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Roberts JB, Rice SJ. Osteoarthritis as an Enhanceropathy: Gene Regulation in Complex Musculoskeletal Disease. Curr Rheumatol Rep 2024; 26:222-234. [PMID: 38430365 PMCID: PMC11116181 DOI: 10.1007/s11926-024-01142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2024] [Indexed: 03/03/2024]
Abstract
PURPOSE OF REVIEW Osteoarthritis is a complex and highly polygenic disease. Over 100 reported osteoarthritis risk variants fall in non-coding regions of the genome, ostensibly conferring functional effects through the disruption of regulatory elements impacting target gene expression. In this review, we summarise the progress that has advanced our knowledge of gene enhancers both within the field of osteoarthritis and more broadly in complex diseases. RECENT FINDINGS Advances in technologies such as ATAC-seq have facilitated our understanding of chromatin states in specific cell types, bolstering the interpretation of GWAS and the identification of effector genes. Their application to osteoarthritis research has revealed enhancers as the principal regulatory element driving disease-associated changes in gene expression. However, tissue-specific effects in gene regulatory mechanisms can contribute added complexity to biological interpretation. Understanding gene enhancers and their altered activity in specific cell and tissue types is the key to unlocking the genetic complexity of osteoarthritis. The use of single-cell technologies in osteoarthritis research is still in its infancy. However, such tools offer great promise in improving our functional interpretation of osteoarthritis GWAS and the identification of druggable targets. Large-scale collaborative efforts will be imperative to understand tissue and cell-type specific molecular mechanisms underlying enhancer function in disease.
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Affiliation(s)
- Jack B Roberts
- Skeletal Research Group, International Centre for Life, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, UK
| | - Sarah J Rice
- Skeletal Research Group, International Centre for Life, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, UK.
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Moses E, Atlan T, Sun X, Franek R, Siddiqui A, Marinov GK, Shifman S, Zucker DM, Oron-Gottesman A, Greenleaf WJ, Cohen E, Ram O, Harel I. The killifish germline regulates longevity and somatic repair in a sex-specific manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.572041. [PMID: 38187630 PMCID: PMC10769255 DOI: 10.1101/2023.12.18.572041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Classical evolutionary theories propose tradeoffs between reproduction, damage repair, and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. Here, we use the turquoise killifish ( N. furzeri ) to genetically arrest germline development at discrete stages, and examine how different modes of infertility impact life-history. We first construct a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. Next, we show that germline depletion - but not arresting germline differentiation - enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted C. elegans . Our results therefore demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.
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Xu D, Zhang C, Bi X, Xu J, Guo S, Li P, Shen Y, Cai J, Zhang N, Tian G, Zhang H, Wang H, Li Q, Jiang H, Wang B, Li X, Li Y, Li K. Mapping enhancer and chromatin accessibility landscapes charts the regulatory network of Alzheimer's disease. Comput Biol Med 2024; 168:107802. [PMID: 38056211 DOI: 10.1016/j.compbiomed.2023.107802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/20/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Enhancers are regulatory elements that target and modulate gene expression and play a role in human health and disease. However, the roles of enhancer regulatory circuit abnormalities driven by epigenetic alterations in Alzheimer's disease (AD) are unclear. METHODS In this study, a multiomic integrative analysis was performed to map enhancer and chromatin accessibility landscapes and identify regulatory network abnormalities in AD. We identified differentially methylated enhancers and constructed regulatory networks across brain regions using AD brain tissue samples. Through the integration of snATAC-seq and snRNA-seq datasets, we mapped enhancers with DNA methylation alterations (DMA) and chromatin accessibility landscapes. Core regulatory triplets that contributed to AD neuropathology in specific cell types were further prioritized. RESULTS We revealed widespread DNA methylation alterations (DMA) in the enhancers of AD patients across different brain regions. In addition, the genome-wide transcription factor (TF) binding profiles showed that enhancers with DMA are pervasively regulated by TFs. The TF-enhancer-gene regulatory network analysis identified core regulatory triplets that are associated with brain and immune cell proportions and play important roles in AD pathogenesis. Enhancer regulatory circuits with DMA exhibited distinct chromatin accessibility patterns, which were further characterized at single-cell resolutions. CONCLUSIONS Our study comprehensively investigated DNA methylation-mediated regulatory circuit abnormalities and provided novel insights into the potential pathogenesis of AD.
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Affiliation(s)
- Dahua Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Chunrui Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100020, China
| | - Xiaoman Bi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Jiankai Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shengnan Guo
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Peihu Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Yutong Shen
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Jiale Cai
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Nihui Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Guanghui Tian
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Haifei Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Hong Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Qifu Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Hongyan Jiang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China
| | - Bo Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China.
| | - Xia Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China.
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China.
| | - Kongning Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan General Hospital, Hainan Affiliated Hospital, Hainan Medical University, Haikou 571199, China.
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Stefan K, Barski A. Cis-regulatory atlas of primary human CD4+ T cells. BMC Genomics 2023; 24:253. [PMID: 37170195 PMCID: PMC10173520 DOI: 10.1186/s12864-023-09288-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/31/2023] [Indexed: 05/13/2023] Open
Abstract
Cis-regulatory elements (CRE) are critical for coordinating gene expression programs that dictate cell-specific differentiation and homeostasis. Recently developed self-transcribing active regulatory region sequencing (STARR-Seq) has allowed for genome-wide annotation of functional CREs. Despite this, STARR-Seq assays are only employed in cell lines, in part, due to difficulties in delivering reporter constructs. Herein, we implemented and validated a STARR-Seq-based screen in human CD4+ T cells using a non-integrating lentiviral transduction system. Lenti-STARR-Seq is the first example of a genome-wide assay of CRE function in human primary cells, identifying thousands of functional enhancers and negative regulatory elements (NREs) in human CD4+ T cells. We find an unexpected difference in nucleosome organization between enhancers and NRE: enhancers are located between nucleosomes, whereas NRE are occupied by nucleosomes in their endogenous locations. We also describe chromatin modification, eRNA production, and transcription factor binding at both enhancers and NREs. Our findings support the idea of silencer repurposing as enhancers in alternate cell types. Collectively, these data suggest that Lenti-STARR-Seq is a successful approach for CRE screening in primary human cell types, and provides an atlas of functional CREs in human CD4+ T cells.
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Affiliation(s)
- Kurtis Stefan
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7028, Cincinnati, OH, 45229-3026, USA
- Medical Scientist Training Program (MSTP), University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7028, Cincinnati, OH, 45229-3026, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229-3026, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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Sahinyan K, Lazure F, Blackburn DM, Soleimani VD. Decline of regenerative potential of old muscle stem cells: contribution to muscle aging. FEBS J 2023; 290:1267-1289. [PMID: 35029021 DOI: 10.1111/febs.16352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 01/01/2023]
Abstract
Muscle stem cells (MuSCs) are required for life-long muscle regeneration. In general, aging has been linked to a decline in the numbers and the regenerative potential of MuSCs. Muscle regeneration depends on the proper functioning of MuSCs, which is itself dependent on intricate interactions with its niche components. Aging is associated with both cell-intrinsic and niche-mediated changes, which can be the result of transcriptional, posttranscriptional, or posttranslational alterations in MuSCs or in the components of their niche. The interplay between cell intrinsic alterations in MuSCs and changes in the stem cell niche environment during aging and its impact on the number and the function of MuSCs is an important emerging area of research. In this review, we discuss whether the decline in the regenerative potential of MuSCs with age is the cause or the consequence of aging skeletal muscle. Understanding the effect of aging on MuSCs and the individual components of their niche is critical to develop effective therapeutic approaches to diminish or reverse the age-related defects in muscle regeneration.
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Affiliation(s)
- Korin Sahinyan
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Felicia Lazure
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Darren M Blackburn
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
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Zheng X, Wu W, Zhou Q, Lian Y, Xiang Y, Zhao X. Targeted bisulfite resequencing of differentially methylated cytosines in pre-eclampsia reveals a skewed dynamic balance in the DNA methylation of enhancers. Clin Sci (Lond) 2023; 137:265-279. [PMID: 36645190 DOI: 10.1042/cs20220644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/17/2023]
Abstract
Pre-eclampsia (PE) is a major hypertensive disorder of pregnancy. Widespread differentially methylated cytosines (DMCs) with modest changes in methylation level are associated with PE, whereas their cause and biological significance remain unknown. We aimed to clarify DNA methylation patterns around DMCs in 103 placentas using MethylCap targeted bisulfite re-sequencing (MethylCap-seq) assays of 690 selected DMCs. We verified the MethylCap-seq method, then validated 677 (98.1%) of DMCs (vDMCs) in an independent cohort. The validated DMCs were strongly enriched in active placenta-specific enhancers and showed highly dynamic methylation levels. We found high epigenetic heterogeneity between vDMCs and adjacent CpG sites (r2 < 0.2) and a significant decrease in PE in the discovery and replication cohorts (P = 2.00 × 10-24 and 6.43 × 10-9, respectively). We replicated the methylation changes in a hypoxia/reoxygenation cell model. We constructed 112 methylation haplotype blocks and found that the frequencies of unmethylated haplotypes (UMHs) were dynamic with gestational age (GA) and were altered in maternal plasma of patients with PE. Our results uncovered additional DNA methylation features in PE placentas and suggested a model of skewed DNA methylation balance of enhancers in PE.
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Affiliation(s)
- Xiaoguo Zheng
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, 200030, Shanghai, China
| | - Weibin Wu
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, 200030, Shanghai, China
| | - Qian Zhou
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Yahan Lian
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, 200030, Shanghai, China
| | - Yuqian Xiang
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, 200030, Shanghai, China
| | - Xinzhi Zhao
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, 200030, Shanghai, China
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Hattori N, Liu YY, Ushijima T. DNA Methylation Analysis. Methods Mol Biol 2023; 2691:165-183. [PMID: 37355545 DOI: 10.1007/978-1-0716-3331-1_13] [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: 06/26/2023]
Abstract
DNA methylation of promoter CpG islands silences their downstream genes, and enhancer methylation can be associated with decreased or increased gene expression. DNA methylation alterations in normal and diseased cells provide rich information, such as tissue origin, disease risk, patient response, and prognosis. DNA methylation status is detected by bisulfite conversion, which converts unmethylated cytosines into uracils but methylated cytosines very inefficiently. A genome-wide DNA methylation analysis is conducted by a BeadChip microarray or next-generation sequencing (NGS) of bisulfite-treated DNA. A region-specific DNA methylation analysis can be conducted by various methods, such as methylation-specific PCR (MSP), quantitative MSP, and bisulfite sequencing. This chapter provides protocols for bisulfite-mediated conversion, a BeadChip array-based method (Infinium), quantitative MSP, and bisulfite sequencing.
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Affiliation(s)
- Naoko Hattori
- Division of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Yu-Yu Liu
- Division of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan.
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Disatham J, Brennan L, Jiao X, Ma Z, Hejtmancik JF, Kantorow M. Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation. Epigenetics Chromatin 2022; 15:8. [PMID: 35246225 PMCID: PMC8897925 DOI: 10.1186/s13072-022-00440-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/16/2022] [Indexed: 12/13/2022] Open
Abstract
Background Methylation at cytosines (mCG) is a well-known regulator of gene expression, but its requirements for cellular differentiation have yet to be fully elucidated. A well-studied cellular differentiation model system is the eye lens, consisting of a single anterior layer of epithelial cells that migrate laterally and differentiate into a core of fiber cells. Here, we explore the genome-wide relationships between mCG methylation, chromatin accessibility and gene expression during differentiation of eye lens epithelial cells into fiber cells. Results Whole genome bisulfite sequencing identified 7621 genomic loci exhibiting significant differences in mCG levels between lens epithelial and fiber cells. Changes in mCG levels were inversely correlated with the differentiation state-specific expression of 1285 genes preferentially expressed in either lens fiber or lens epithelial cells (Pearson correlation r = − 0.37, p < 1 × 10–42). mCG levels were inversely correlated with chromatin accessibility determined by assay for transposase-accessible sequencing (ATAC-seq) (Pearson correlation r = − 0.86, p < 1 × 10–300). Many of the genes exhibiting altered regions of DNA methylation, chromatin accessibility and gene expression levels in fiber cells relative to epithelial cells are associated with lens fiber cell structure, homeostasis and transparency. These include lens crystallins (CRYBA4, CRYBB1, CRYGN, CRYBB2), lens beaded filament proteins (BFSP1, BFSP2), transcription factors (HSF4, SOX2, HIF1A), and Notch signaling pathway members (NOTCH1, NOTCH2, HEY1, HES5). Analysis of regions exhibiting cell-type specific alterations in DNA methylation revealed an overrepresentation of consensus sequences of multiple transcription factors known to play key roles in lens cell differentiation including HIF1A, SOX2, and the MAF family of transcription factors. Conclusions Collectively, these results link DNA methylation with control of chromatin accessibility and gene expression changes required for eye lens differentiation. The results also point to a role for DNA methylation in the regulation of transcription factors previously identified to be important for lens cell differentiation. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00440-z.
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Affiliation(s)
- Joshua Disatham
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Lisa Brennan
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhiwei Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marc Kantorow
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA.
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Pterostilbene Changes Epigenetic Marks at Enhancer Regions of Oncogenes in Breast Cancer Cells. Antioxidants (Basel) 2021; 10:antiox10081232. [PMID: 34439480 PMCID: PMC8388921 DOI: 10.3390/antiox10081232] [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: 06/06/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic aberrations are linked to sporadic breast cancer. Interestingly, certain dietary polyphenols with anti-cancer effects, such as pterostilbene (PTS), have been shown to regulate gene expression by altering epigenetic patterns. Our group has proposed the involvement of DNA methylation and DNA methyltransferase 3B (DNMT3B) as vital players in PTS-mediated suppression of candidate oncogenes and suggested a role of enhancers as target regions. In the present study, we assess a genome-wide impact of PTS on epigenetic marks at enhancers in highly invasive MCF10CA1a breast cancer cells. Following chromatin immunoprecipitation (ChIP)-sequencing in MCF10CA1a cells treated with 7 μM PTS for 9 days, we discovered that PTS leads to increased binding of DNMT3B at enhancers of 77 genes, and 17 of those genes display an overlapping decrease in the occupancy of trimethylation at lysine 36 of histone 3 (H3K36me3), a mark of active enhancers. We selected two genes, PITPNC1 and LINC00910, and found that their enhancers are hypermethylated in response to PTS. These changes coincided with the downregulation of gene expression. Of importance, we showed that 6 out of 17 target enhancers, including PITPNC1 and LINC00910, are bound by an oncogenic transcription factor OCT1 in MCF10CA1a cells. Indeed, the six enhancers corresponded to genes with established or putative cancer-driving functions. PTS led to a decrease in OCT1 binding at those enhancers, and OCT1 depletion resulted in PITPNC1 and LINC00910 downregulation, further demonstrating a role for OCT1 in transcriptional regulation. Our findings provide novel evidence for the epigenetic regulation of enhancer regions by dietary polyphenols in breast cancer cells.
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