach to classifying PitNETs according to the most recent classification recommended by the 2017 WHO and to explore their biological and clinical relevance in these tumors.
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Affiliation(s)
- Maritza S Mosella
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA.,Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Thais S Sabedot
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Tiago C Silva
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Tathiane M Malta
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Felipe Segato Dezem
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Karam P Asmaro
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Michael Wells
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Abir Mukherjee
- Department of Pathology, Henry Ford Health System, Detroit, Michigan, USA
| | - Laila M Poisson
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA.,Center for Bioinformatics, Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - James Snyder
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Ana C deCarvalho
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Tobias Walbert
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
| | - Todd Aho
- Department of Radiology, Henry Ford Health System, Detroit, Michigan, USA
| | - Steven Kalkanis
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Paula C Elias
- Internal Medicine Department, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Sonir R Antonini
- Department of Pediatrics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Jack Rock
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan, USA
| | - Houtan Noushmehr
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA.,Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Margaret Castro
- Internal Medicine Department, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Ana Valeria Castro
- Hermelin Brain Tumor Center, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan, USA
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138
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Zinghirino F, Pappalardo XG, Messina A, Nicosia G, De Pinto V, Guarino F. VDAC Genes Expression and Regulation in Mammals. Front Physiol 2021; 12:708695. [PMID: 34421651 PMCID: PMC8374620 DOI: 10.3389/fphys.2021.708695] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022] Open
Abstract
VDACs are pore-forming proteins, coating the mitochondrial outer membrane, and playing the role of main regulators for metabolites exchange between cytosol and mitochondria. In mammals, three isoforms have evolutionary originated, VDAC1, VDAC2, and VDAC3. Despite similarity in sequence and structure, evidence suggests different biological roles in normal and pathological conditions for each isoform. We compared Homo sapiens and Mus musculus VDAC genes and their regulatory elements. RNA-seq transcriptome analysis shows that VDAC isoforms are expressed in human and mouse tissues at different levels with a predominance of VDAC1 and VDAC2 over VDAC3, with the exception of reproductive system. Numerous transcript variants for each isoform suggest specific context-dependent regulatory mechanisms. Analysis of VDAC core promoters has highlighted that, both in a human and a mouse, VDAC genes show features of TATA-less ones. The level of CG methylation of the human VDAC genes revealed that VDAC1 promoter is less methylated than other two isoforms. We found that expression of VDAC genes is mainly regulated by transcription factors involved in controlling cell growth, proliferation and differentiation, apoptosis, and bioenergetic metabolism. A non-canonical initiation site termed "the TCT/TOP motif," the target for translation regulation by the mTOR pathway, was identified in human VDAC2 and VDAC3 and in every murine VDACs promoter. In addition, specific TFBSs have been identified in each VDAC promoter, supporting the hypothesis that there is a partial functional divergence. These data corroborate our experimental results and reinforce the idea that gene regulation could be the key to understanding the evolutionary specialization of VDAC isoforms.
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Affiliation(s)
- Federica Zinghirino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Angela Messina
- Section of Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
- we.MitoBiotech.srl, Catania, Italy
| | - Giuseppe Nicosia
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- we.MitoBiotech.srl, Catania, Italy
- Section of Catania, National Institute of Biostructures and Biosystems, Catania, Italy
| | - Francesca Guarino
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- we.MitoBiotech.srl, Catania, Italy
- Section of Catania, National Institute of Biostructures and Biosystems, Catania, Italy
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139
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Janowski M, Milewska M, Zare P, Pękowska A. Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue. Pharmaceuticals (Basel) 2021; 14:765. [PMID: 34451862 PMCID: PMC8399958 DOI: 10.3390/ph14080765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/26/2022] Open
Abstract
Neurological disorders (NDs) comprise a heterogeneous group of conditions that affect the function of the nervous system. Often incurable, NDs have profound and detrimental consequences on the affected individuals' lives. NDs have complex etiologies but commonly feature altered gene expression and dysfunctions of the essential chromatin-modifying factors. Hence, compounds that target DNA and histone modification pathways, the so-called epidrugs, constitute promising tools to treat NDs. Yet, targeting the entire epigenome might reveal insufficient to modify a chosen gene expression or even unnecessary and detrimental to the patients' health. New technologies hold a promise to expand the clinical toolkit in the fight against NDs. (Epi)genome engineering using designer nucleases, including CRISPR-Cas9 and TALENs, can potentially help restore the correct gene expression patterns by targeting a defined gene or pathway, both genetically and epigenetically, with minimal off-target activity. Here, we review the implication of epigenetic machinery in NDs. We outline syndromes caused by mutations in chromatin-modifying enzymes and discuss the functional consequences of mutations in regulatory DNA in NDs. We review the approaches that allow modifying the (epi)genome, including tools based on TALENs and CRISPR-Cas9 technologies, and we highlight how these new strategies could potentially change clinical practices in the treatment of NDs.
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Affiliation(s)
| | | | | | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur Street, 02-093 Warsaw, Poland; (M.J.); (M.M.); (P.Z.)
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140
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Chiang PC, Li PT, Lee MJ, Chen CT. DNA Hypermethylation Involves in the Down-Regulation of Chloride Intracellular Channel 4 (CLIC4) Induced by Photodynamic Therapy. Biomedicines 2021; 9:biomedicines9080927. [PMID: 34440131 PMCID: PMC8394338 DOI: 10.3390/biomedicines9080927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
The altered expression of chloride intracellular channel 4 (CLIC4) was reported to correlate with tumor progression. Previously, we have shown that the reduced cellular invasion induced by photodynamic therapy (PDT) is associated with suppression of CLIC4 expression in PDT-treated cells. Herein, we attempted to decipher the regulatory mechanisms involved in PDT-mediated CLIC4 suppression in A375 and MDA-MB-231 cells in vitro. We found that PDT can increase the expression and enzymatic activity of DNA methyltransferase 1 (DNMT1). Bisulfite sequencing PCR further revealed that PDT can induce hypermethylation in the CLIC4 promoter region. Silencing DNMT1 rescues the PDT-induced CLIC4 suppression and inhibits hypermethylation in its promoter. Furthermore, we found tumor suppressor p53 involves in the increased DNMT1 expression of PDT-treated cells. Finally, by comparing CLIC4 expression in lung malignant cells and normal lung fibroblasts, the extent of methylation in CLIC4 promoter was found to be inversely proportional to its expression. Taken together, our results indicate that CLIC4 suppression induced by PDT is modulated by DNMT1-mediated hypermethylation and depends on the status of p53, which provides a possible mechanistic basis for regulating CLIC4 expression in tumorigenesis.
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Affiliation(s)
- Pei-Chi Chiang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan; (P.-C.C.); (P.-T.L.)
| | - Pei-Tzu Li
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan; (P.-C.C.); (P.-T.L.)
| | - Ming-Jen Lee
- Department of Neurology and Medical Genetics, National Taiwan University Hospital, Taipei 10012, Taiwan;
| | - Chin-Tin Chen
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan; (P.-C.C.); (P.-T.L.)
- Correspondence:
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141
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Yamazaki J, Meagawa S, Jelinek J, Yokoyama S, Nagata N, Yuki M, Takiguchi M. Obese status is associated with accelerated DNA methylation change in peripheral blood of senior dogs. Res Vet Sci 2021; 139:193-199. [PMID: 34358922 DOI: 10.1016/j.rvsc.2021.07.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/29/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Obesity and its associated comorbidities constitute a major and growing health problem worldwide not only involved with people but also dogs and cats. Although few genetic mutations have been associated with obesity in dogs, molecular mechanism remains to be clearly understood. Given the fact that DNA methylation leads to gene expression variability and has plasticity affected by metabolic phenotypes such as obesity in human, the objective of this study is to identify obesity-associated differentially methylated cytosine-phosphate-guanine (CpG) dinucleotide sites in dogs. With genome-wide DNA methylation analysis using next-generation sequencing for blood samples from fourteen Miniature dachshunds with body condition score (BCS) 4-5 and BCS ≥6, over 100,000 sites could be analysed to identify genomic locations of differentially methylated CpG sites. As a result, 191 differentially methylated CpG sites (89 CpG sites were hypermethylated in BCS ≥6 and 102 were hypermethylated in BCS 4-5) were identified. These sites included promoter regions of Kisspeptin receptor (KISS1R) and Calcyphosine 2 (CAPS2) genes which were subsequently validated by bisulfite-pyrosequencing for another set of 157 dog blood samples. KISS1R methylation levels were found to be higher in BCS ≥6 group than BCS 4-5 in senior (>84 months) dogs. Especially male dogs but not female dogs as well as uncastrated male dogs but not castrated male dogs showed this trend. DNA methylation of KISS1R gene will be useful for understanding of comprehensive epigenetic change in obese dogs.
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Affiliation(s)
- Jumpei Yamazaki
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan; One Health Research Center, Hokkaido University, Japan.
| | - Shinji Meagawa
- Department of Pediatrics, MD Anderson Cancer Center, Houston, Tx, USA
| | | | - Shoko Yokoyama
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | - Noriyuki Nagata
- Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan
| | - Masashi Yuki
- Yuki Animal Hospital, 2-99 Kiba-cho, Minato-ku, Aichi, Japan
| | - Mitsuyoshi Takiguchi
- Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido University, Japan
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142
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Pei WD, Zhang Y, Yin TL, Yu Y. Epigenome editing by CRISPR/Cas9 in clinical settings: possibilities and challenges. Brief Funct Genomics 2021; 19:215-228. [PMID: 31819946 DOI: 10.1093/bfgp/elz035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/24/2019] [Accepted: 11/05/2019] [Indexed: 12/26/2022] Open
Abstract
Epigenome editing is a promising approach for both basic research and clinical application. With the convergence of techniques from different fields, regulating gene expression artificially becomes possible. From a clinical point of view, targeted epigenome editing by CRISPR/Cas9 of disease-related genes offers novel therapeutic avenues for many diseases. In this review, we summarize the EpiEffectors used in epigenome editing by CRISPR/Cas9, current applications of epigenome editing and progress made in this field. Moreover, application challenges such as off-target effects, inefficient delivery, stability and immunogenicity are discussed. In conclusion, epigenome editing by CRISPR/Cas9 has broad prospects in the clinic, and future work will promote the application of this technology.
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Affiliation(s)
- Wen-Di Pei
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191 China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, PR China
| | - Tai-Lang Yin
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Yang Yu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191 China.,Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing, 100191 China
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143
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Smith CL, Poleshko A, Epstein JA. The nuclear periphery is a scaffold for tissue-specific enhancers. Nucleic Acids Res 2021; 49:6181-6195. [PMID: 34023908 PMCID: PMC8216274 DOI: 10.1093/nar/gkab392] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 02/06/2023] Open
Abstract
Nuclear architecture influences gene regulation and cell identity by controlling the three-dimensional organization of genes and their distal regulatory sequences, which may be far apart in linear space. The genome is functionally and spatially segregated in the eukaryotic nucleus with transcriptionally active regions in the nuclear interior separated from repressive regions, including those at the nuclear periphery. Here, we describe the identification of a novel type of nuclear peripheral chromatin domain that is enriched for tissue-specific transcriptional enhancers. Like other chromatin at the nuclear periphery, these regions are marked by H3K9me2. But unlike the nuclear peripheral Lamina-Associated Domains (LADs), these novel, enhancer-rich domains have limited Lamin B interaction. We therefore refer to them as H3K9me2-Only Domains (KODs). In mouse embryonic stem cells, KODs are found in Hi-C-defined A compartments and feature relatively accessible chromatin. KODs are characterized by low gene expression and enhancers located in these domains bear the histone marks of an inactive or poised state. These results indicate that KODs organize a subset of inactive, tissue-specific enhancers at the nuclear periphery. We hypothesize that KODs may play a role in facilitating and perhaps constraining the enhancer-promoter interactions underlying spatiotemporal regulation of gene expression programs in differentiation and development.
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Affiliation(s)
- Cheryl L Smith
- Department of Cell and Developmental Biology and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA 19104, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA 19104, USA
| | - Jonathan A Epstein
- Department of Medicine and Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA 19104, USA
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144
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Ahn J, Heo S, Lee J, Bang D. Introduction to Single-Cell DNA Methylation Profiling Methods. Biomolecules 2021; 11:1013. [PMID: 34356635 PMCID: PMC8301785 DOI: 10.3390/biom11071013] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is an epigenetic mechanism that is related to mammalian cellular differentiation, gene expression regulation, and disease. In several studies, DNA methylation has been identified as an effective marker to identify differences between cells. In this review, we introduce single-cell DNA-methylation profiling methods, including experimental strategies and approaches to computational data analysis. Furthermore, the blind spots of the basic analysis and recent alternatives are briefly described. In addition, we introduce well-known applications and discuss future development.
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Affiliation(s)
- Jongseong Ahn
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
| | - Sunghoon Heo
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
| | - Jihyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
- Department of Biomedical Science and Technology, Kyung Hee University, Seoul 02447, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
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145
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Grencewicz DJ, Romigh T, Thacker S, Abbas A, Jaini R, Luse D, Eng C. Redefining the PTEN promoter: Identification of novel upstream transcription start regions. Hum Mol Genet 2021; 30:2135-2148. [PMID: 34218272 DOI: 10.1093/hmg/ddab175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 11/14/2022] Open
Abstract
Germline mutation of PTEN is causally observed in Cowden syndrome (CS) and is one of the most common, penetrant risk genes for autism spectrum disorder (ASD). However, the majority of individuals who present with CS-like clinical features are PTEN-mutation negative. Reassessment of PTEN promoter regulation may help explain abnormal PTEN dosage, as only the minimal promoter and coding regions are currently included in diagnostic PTEN mutation analysis. Therefore, we reanalyzed the architecture of the PTEN promoter using next-generation sequencing datasets. Specifically, run-on sequencing assays identified two additional transcription start regions (TSRs) at -2053 and - 1906 basepairs from the canonical start of PTEN, thus extending the PTEN 5'UTR and redefining the PTEN promoter. We show that these novel upstream TSRs are active in cancer cell lines, human cancer, and normal tissue. Further, these TSRs can produce novel PTEN transcripts due to the introduction of new splice donors at -2041, -1826, and - 1355, which may allow for splicing out of the PTEN 5'UTR or the first and second exon in upstream-initiated transcripts. Combining ENCODE ChIP-seq and pertinent literature, we also compile and analyze all transcription factors (TFs) binding at the redefined PTEN locus. Enrichment analyses suggest that TFs bind specifically to the upstream TSRs may be implicated in inflammatory processes. Together, these data redefine the architecture of the PTEN promoter, an important step toward a comprehensive model of PTEN transcription regulation, a basis for future investigations into the new promoters' role in disease pathogenesis.
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Affiliation(s)
- Dennis J Grencewicz
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Todd Romigh
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Stetson Thacker
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ata Abbas
- Division of Hematology and Oncology, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Developmental Therapeutics Program, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ritika Jaini
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Developmental Therapeutics Program, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Donal Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Center for Personalized Genetic Healthcare, Cleveland Clinic Community Care and Population Health, Cleveland, OH 44195, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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146
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Komijani M, Momeni HR, Shaykh-Baygloo N, Ghafarizadeh AA, Maleki P, Tahsili MR. Association of Herpes simplex virus I&II infections with rs187084 SNP of TLR9 and male infertility. Andrologia 2021; 53:e14163. [PMID: 34216052 DOI: 10.1111/and.14163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 11/29/2022] Open
Abstract
Since TLR9 recognises unmethylated CpG motifs in viral DNA, its polymorphisms may contribute to the susceptibility to Herpes simplex virus I&II infection. In the present study, to evaluate the role of rs187084 SNP (single nucleotide polymorphism) of TLR9 in Herpes simplex virus I&II infection and male infertility, 103 infertile and 27 fertile blood and semen samples were analysed. We assessed the micro and macro properties of semen specimens and the presence of HSV immunoglobulins. Tetra-primer ARMS PCR was used to detect SNP and to investigate the genotype distribution of TLR9-rs187084 SNPs, and the correlation between polymorphisms of TLR9 gene and male infertility. Moreover, the odds ratio (OR) and 95% confidence intervals were used to estimate the strength of the association. Based on our finding, a significant correlation was observed between HSV infection, agglutination and polymorphism (TT) under dominant (OR = 1.28, 95% CI = 0.94-1.75) and recessive (OR = 0.44, 95% CI = 0.21-0.94) models for the data, which was complied with Hardy-Weinberg equilibrium (HWE) (OR = 2.91, 95% CI = 1.02-8.30). The result showed a significant association between HSV IgM and agglutination in HSV infection (p < .001), and in addition, there were associations between alleles so that rs187084 SNP might be considered as a risk factor for the incidence of HSV infection.
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Affiliation(s)
- Majid Komijani
- Department of Biology, Faculty of Science, Arak University, Arak, Iran
| | - Hamid Reza Momeni
- Department of Biology, Faculty of Science, Arak University, Arak, Iran
| | | | | | - Parisa Maleki
- Department of Biology, Faculty of Science, Arak University, Arak, Iran
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147
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Pachano T, Sánchez-Gaya V, Ealo T, Mariner-Faulí M, Bleckwehl T, Asenjo HG, Respuela P, Cruz-Molina S, Muñoz-San Martín M, Haro E, van IJcken WFJ, Landeira D, Rada-Iglesias A. Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness. Nat Genet 2021; 53:1036-1049. [PMID: 34183853 PMCID: PMC7611182 DOI: 10.1038/s41588-021-00888-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 05/17/2021] [Indexed: 12/12/2022]
Abstract
CpG islands (CGIs) represent a widespread feature of vertebrate genomes, being associated with ~70% of all gene promoters. CGIs control transcription initiation by conferring nearby promoters with unique chromatin properties. In addition, there are thousands of distal or orphan CGIs (oCGIs) whose functional relevance is barely known. Here we show that oCGIs are an essential component of poised enhancers that augment their long-range regulatory activity and control the responsiveness of their target genes. Using a knock-in strategy in mouse embryonic stem cells, we introduced poised enhancers with or without oCGIs within topologically associating domains harboring genes with different types of promoters. Analysis of the resulting cell lines revealed that oCGIs act as tethering elements that promote the physical and functional communication between poised enhancers and distally located genes, particularly those with large CGI clusters in their promoters. Therefore, by acting as genetic determinants of gene-enhancer compatibility, CGIs can contribute to gene expression control under both physiological and potentially pathological conditions.
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Affiliation(s)
- Tomas Pachano
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Víctor Sánchez-Gaya
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Thais Ealo
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Maria Mariner-Faulí
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Tore Bleckwehl
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Helena G Asenjo
- Centre for Genomics and Oncological Research (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Virgen de las Nieves, Granada, Spain
| | - Patricia Respuela
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Sara Cruz-Molina
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - María Muñoz-San Martín
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | - Endika Haro
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain
| | | | - David Landeira
- Centre for Genomics and Oncological Research (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Virgen de las Nieves, Granada, Spain
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Santander, Spain.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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148
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Guiblet WM, DeGiorgio M, Cheng X, Chiaromonte F, Eckert KA, Huang YF, Makova KD. Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. Genome Res 2021; 31:1136-1149. [PMID: 34187812 PMCID: PMC8256861 DOI: 10.1101/gr.269589.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
Approximately 1% of the human genome has the ability to fold into G-quadruplexes (G4s)-noncanonical strand-specific DNA structures forming at G-rich motifs. G4s regulate several key cellular processes (e.g., transcription) and have been hypothesized to participate in others (e.g., firing of replication origins). Moreover, G4s differ in their thermostability, and this may affect their function. Yet, G4s may also hinder replication, transcription, and translation and may increase genome instability and mutation rates. Therefore, depending on their genomic location, thermostability, and functionality, G4 loci might evolve under different selective pressures, which has never been investigated. Here we conducted the first genome-wide analysis of G4 distribution, thermostability, and selection. We found an overrepresentation, high thermostability, and purifying selection for G4s within genic components in which they are expected to be functional-promoters, CpG islands, and 5' and 3' UTRs. A similar pattern was observed for G4s within replication origins, enhancers, eQTLs, and TAD boundary regions, strongly suggesting their functionality. In contrast, G4s on the nontranscribed strand of exons were underrepresented, were unstable, and evolved neutrally. In general, G4s on the nontranscribed strand of genic components had lower density and were less stable than those on the transcribed strand, suggesting that the former are avoided at the RNA level. Across the genome, purifying selection was stronger at stable G4s. Our results suggest that purifying selection preserves the sequences of functional G4s, whereas nonfunctional G4s are too costly to be tolerated in the genome. Thus, G4s are emerging as fundamental, functional genomic elements.
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Affiliation(s)
- Wilfried M Guiblet
- Bioinformatics and Genomics Graduate Program, Penn State University, University Park, Pennsylvania 16802, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, USA
| | - Xiaoheng Cheng
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Sant'Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Kristin A Eckert
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Department of Pathology, Penn State University, College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Yi-Fei Huang
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
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149
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Garribba L, Vogel I, Lerdrup M, Gonçalves Dinis MM, Ren L, Liu Y. Folate Deficiency Triggers the Abnormal Segregation of a Region With Large Cluster of CG-Rich Trinucleotide Repeats on Human Chromosome 2. Front Genet 2021; 12:695124. [PMID: 34276797 PMCID: PMC8281231 DOI: 10.3389/fgene.2021.695124] [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: 04/14/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Folate deficiency is associated with a broad range of human disorders, including anemia, fetal neural tube defects, age-associated dementia and several types of cancer. It is well established that a subgroup of rare fragile sites (RFSs) containing expanded CGG trinucleotide repeat (TNR) sequences display instability when cells are deprived of folate. However, given that folate sensitive RFSs exist in a very small percentage of the population, they are unlikely to be the cause of the widespread health problems associated with folate deficiency. We hypothesized that folate deficiency could specifically affect DNA replication at regions containing CG-rich repeat sequences. For this, we identified a region on human chromosome 2 (Chr2) comprising more than 300 CG-rich TNRs (termed “FOLD1”) by examining the human genome database. Via the analysis of chromosome shape and segregation in mitosis, we demonstrate that, when human cells are cultured under folate stress conditions, Chr2 is prone to display a “kink” or “bending” at FOLD1 in metaphase and nondisjunction in anaphase. Furthermore, long-term folate deprivation causes Chr2 aneuploidy. Our results provide new evidence on the abnormalities folate deficiency could cause in human cells. This could facilitate future studies on the deleterious health conditions associated with folate deficiency.
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Affiliation(s)
- Lorenza Garribba
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ivan Vogel
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mads Lerdrup
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marisa M Gonçalves Dinis
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Liqun Ren
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ying Liu
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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150
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Angeloni A, Bogdanovic O. Sequence determinants, function, and evolution of CpG islands. Biochem Soc Trans 2021; 49:1109-1119. [PMID: 34156435 PMCID: PMC8286816 DOI: 10.1042/bst20200695] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/25/2022]
Abstract
In vertebrates, cytosine-guanine (CpG) dinucleotides are predominantly methylated, with ∼80% of all CpG sites containing 5-methylcytosine (5mC), a repressive mark associated with long-term gene silencing. The exceptions to such a globally hypermethylated state are CpG-rich DNA sequences called CpG islands (CGIs), which are mostly hypomethylated relative to the bulk genome. CGIs overlap promoters from the earliest vertebrates to humans, indicating a concerted evolutionary drive compatible with CGI retention. CGIs are characterised by DNA sequence features that include DNA hypomethylation, elevated CpG and GC content and the presence of transcription factor binding sites. These sequence characteristics are congruous with the recruitment of transcription factors and chromatin modifying enzymes, and transcriptional activation in general. CGIs colocalize with sites of transcriptional initiation in hypermethylated vertebrate genomes, however, a growing body of evidence indicates that CGIs might exert their gene regulatory function in other genomic contexts. In this review, we discuss the diverse regulatory features of CGIs, their functional readout, and the evolutionary implications associated with CGI retention in vertebrates and possibly in invertebrates.
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Affiliation(s)
- Allegra Angeloni
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, Australia
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, Australia
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