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Zhou Y, Yu H, Zhang D, Wang Z, Li Q, An X, Zhang S, Li Z. Imprinted lncRNA KCNQ1OT1 regulates CDKN1C expression through promoter binding and chromatin folding in pigs. Gene 2024; 923:148590. [PMID: 38772516 DOI: 10.1016/j.gene.2024.148590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024]
Abstract
Long noncoding RNAs (lncRNAs) are implicated in a number of regulatory functions in eukaryotic genomes. In humans, KCNQ1OT1 is a 91 kb imprinted lncRNA that inhibits multiple surrounding genes in cis. Among them, CDKN1C is closely related to KCNQ1OT1 and is involved in multiple epigenetic disorders. Here, we found that pigs also had a relatively conserved paternal allele expressing KCNQ1OT1 and had a shorter 5' end (∼27 kb) compared to human KCNQ1OT1. Knockdown of KCNQ1OT1 using antisense oligonucleotides (ASO) showed that upregulation of CDKN1C expression in pigs. However, porcine KCNQ1OT1 did not affect the DNA methylation status of the CpG islands in the promoters of KCNQ1OT1 and CDKN1C. Inhibition of DNA methyltransferase using Decitabine treatment resulted in a significant increase in both KCNQ1OT1 and CDKN1C expression, suggesting that the regulation between KCNQ1OT1 and CDKN1C may not be dependent on RNA interference. Further use of chromosome conformation capture and reverse transcription-associated trap detection in the region where CDKN1C was located revealed that KCNQ1OT1 bound to the CDKN1C promoter and affected chromosome folding. Phenotypically, inhibition of KCNQ1OT1 at the cumulus-oocyte complex promoted cumulus cell transformation, and to upregulated the expression of ALPL at the early stage of osteogenic differentiation of porcine bone marrow mesenchymal stem cells. Our results confirm that the expression of KCNQ1OT1 imprinting in pigs as well as porcine KCNQ1OT1 regulates the expression of CDKN1C through direct promoter binding and chromatin folding alteration. And this regulatory mechanism played an important role in cell differentiation.
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Affiliation(s)
- Yongfeng Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Hao Yu
- College of Animal Science, Jilin University, Changchun, China
| | - Daoyu Zhang
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Zhengzhu Wang
- Shenzhen University Affiliated South China Hospital, Shenzhen, China
| | - Qi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China.
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2
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Hsu CY, Jasim SA, Pallathadka H, Kumar A, Konnova K, Qasim MT, Alubiady MHS, Pramanik A, Al-Ani AM, Abosaoda MK. A comprehensive insight into the contribution of epigenetics in male infertility; focusing on immunological modifications. J Reprod Immunol 2024; 164:104274. [PMID: 38865894 DOI: 10.1016/j.jri.2024.104274] [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: 04/16/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024]
Abstract
Numerous recent studies have examined the impact epigenetics-including DNA methylation-has on spermatogenesis and male infertility. Differential methylation of several genes has been linked to compromised spermatogenesis and/or reproductive failure. Specifically, male infertility has been frequently associated with DNA methylation abnormalities of MEST and H19 inside imprinted genes and MTHFR within non-imprinted genes. Microbial infections mainly result in male infertility because of the immune response triggered by the bacteria' accumulation of immune cells, proinflammatory cytokines, and chemokines. Thus, bacterially produced epigenetic dysregulations may impact host cell function, supporting host defense or enabling pathogen persistence. So, it is possible to think of pathogenic bacteria as potential epimutagens that can alter the epigenome. It has been demonstrated that dysregulated levels of LncRNA correlate with motility and sperm count in ejaculated spermatozoa from infertile males. Therefore, a thorough understanding of the relationship between decreased reproductive capacity and sperm DNA methylation status should aid in creating new diagnostic instruments for this condition. To fully understand the mechanisms influencing sperm methylation and how they relate to male infertility, more research is required.
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Affiliation(s)
- Chou-Yi Hsu
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| | | | | | - Ashwani Kumar
- Department of Life Sciences, School of Sciences, Jain (Deemed-to-be) University, Bengaluru, Karnataka 560069, India; Department of Pharmacy, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Karina Konnova
- Assistant of the Department of Propaedeutics of Dental Diseases. Sechenov First Moscow State Medical University, Russia
| | - Maytham T Qasim
- College of Health and Medical Technology, Al-Ayen University, Thi-Qar 64001, Iraq
| | | | - Atreyi Pramanik
- School of Applied and Life Sciences, Divison of Research and Innovation, Uttaranchal University, Dehradun, Uttarakhand, India
| | | | - Munther Kadhim Abosaoda
- College of Technical Engineering, the Islamic University, Najaf, Iraq; College of Technical Engineering, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq; College of Technical Engineering, the Islamic University of Babylon, Babylon, Iraq
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3
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van Breugel ME, Gerber A, van Leeuwen F. The choreography of chromatin in RNA polymerase III regulation. Biochem Soc Trans 2024; 52:1173-1189. [PMID: 38666598 PMCID: PMC11346459 DOI: 10.1042/bst20230770] [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: 03/07/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
Regulation of eukaryotic gene expression involves a dynamic interplay between the core transcriptional machinery, transcription factors, and chromatin organization and modification. While this applies to transcription by all RNA polymerase complexes, RNA polymerase III (RNAPIII) seems to be atypical with respect to its mechanisms of regulation. One distinctive feature of most RNAPIII transcribed genes is that they are devoid of nucleosomes, which relates to the high levels of transcription. Moreover, most of the regulatory sequences are not outside but within the transcribed open chromatin regions. Yet, several lines of evidence suggest that chromatin factors affect RNAPIII dynamics and activity and that gene sequence alone does not explain the observed regulation of RNAPIII. Here we discuss the role of chromatin modification and organization of RNAPIII transcribed genes and how they interact with the core transcriptional RNAPIII machinery and regulatory DNA elements in and around the transcribed genes.
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Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Alan Gerber
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam 1081HV, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
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4
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Zhong Y, Zhou X, Pan Z, Zhang J, Pan J. Role of epigenetic regulatory mechanisms in age-related bone homeostasis imbalance. FASEB J 2024; 38:e23642. [PMID: 38690719 DOI: 10.1096/fj.202302665r] [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: 12/24/2023] [Revised: 03/05/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
Alterations to the human organism that are brought about by aging are comprehensive and detrimental. Of these, an imbalance in bone homeostasis is a major outward manifestation of aging. In older adults, the decreased osteogenic activity of bone marrow mesenchymal stem cells and the inhibition of bone marrow mesenchymal stem cell differentiation lead to decreased bone mass, increased risk of fracture, and impaired bone injury healing. In the past decades, numerous studies have reported the epigenetic alterations that occur during aging, such as decreased core histones, altered DNA methylation patterns, and abnormalities in noncoding RNAs, which ultimately lead to genomic abnormalities and affect the expression of downstream signaling osteoporosis treatment and promoter of fracture healing in older adults. The current review summarizes the impact of epigenetic regulation mechanisms on age-related bone homeostasis imbalance.
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Affiliation(s)
- Yunyu Zhong
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xueer Zhou
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zijian Pan
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jiankang Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jian Pan
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
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5
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Wang L, Xiao J, Zhang B, Hou A. Epigenetic modifications in the development of bronchopulmonary dysplasia: a review. Pediatr Res 2024:10.1038/s41390-024-03167-7. [PMID: 38570557 DOI: 10.1038/s41390-024-03167-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 02/25/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
While perinatal medicine advancements have bolstered survival outcomes for premature infants, bronchopulmonary dysplasia (BPD) continues to threaten their long-term health. Gene-environment interactions, mediated by epigenetic modifications such as DNA methylation, histone modification, and non-coding RNA regulation, take center stage in BPD pathogenesis. Recent discoveries link methylation variations across biological pathways with BPD. Also, the potential reversibility of histone modifications fuels new treatment avenues. The review also highlights the promise of utilizing mesenchymal stem cells and their exosomes as BPD therapies, given their ability to modulate non-coding RNA, opening novel research and intervention possibilities. IMPACT: The complexity and universality of epigenetic modifications in the occurrence and development of bronchopulmonary dysplasia were thoroughly discussed. Both molecular and cellular mechanisms contribute to the diverse nature of epigenetic changes, suggesting the need for deeper biochemical techniques to explore these molecular alterations. The utilization of innovative cell-specific drug delivery methods like exosomes and extracellular vesicles holds promise in achieving precise epigenetic regulation.
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Affiliation(s)
- Lichuan Wang
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Jun Xiao
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Bohan Zhang
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Ana Hou
- Department of Pediatrics, Sheng Jing Hospital of China Medical University, Shenyang, China.
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6
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Liu R, Li Y, Zheng Q, Ding M, Zhou H, Li X. Epigenetic modification in liver fibrosis: Promising therapeutic direction with significant challenges ahead. Acta Pharm Sin B 2024; 14:1009-1029. [PMID: 38486982 PMCID: PMC10935124 DOI: 10.1016/j.apsb.2023.10.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 03/17/2024] Open
Abstract
Liver fibrosis, characterized by scar tissue formation, can ultimately result in liver failure. It's a major cause of morbidity and mortality globally, often associated with chronic liver diseases like hepatitis or alcoholic and non-alcoholic fatty liver diseases. However, current treatment options are limited, highlighting the urgent need for the development of new therapies. As a reversible regulatory mechanism, epigenetic modification is implicated in many biological processes, including liver fibrosis. Exploring the epigenetic mechanisms involved in liver fibrosis could provide valuable insights into developing new treatments for chronic liver diseases, although the current evidence is still controversial. This review provides a comprehensive summary of the regulatory mechanisms and critical targets of epigenetic modifications, including DNA methylation, histone modification, and RNA modification, in liver fibrotic diseases. The potential cooperation of different epigenetic modifications in promoting fibrogenesis was also highlighted. Finally, available agonists or inhibitors regulating these epigenetic mechanisms and their potential application in preventing liver fibrosis were discussed. In summary, elucidating specific druggable epigenetic targets and developing more selective and specific candidate medicines may represent a promising approach with bright prospects for the treatment of chronic liver diseases.
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Affiliation(s)
- Runping Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102400, China
| | - Yajing Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102400, China
| | - Qi Zheng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102400, China
| | - Mingning Ding
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102400, China
| | - Huiping Zhou
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 22460, USA
| | - Xiaojiaoyang Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102400, China
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7
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Malhi NK, Southerland KW, Lai L, Chen ZB. Epigenetic Regulation of Angiogenesis in Peripheral Artery Disease. Methodist Debakey Cardiovasc J 2023; 19:47-57. [PMID: 38028966 PMCID: PMC10655766 DOI: 10.14797/mdcvj.1294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 12/01/2023] Open
Abstract
Peripheral arterial disease (PAD) represents a global health concern with a rising prevalence attributed to factors such as obesity, diabetes, aging, and smoking. Among patients with PAD, chronic limb-threatening ischemia (CLTI) is the most severe manifestation, associated with substantial morbidity and mortality. While revascularization remains the primary therapy for CLTI, not all patients are candidates for such interventions, highlighting the need for alternative approaches. Impaired angiogenesis, the growth of new blood vessels, is a central feature of PAD, and despite decades of research, effective clinical treatments remain elusive. Epigenetics, the study of heritable changes in gene expression, has gained prominence in understanding PAD pathogenesis. Here, we explore the role of epigenetic regulation in angiogenesis within the context of PAD, with a focus on long non-coding RNAs and fibroblast-endothelial cell transdifferentiation. Additionally, we discuss the interplay between metabolic control and epigenetic regulation, providing insights into potential novel therapeutic avenues for improving PAD treatments. This review aims to offer a concise update on the application of epigenetics in angiogenesis and PAD research, inspiring further investigations in this promising field.
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Affiliation(s)
| | | | - Li Lai
- Houston Methodist Research Institute, Houston, Texas, US
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8
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Tregub PP, Ibrahimli I, Averchuk AS, Salmina AB, Litvitskiy PF, Manasova ZS, Popova IA. The Role of microRNAs in Epigenetic Regulation of Signaling Pathways in Neurological Pathologies. Int J Mol Sci 2023; 24:12899. [PMID: 37629078 PMCID: PMC10454825 DOI: 10.3390/ijms241612899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
In recent times, there has been a significant increase in researchers' interest in the functions of microRNAs and the role of these molecules in the pathogenesis of many multifactorial diseases. This is related to the diagnostic and prognostic potential of microRNA expression levels as well as the prospects of using it in personalized targeted therapy. This review of the literature analyzes existing scientific data on the involvement of microRNAs in the molecular and cellular mechanisms underlying the development of pathologies such as Alzheimer's disease, cerebral ischemia and reperfusion injury, and dysfunction of the blood-brain barrier.
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Affiliation(s)
- Pavel P. Tregub
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Scientific and Educational Resource Center “Innovative Technologies of Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis”, RUDN University, 117198 Moscow, Russia
- Research Center of Neurology, 125367 Moscow, Russia
| | - Irada Ibrahimli
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | | | - Alla B. Salmina
- Research Center of Neurology, 125367 Moscow, Russia
- Research Institute of Molecular Medicine and Pathobiochemistry, Prof. V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
| | - Peter F. Litvitskiy
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Zaripat Sh. Manasova
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Inga A. Popova
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
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9
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Jiao J, Lv Z, Wang Y, Fan L, Yang A. The off-target effects of AID in carcinogenesis. Front Immunol 2023; 14:1221528. [PMID: 37600817 PMCID: PMC10436223 DOI: 10.3389/fimmu.2023.1221528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) plays a crucial role in promoting B cell diversification through somatic hypermutation (SHM) and class switch recombination (CSR). While AID is primarily associated with the physiological function of humoral immune response, it has also been linked to the initiation and progression of lymphomas. Abnormalities in AID have been shown to disrupt gene networks and signaling pathways in both B-cell and T-cell lineage lymphoblastic leukemia, although the full extent of its role in carcinogenesis remains unclear. This review proposes an alternative role for AID and explores its off-target effects in regulating tumorigenesis. In this review, we first provide an overview of the physiological function of AID and its regulation. AID plays a crucial role in promoting B cell diversification through SHM and CSR. We then discuss the off-target effects of AID, which includes inducing mutations of non-Igs, epigenetic modification, and the alternative role as a cofactor. We also explore the networks that keep AID in line. Furthermore, we summarize the off-target effects of AID in autoimmune diseases and hematological neoplasms. Finally, we assess the off-target effects of AID in solid tumors. The primary focus of this review is to understand how and when AID targets specific gene loci and how this affects carcinogenesis. Overall, this review aims to provide a comprehensive understanding of the physiological and off-target effects of AID, which will contribute to the development of novel therapeutic strategies for autoimmune diseases, hematological neoplasms, and solid tumors.
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Affiliation(s)
- Junna Jiao
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhuangwei Lv
- School of Forensic Medicine, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yurong Wang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Liye Fan
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Angang Yang
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
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Meng F, Zhang X, Wang Y, Lin J, Tang Y, Zhang G, Qiu B, Zeng X, Liu W, He X. Hsa_circ_0021727 (circ-CD44) promotes ESCC progression by targeting miR-23b-5p to activate the TAB1/NFκB pathway. Cell Death Dis 2023; 14:9. [PMID: 36609391 PMCID: PMC9822936 DOI: 10.1038/s41419-022-05541-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is characterized by high morbidity and mortality. Circular RNAs (circRNAs) play an important role in tumor progression. We discovered an aberrantly expressed circRNA (hsa_circ_0021727) in patients with ESCC. However, the mechanism of action of hsa_circ_0021727 in tumors is unclear. The present study aimed to investigate the biological role of hsa_circ_0021727 and its mechanism in ESCC progression. We screened for the expression of hsa_circ_0021727 in ESCC patients. Patients with ESCC with high expression of hsa_circ_0021727 had shorter survival than those with low expression. Hsa_circ_0021727 promoted the proliferation, invasion, and migration of ESCC cells. However, miR-23b-5p inhibited this ability of hsa_circ_0021727. MiR-23b-5p acts by targeting TAK1-binding protein 1 (TAB1). Upregulation of TAB1 can activate the nuclear factor kappa B (NFκB) pathway. Hsa_circ_0021727 promoted ESCC progression by activating TAB1/NFκB pathway by sponging miR-23b-5p. In addition, in vivo experiments also confirmed that hsa_circ_0021727 could promote the proliferation, invasion, and migration of ESCC cells. In short, hsa_circ_0021727 promotes ESCC progression by targeting miR-23b-5p to activate the TAB1/NFκB pathway. These findings might provide potential targets to treat ESCC.
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Affiliation(s)
- Fan Meng
- Digestive System Department, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xiaokang Zhang
- Jiangxi Provincial Branch of China Clinical Medical Research Center for Geriatric Diseases, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yanting Wang
- Department of Respiratory and Critical Illness Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Jie Lin
- Department of Respiratory and Critical Illness Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yulin Tang
- Department of Respiratory and Critical Illness Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Guisheng Zhang
- Digestive System Department, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Binqiang Qiu
- Department of Respiratory and Critical Illness Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xingdu Zeng
- Department of Respiratory and Critical Illness Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Weiyou Liu
- Jiangxi Provincial Branch of China Clinical Medical Research Center for Geriatric Diseases, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Department of Respiratory and Critical Illness Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xin He
- Jiangxi Provincial Branch of China Clinical Medical Research Center for Geriatric Diseases, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China.
- Department of Respiratory and Critical Illness Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China.
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Epigenetics in fetal alcohol spectrum disorder. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:211-239. [PMID: 37019593 DOI: 10.1016/bs.pmbts.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During pregnancy, alcohol abuse and its detrimental effects on developing offspring are major public health, economic and social challenges. The prominent characteristic attributes of alcohol (ethanol) abuse during pregnancy in humans are neurobehavioral impairments in offspring due to damage to the central nervous system (CNS), causing structural and behavioral impairments that are together named fetal alcohol spectrum disorder (FASD). Development-specific alcohol exposure paradigms were established to recapitulate the human FASD phenotypes and establish the underlying mechanisms. These animal studies have offered some critical molecular and cellular underpinnings likely to account for the neurobehavioral impairments associated with prenatal ethanol exposure. Although the pathogenesis of FASD remains unclear, emerging literature proposes that the various genomic and epigenetic components that cause the imbalance in gene expression can significantly contribute to the development of this disease. These studies acknowledged numerous immediate and enduring epigenetic modifications, such as methylation of DNA, post-translational modifications (PTMs) of histone proteins, and regulatory networks related to RNA, using many molecular approaches. Methylated DNA profiles, PTMs of histone proteins, and RNA-regulated expression of genes are essential for synaptic and cognitive behavior. Thus, offering a solution to many neuronal and behavioral impairments reported in FASD. In the current chapter, we review the recent advances in different epigenetic modifications that cause the pathogenesis of FASD. The information discussed can help better explain the pathogenesis of FASD and thereby might provide a basis for finding novel therapeutic targets and innovative treatment strategies.
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12
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Differential Expression Analysis of tRNA-Derived Small RNAs from Subcutaneous Adipose Tissue of Obese and Lean Pigs. Animals (Basel) 2022; 12:ani12243561. [PMID: 36552481 PMCID: PMC9774726 DOI: 10.3390/ani12243561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Epigenetic factors, including non-coding RNA regulation, play a vital role in the development of obesity and have been well researched. Transfer RNA-derived small RNA (tsRNA) is a class of non-coding RNA proven to be involved in various aspects of mammalian biology. Here we take pigs as a model for obesity research and use tsRNA-seq to investigate the difference in tsRNA expression in the subcutaneous adipose tissue of obese and lean pigs to elucidate the role of tsRNA in obesity development. A total of 482 tsRNAs were identified in pig adipose tissue, of which 123 were significantly differentially accumulated tsRNAs compared with the control group. The tRF-5c was the main type of these tsRNAs. The largest number of tsRNAs produced was the Gly-carrying tRNA, which produced 81 tsRNAs. Functional enrichment analysis revealed that differential tsRNAs indirectly participated in MAPK, AMPK, insulin resistance, the TNF signaling pathway, adipocytokine signaling pathway, and other signaling pathways by interacting with target genes. These are involved in bioenergetic metabolic regulatory processes, suggesting that tsRNAs may influence these pathways to mediate the regulation of energy metabolism in porcine adipocytes to promote lipid deposition, thus contributing to obesity. Our findings suggest a potential function of tsRNA in regulating obesity development.
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13
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Yang Z, Xu F, Teschendorff AE, Zhao Y, Yao L, Li J, He Y. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci 2022; 9:1067406. [PMID: 36533073 PMCID: PMC9755597 DOI: 10.3389/fmolb.2022.1067406] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feng Xu
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yao
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Li
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yungang He
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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14
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Basavarajappa BS, Subbanna S. Molecular Insights into Epigenetics and Cannabinoid Receptors. Biomolecules 2022; 12:1560. [PMID: 36358910 PMCID: PMC9687363 DOI: 10.3390/biom12111560] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/29/2022] [Accepted: 10/22/2022] [Indexed: 09/22/2023] Open
Abstract
The actions of cannabis are mediated by G protein-coupled receptors that are part of an endogenous cannabinoid system (ECS). ECS consists of the naturally occurring ligands N-arachidonylethanolamine (anandamide) and 2-arachidonoylglycerol (2-AG), their biosynthetic and degradative enzymes, and the CB1 and CB2 cannabinoid receptors. Epigenetics are heritable changes that affect gene expression without changing the DNA sequence, transducing external stimuli in stable alterations of the DNA or chromatin structure. Cannabinoid receptors are crucial candidates for exploring their functions through epigenetic approaches due to their significant roles in health and diseases. Epigenetic changes usually promote alterations in the expression of genes and proteins that can be evaluated by various transcriptomic and proteomic analyses. Despite the exponential growth of new evidence on the critical functions of cannabinoid receptors, much is still unknown regarding the contribution of various genetic and epigenetic factors that regulate cannabinoid receptor gene expression. Recent studies have identified several immediate and long-lasting epigenetic changes, such as DNA methylation, DNA-associated histone proteins, and RNA regulatory networks, in cannabinoid receptor function. Thus, they can offer solutions to many cellular, molecular, and behavioral impairments found after modulation of cannabinoid receptor activities. In this review, we discuss the significant research advances in different epigenetic factors contributing to the regulation of cannabinoid receptors and their functions under both physiological and pathological conditions. Increasing our understanding of the epigenetics of cannabinoid receptors will significantly advance our knowledge and could lead to the identification of novel therapeutic targets and innovative treatment strategies for diseases associated with altered cannabinoid receptor functions.
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Affiliation(s)
- Balapal S. Basavarajappa
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
- Molecular Imaging and Neuropathology Area, New York State Psychiatric Institute, New York, NY 10032, USA
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Psychiatry, New York University Langone Medical Center, New York, NY 10016, USA
| | - Shivakumar Subbanna
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
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15
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Reardon RM, Walsh AK, Larsen CI, Schmidberger LH, Morrow LA, Thompson AE, Wellik IM, Thompson JS. An epigenetically inherited UV hyper-resistance phenotype in Saccharomyces cerevisiae. Epigenetics Chromatin 2022; 15:31. [PMID: 35986361 PMCID: PMC9392361 DOI: 10.1186/s13072-022-00464-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
Background Epigenetics refers to inheritable phenotypic changes that occur in the absence of genetic alteration. Such adaptations can provide phenotypic plasticity in reaction to environmental cues. While prior studies suggest that epigenetics plays a role in the response to DNA damage, no direct demonstration of epigenetically inheritable processes have been described in this context. Results Here we report the identification of an epigenetic response to ultraviolet (UV) radiation in the baker’s yeast Saccharomyces cerevisiae. Cells that have been previously exposed to a low dosage of UV exhibit dramatically increased survival following subsequent UV exposure, which we refer to as UV hyper-resistance (UVHR). This phenotypic change persists for multiple mitotic generations, without any indication of an underlying genetic basis. Pre-exposed cells experience a notable reduction in the amount of DNA damage caused by the secondary UV exposure. While the mechanism for the protection is not fully characterized, our results suggest that UV-induced cell size increases and/or cell wall changes are contributing factors. In addition, we have identified two histone modifications, H3K56 acetylation and H3K4 methylation, that are important for UVHR, potentially serving as mediators of UV protective gene expression patterns, as well as epigenetic marks to propagate the phenotype across cell generations. Conclusions Exposure to UV radiation triggers an epigenetically inheritable protective response in baker’s yeast that increases the likelihood of survival in response to subsequent UV exposures. These studies provide the first demonstration of an epigenetically inheritable dimension of the cellular response to DNA damage. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00464-5.
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