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Zhang J, Tong L, Liu Y, Li X, Wang J, Lin R, Zhou Z, Chen Y, Chen Y, Liu Y, Chen D. The regulatory role of m 6A modification in the maintenance and differentiation of embryonic stem cells. Genes Dis 2024; 11:101199. [PMID: 38947741 PMCID: PMC11214295 DOI: 10.1016/j.gendis.2023.101199] [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: 08/24/2023] [Revised: 10/28/2023] [Accepted: 11/11/2023] [Indexed: 07/02/2024] Open
Abstract
As the most prevalent and reversible internal epigenetic modification in eukaryotic mRNAs, N 6-methyladenosine (m6A) post-transcriptionally regulates the processing and metabolism of mRNAs involved in diverse biological processes. m6A modification is regulated by m6A writers, erasers, and readers. Emerging evidence suggests that m6A modification plays essential roles in modulating the cell-fate transition of embryonic stem cells. Mechanistic investigation of embryonic stem cell maintenance and differentiation is critical for understanding early embryonic development, which is also the premise for the application of embryonic stem cells in regenerative medicine. This review highlights the current knowledge of m6A modification and its essential regulatory contribution to the cell fate transition of mouse and human embryonic stem cells.
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Affiliation(s)
- Jin Zhang
- Center for Reproductive Medicine of the Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Lingling Tong
- Center for Reproductive Medicine of the Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yuchen Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Xiang Li
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Jiayi Wang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Ruoxin Lin
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Ziyu Zhou
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yunbing Chen
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yanxi Chen
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yirong Liu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
| | - Di Chen
- Center for Reproductive Medicine of the Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
- National Key Laboratory of Biobased Transportation Fuel Technology, Haining, Zhejiang 314400, China
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2
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Yuan Z, Lei Y, Wan B, Yang M, Jiang Y, Tian C, Wang Z, Wang W. Cadmium exposure elicited dynamic RNA m 6A modification and epi-transcriptomic regulation in the Pacific whiteleg shrimp Litopenaeus vannamei. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101307. [PMID: 39126882 DOI: 10.1016/j.cbd.2024.101307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/05/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
N6-methyladenosine (m6A) methylation is the most prevalent post-transcriptional RNA modification in eukaryotic organisms, but its roles in the regulation of physiological resistance of marine crustaceans to heavy metal pollutants are poorly understood. In this study, the transcriptome-wide m6A RNA methylation profiles and dynamic m6A changes induced by acute Cd2+ exposure in the the pacific whiteleg shrimp Litopenaeus vannamei were comprehensively analyzed. Cd2+ toxicity caused a significant reduction in global RNA m6A methylation level, with major m6A regulators including the m6A methyltransferase METTL3 and the m6A binding protein YTHDF2 showing declined expression. Totally, 11,467 m6A methylation peaks from 6415 genes and 17,291 peaks within 7855 genes were identified from the Cd2+ exposure group and the control group, respectively. These m6A peaks were predominantly enriched in the 3' untranslated region (UTR) and around the start codon region of the transcripts. 7132 differentially expressed genes (DEGs) and 7382 differentially m6A-methylated genes (DMGs) were identified. 3186 genes showed significant changes in both gene expression and m6A methylation levels upon cadmium exposure, and they were related to a variety of biological processes and gene pathways. Notably, an array of genes associated with antioxidation homeostasis, transmembrane transporter activity and intracellular detoxification processes were significantly enriched, demonstrating that m6A modification may mediate the physiological responses of shrimp to cadmium toxicity via regulating ROS balance, Cd2+ transport and toxicity mitigation. The study would contribute to a deeper understanding of the evolutionary and functional significance of m6A methylation to the physiological resilience of decapod crustaceans to heavy metal toxicants.
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Affiliation(s)
- Zhixiang Yuan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yiguo Lei
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Boquan Wan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Miao Yang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yue Jiang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Changxu Tian
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhongduo Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Wei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China.
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Wang M, Wang L, Huang Y, Qiao Z, Yi S, Zhang W, Wang J, Yang G, Cui X, Kou X, Zhao Y, Wang H, Jiang C, Gao S, Chen J. Loss of Tet hydroxymethylase activity causes mouse embryonic stem cell differentiation bias and developmental defects. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2631-x. [PMID: 39037697 DOI: 10.1007/s11427-024-2631-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 05/23/2024] [Indexed: 07/23/2024]
Abstract
The TET family is well known for active DNA demethylation and plays important roles in regulating transcription, the epigenome and development. Nevertheless, previous studies using knockdown (KD) or knockout (KO) models to investigate the function of TET have faced challenges in distinguishing its enzymatic and nonenzymatic roles, as well as compensatory effects among TET family members, which has made the understanding of the enzymatic role of TET not accurate enough. To solve this problem, we successfully generated mice catalytically inactive for specific Tet members (Tetm/m). We observed that, compared with the reported KO mice, mutant mice exhibited distinct developmental defects, including growth retardation, sex imbalance, infertility, and perinatal lethality. Notably, Tetm/m mouse embryonic stem cells (mESCs) were successfully established but entered an impaired developmental program, demonstrating extended pluripotency and defects in ectodermal differentiation caused by abnormal DNA methylation. Intriguingly, Tet3, traditionally considered less critical for mESCs due to its lower expression level, had a significant impact on the global hydroxymethylation, gene expression, and differentiation potential of mESCs. Notably, there were common regulatory regions between Tet1 and Tet3 in pluripotency regulation. In summary, our study provides a more accurate reference for the functional mechanism of Tet hydroxymethylase activity in mouse development and ESC pluripotency regulation.
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Affiliation(s)
- Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Liping Wang
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai, 200065, China
| | - Yanxin Huang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Zhibin Qiao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Shanru Yi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Weina Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Jing Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Guang Yang
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai, 200065, China
| | - Xinyu Cui
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai, 200065, China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Yanhong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Cizhong Jiang
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China.
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai, 200065, China.
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China.
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China.
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China.
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Li X, Bie L, Wang Y, Hong Y, Zhou Z, Fan Y, Yan X, Tao Y, Huang C, Zhang Y, Sun X, Li JXH, Zhang J, Chang Z, Xi Q, Meng A, Shen X, Xie W, Liu N. LINE-1 transcription activates long-range gene expression. Nat Genet 2024; 56:1494-1502. [PMID: 38849613 DOI: 10.1038/s41588-024-01789-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024]
Abstract
Long interspersed nuclear element-1 (LINE-1 or L1) is a retrotransposon group that constitutes 17% of the human genome and shows variable expression across cell types. However, the control of L1 expression and its function in gene regulation are incompletely understood. Here we show that L1 transcription activates long-range gene expression. Genome-wide CRISPR-Cas9 screening using a reporter driven by the L1 5' UTR in human cells identifies functionally diverse genes affecting L1 expression. Unexpectedly, altering L1 expression by knockout of regulatory genes impacts distant gene expression. L1s can physically contact their distal target genes, with these interactions becoming stronger upon L1 activation and weaker when L1 is silenced. Remarkably, L1s contact and activate genes essential for zygotic genome activation (ZGA), and L1 knockdown impairs ZGA, leading to developmental arrest in mouse embryos. These results characterize the regulation and function of L1 in long-range gene activation and reveal its importance in mammalian ZGA.
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Affiliation(s)
- Xiufeng Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Luyao Bie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Wang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yaqiang Hong
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ziqiang Zhou
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yiming Fan
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohan Yan
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yibing Tao
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Chunyi Huang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yongyan Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xueyan Sun
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - John Xiao He Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zai Chang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiaoran Xi
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Anming Meng
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohua Shen
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Nian Liu
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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5
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Feng Y, Shen J, Lin Z, Chen Z, Zhou M, Ma X. PXR Activation Relieves Deoxynivalenol-Induced Liver Oxidative Stress Via Malat1 LncRNA m 6A Demethylation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308742. [PMID: 38654691 PMCID: PMC11220637 DOI: 10.1002/advs.202308742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/28/2024] [Indexed: 04/26/2024]
Abstract
Deoxynivalenol (DON) is a prevalent toxin causing severe liver damage through hepatocellular oxidative stress. However, the underlying mechanisms and effective therapeutic approaches remain unknown. Here, the unique role of the xenobiotic metabolism factor pregnane X receptor (PXR) in mediating DON-induced hepatocellular oxidative stress is investigated. Treatment with the PXR agonist 3-indole-propionic acid (IPA) alleviates DON-induced oxidative stress and liver injury both in vitro and in vivo. Mechanistically, it is discovered for the first time that PXR agonist IPA directly transactivates the m6A demethylase FTO expression, leading to site-specific demethylation and decreased abundance of YTHDC1-bound Malat1 lncRNA at single-nucleotide resolution. The diminished m6A modification of Malat1 lncRNA reduces its stability and augments antioxidant pathways governed by NRF2, consequently mitigating DON-induced liver injury. Furthermore, Malat1 knockout mice exhibit decreased DON-induced liver injury, emphasizing the role of Malat1 lncRNA in oxidative stress. Collectively, the findings establish that PXR-mediated m6A-dependent Malat1 lncRNA expression determines hepatocyte oxidative stress via m6A demethylase FTO, providing valuable insights into the potential mechanisms underlying DON-induced liver injury and offers potential therapeutic strategies for its treatment.
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Affiliation(s)
- Yue Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Jiakun Shen
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Zishen Lin
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Zeyi Chen
- College of Life SciencesHenan Agricultural UniversityZhengzhou450046China
| | - Min Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijing100193China
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6
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Su Z, Dong Y, Sun J, Wu Y, Wei Q, Liang Y, Lin Z, Li Y, Shen L, Xi C, Wu L, Xu Y, Liu Y, Yin J, Wang H, Shi K, Le R, Gao S, Xu X. RNA m 6A modification regulates cell fate transition between pluripotent stem cells and 2-cell-like cells. Cell Prolif 2024:e13696. [PMID: 38952035 DOI: 10.1111/cpr.13696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 07/03/2024] Open
Abstract
N6-methyladenosine (m6A) exerts essential roles in early embryos, especially in the maternal-to-zygotic transition stage. However, the landscape and roles of RNA m6A modification during the transition between pluripotent stem cells and 2-cell-like (2C-like) cells remain elusive. Here, we utilised ultralow-input RNA m6A immunoprecipitation to depict the dynamic picture of transcriptome-wide m6A modifications during 2C-like transitions. We found that RNA m6A modification was preferentially enriched in zygotic genome activation (ZGA) transcripts and MERVL with high expression levels in 2C-like cells. During the exit of the 2C-like state, m6A facilitated the silencing of ZGA genes and MERVL. Notably, inhibition of m6A methyltransferase METTL3 and m6A reader protein IGF2BP2 is capable of significantly delaying 2C-like state exit and expanding 2C-like cells population. Together, our study reveals the critical roles of RNA m6A modification in the transition between 2C-like and pluripotent states, facilitating the study of totipotency and cell fate decision in the future.
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Affiliation(s)
- Zhongqu Su
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yu Dong
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiatong Sun
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - You Wu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qingqing Wei
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yuwei Liang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhiyi Lin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yujun Li
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lu Shen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chenxiang Xi
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Li Wu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yiliang Xu
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yingdong Liu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiqing Yin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Kerong Shi
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Tai'an, Shandong, China
| | - Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaocui Xu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, China
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7
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Zhang S, Xiao X, Yi Y, Wang X, Zhu L, Shen Y, Lin D, Wu C. Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets. Signal Transduct Target Ther 2024; 9:149. [PMID: 38890350 PMCID: PMC11189549 DOI: 10.1038/s41392-024-01848-7] [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: 01/01/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 06/20/2024] Open
Abstract
Tumorigenesis is a multistep process, with oncogenic mutations in a normal cell conferring clonal advantage as the initial event. However, despite pervasive somatic mutations and clonal expansion in normal tissues, their transformation into cancer remains a rare event, indicating the presence of additional driver events for progression to an irreversible, highly heterogeneous, and invasive lesion. Recently, researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution, independently of inducing mutations. Additionally, clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into tumors. However, the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully understood. In this review, we summarize the genetic, epigenetic, and external driver events, and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution. A deeper understanding of the earliest molecular events holds promise for translational applications, predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyi Xiao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yonglin Yi
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lingxuan Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Changping Laboratory, 100021, Beijing, China
| | - Yanrong Shen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- CAMS Oxford Institute, Chinese Academy of Medical Sciences, 100006, Beijing, China.
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8
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Xu W, Shen H. m 6A regulates heterochromatin in mammalian embryonic stem cells. Curr Opin Genet Dev 2024; 86:102196. [PMID: 38669774 DOI: 10.1016/j.gde.2024.102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
As the most well-studied modification in mRNA, m6A has been shown to regulate multiple biological processes, including RNA degradation, processing, and translation. Recent studies showed that m6A modification is enriched in chromatin-associated RNAs and nascent RNAs, suggesting m6A might play regulatory roles in chromatin contexts. Indeed, in the past several years, a number of studies have clarified how m6A and its modulators regulate different types of chromatin states. Specifically, in the past 2-3 years, several studies discovered the roles of m6A and/or its modulators in regulating constitutive and facultative heterochromatin, shedding interesting lights on RNA-dependent heterochromatin formation in mammalian cells. This review will summarize and discuss the mechanisms underlying m6A's regulation in different types of heterochromatin, with a specific emphasis on the regulation in mammalian embryonic stem cells, which exhibit distinct features of multiple heterochromatin marks.
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Affiliation(s)
- Wenqi Xu
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Hongjie Shen
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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9
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Wang Y, Huang H, Chen J, Weng H. Crosstalk between histone/DNA modifications and RNA N 6-methyladenosine modification. Curr Opin Genet Dev 2024; 86:102205. [PMID: 38776766 DOI: 10.1016/j.gde.2024.102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal RNA modification in eukaryotic messenger RNAs (mRNAs), regulating gene expression at the transcription and post-transcription levels. Complex interplay between m6A and other well-studied epigenetic modifications, including histone modifications and DNA modification, has been extensively reported in recent years. The crosstalk between RNA m6A modification and histone/DNA modifications plays a critical role in establishing the chromatin state for the precise and specific fine-tuning of gene expression and undoubtedly has profound impacts on both physiological and pathological processes. In this review, we discuss the crosstalk between RNA m6A modification and histone/DNA modifications, emphasizing their sophisticated communications and the mechanisms underlying to gain a comprehensive view of the biological relevance of m6A-based epigenetic network.
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Affiliation(s)
- Yushuai Wang
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Gehr Family Center for Leukemia Research & City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA.
| | - Hengyou Weng
- Guangzhou National Laboratory, Guangzhou 510005, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China; The First Affiliated Hospital, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou 510005, China.
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10
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Zhang YQ, Li J, Qin Z, Li DM, Ye FZ, Bei SH, Zhang XH, Feng L. METTL5 promotes gastric cancer progression via sphingomyelin metabolism. World J Gastrointest Oncol 2024; 16:1925-1946. [PMID: 38764837 PMCID: PMC11099429 DOI: 10.4251/wjgo.v16.i5.1925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/09/2024] [Accepted: 02/19/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND The treatment of gastric cancer (GC) has caused an enormous social burden worldwide. Accumulating studies have reported that N6-methyladenosine (m6A) is closely related to tumor progression. METTL5 is a m6A methyltransferase that plays a pivotal role in maintaining the metabolic stability of cells. However, its aberrant regulation in GC has not been fully elucidated. AIM To excavate the role of METTL5 in the development of GC. METHODS METTL5 expression and clinicopathological characteristics were analyzed via The Cancer Genome Atlas dataset and further verified via immunohistochemistry, western blotting and real-time quantitative polymerase chain reaction in tissue microarrays and clinical samples. The tumor-promoting effect of METTL5 on HGC-27 and AGS cells was explored in vitro by Cell Counting Kit-8 assays, colony formation assays, scratch healing assays, transwell assays and flow cytometry. The tumor-promoting role of METTL5 in vivo was evaluated in a xenograft tumor model. The EpiQuik m6A RNA Methylation Quantification Kit was used for m6A quantification. Next, liquid chromatography-mass spectrometry was used to evaluate the association between METTL5 and sphingomyelin metabolism, which was confirmed by Enzyme-linked immunosorbent assay and rescue tests. In addition, we investigated whether METTL5 affects the sensitivity of GC cells to cisplatin via colony formation and transwell experiments. RESULTS Our research revealed substantial upregulation of METTL5, which suggested a poor prognosis of GC patients. Increased METTL5 expression indicated distant lymph node metastasis, advanced cancer stage and pathological grade. An increased level of METTL5 correlated with a high degree of m6A methylation. METTL5 markedly promotes the proliferation, migration, and invasion of GC cells in vitro. METTL5 also promotes the growth of GC in animal models. METTL5 knockdown resulted in significant changes in sphingomyelin metabolism, which implies that METTL5 may impact the development of GC via sphingomyelin metabolism. In addition, high METTL5 expression led to cisplatin resistance. CONCLUSION METTL5 was found to be an oncogenic driver of GC and may be a new target for therapy since it facilitates GC carcinogenesis through sphingomyelin metabolism and cisplatin resistance.
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Affiliation(s)
- Ya-Qiong Zhang
- Endoscopy Center, Minhang Hospital Affiliated to Fudan University, Shanghai 201100, China
| | - Jian Li
- Endoscopy Center, Minhang Hospital Affiliated to Fudan University, Shanghai 201100, China
| | - Zhe Qin
- Endoscopy Center, Minhang Hospital Affiliated to Fudan University, Shanghai 201100, China
| | - De-Ming Li
- Endoscopy Center, Minhang Hospital Affiliated to Fudan University, Shanghai 201100, China
| | - Fang-Zhou Ye
- Endoscopy Center, Minhang Hospital Affiliated to Fudan University, Shanghai 201100, China
| | - Song-Hua Bei
- Endoscopy Center, Minhang Hospital Affiliated to Fudan University, Shanghai 201100, China
| | - Xiao-Hong Zhang
- Endoscopy Center, Minhang Hospital Affiliated to Fudan University, Shanghai 201100, China
| | - Li Feng
- Endoscopy Center, Minhang Hospital Affiliated to Fudan University, Shanghai 201100, China
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11
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Wei G. RNA m6A modification, signals for degradation or stabilisation? Biochem Soc Trans 2024; 52:707-717. [PMID: 38629637 PMCID: PMC11088905 DOI: 10.1042/bst20230574] [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: 12/01/2023] [Revised: 03/24/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
The RNA modification N6-methyladenosine (m6A) is conserved across eukaryotes, and profoundly influences RNA metabolism, including regulating RNA stability. METTL3 and METTL14, together with several accessory components, form a 'writer' complex catalysing m6A modification. Conversely, FTO and ALKBH5 function as demethylases, rendering m6A dynamic. Key to understanding the functional significance of m6A is its 'reader' proteins, exemplified by YTH-domain-containing proteins (YTHDFs) canonical reader and insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) non-canonical reader. These proteins play a crucial role in determining RNA stability: YTHDFs mainly promote mRNA degradation through different cytoplasmic pathways, whereas IGF2BPs function to maintain mRNA stability. Additionally, YTHDC1 functions within the nucleus to degrade or protect certain m6A-containing RNAs, and other non-canonical readers also contribute to RNA stability regulation. Notably, m6A regulates retrotransposon LINE1 RNA stability and/or transcription via multiple mechanisms. However, conflicting observations underscore the complexities underlying m6A's regulation of RNA stability depending upon the RNA sequence/structure context, developmental stage, and/or cellular environment. Understanding the interplay between m6A and other RNA regulatory elements is pivotal in deciphering the multifaceted roles m6A plays in RNA stability regulation and broader cellular biology.
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Affiliation(s)
- Guifeng Wei
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
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12
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Olazagoitia‐Garmendia A, Rojas‐Márquez H, Sebastian‐delaCruz M, Agirre‐Lizaso A, Ochoa A, Mendoza‐Gomez LM, Perugorria MJ, Bujanda L, Madrigal AH, Santin I, Castellanos‐Rubio A. m 6A Methylated Long Noncoding RNA LOC339803 Regulates Intestinal Inflammatory Response. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307928. [PMID: 38273714 PMCID: PMC10987157 DOI: 10.1002/advs.202307928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/20/2023] [Indexed: 01/27/2024]
Abstract
Cytokine mediated sustained inflammation increases the risk to develop different complex chronic inflammatory diseases, but the implicated mechanisms remain unclear. Increasing evidence shows that long noncoding RNAs (lncRNAs) play key roles in the pathogenesis of inflammatory disorders, while inflammation associated variants are described to affect their function or essential RNA modifications as N6-methyladenosine (m6A) methylation, increasing predisposition to inflammatory diseases. Here, the functional implication of the intestinal inflammation associated lncRNA LOC339803 in the production of cytokines by intestinal epithelial cells is described. Allele-specific m6A methylation is found to affect YTHDC1 mediated protein binding affinity. LOC339803-YTHDC1 interaction dictates chromatin localization of LOC339803 ultimately inducing the expression of NFκB mediated proinflammatory cytokines and contributing to the development of intestinal inflammation. These findings are confirmed using human intestinal biopsy samples from different intestinal inflammatory conditions and controls. Additionally, it is demonstrated that LOC339803 targeting can be a useful strategy for the amelioration of intestinal inflammation in vitro and ex vivo. Overall, the results support the importance of the methylated LOC339803 lncRNA as a mediator of intestinal inflammation, explaining genetic susceptibility and presenting this lncRNA as a potential novel therapeutic target for the treatment of inflammatory intestinal disorders.
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Affiliation(s)
- Ane Olazagoitia‐Garmendia
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Henar Rojas‐Márquez
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Maialen Sebastian‐delaCruz
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Aloña Agirre‐Lizaso
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
| | - Anne Ochoa
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
| | - Luis Manuel Mendoza‐Gomez
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
- Department of MedicineFaculty of Medicine and NursingUniversity of the Basque CountryUPV/EHUDonostia‐San Sebastián20014Spain
- CIBERehdInstituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Luis Bujanda
- Department of Liver and Gastrointestinal DiseasesBiogipuzkoa Health Research InstituteDonostia University HospitalDonostia‐San Sebastian20014Spain
- Department of MedicineFaculty of Medicine and NursingUniversity of the Basque CountryUPV/EHUDonostia‐San Sebastián20014Spain
- CIBERehdInstituto de Salud Carlos III (ISCIII)Madrid28029Spain
| | - Alain Huerta Madrigal
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of MedicineMedicine FacultyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Gastroenterology DepartmentHospital Universitario de GaldakaoGaldakao48960Spain
| | - Izortze Santin
- Department of Biochemistry and Molecular BiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas CIBERDEMInstituto de Salud Carlos IIIMadrid28029Spain
| | - Ainara Castellanos‐Rubio
- Biobizkaia Health Research InstituteBarakaldo48903Spain
- Department of GeneticsPhysical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioa48940Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas CIBERDEMInstituto de Salud Carlos IIIMadrid28029Spain
- IkerbasqueBasque Foundation for ScienceBilbao48011Spain
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13
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Yao Y, Liu P, Li Y, Wang W, Jia H, Bai Y, Yuan Z, Yang Z. Regulatory role of m 6A epitranscriptomic modifications in normal development and congenital malformations during embryogenesis. Biomed Pharmacother 2024; 173:116171. [PMID: 38394844 DOI: 10.1016/j.biopha.2024.116171] [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: 10/18/2023] [Revised: 01/08/2024] [Accepted: 01/13/2024] [Indexed: 02/25/2024] Open
Abstract
The discovery of N6-methyladenosine (m6A) methylation and its role in translation has led to the emergence of a new field of research. Despite accumulating evidence suggesting that m6A methylation is essential for the pathogenesis of cancers and aging diseases by influencing RNA stability, localization, transformation, and translation efficiency, its role in normal and abnormal embryonic development remains unclear. An increasing number of studies are addressing the development of the nervous and gonadal systems during embryonic development, but only few are assessing that of the immune, hematopoietic, urinary, and respiratory systems. Additionally, these studies are limited by the requirement for reliable embryonic animal models and the difficulty in collecting tissue samples of fetuses during development. Multiple studies on the function of m6A methylation have used suitable cell lines to mimic the complex biological processes of fetal development or the early postnatal phase; hence, the research is still in the primary stage. Herein, we discuss current advances in the extensive biological functions of m6A methylation in the development and maldevelopment of embryos/fetuses and conclude that m6A modification occurs extensively during fetal development. Aberrant expression of m6A regulators is probably correlated with single or multiple defects in organogenesis during the intrauterine life. This comprehensive review will enhance our understanding of the pivotal role of m6A modifications involved in fetal development and examine future research directions in embryogenesis.
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Affiliation(s)
- Yifan Yao
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Peiqi Liu
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yue Li
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Weilin Wang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Huimin Jia
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuzuo Bai
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhonghua Yang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
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14
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Li Z, Fang F, Zafar MI, Wu X, Liu X, Tan X, Luo J, Ye Z, Xiong C, Li H. RNA m 6A modification regulates L1 retrotransposons in human spermatogonial stem cell differentiation in vitro and in vivo. Cell Mol Life Sci 2024; 81:92. [PMID: 38363375 PMCID: PMC10873452 DOI: 10.1007/s00018-024-05119-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/16/2023] [Accepted: 01/07/2024] [Indexed: 02/17/2024]
Abstract
The maintenance of genome integrity in the germline is crucial for mammalian development. Long interspersed element type 1 (LINE-1, L1) is a mobile genetic element that makes up about 17% of the human genome and poses a threat to genome integrity. N6-methyl-adenosine (m6A) plays an essential role in regulating various biological processes. However, the function of m6A modification in L1 retrotransposons and human germline development remains largely unknown. Here we knocked out the m6A methyltransferase METTL3 or the m6A reader YTHDF2 in human embryonic stem cells (hESCs) and discovered that METTL3 and YTHDF2 are crucial for inducing human spermatogonial stem cells (hSSCs) from hESCs in vitro. The removal of METTL3 or YTHDF2 resulted in increased L1 retrotransposition and reduced the efficiency of SSC differentiation in vitro. Further analysis showed that YTHDF2 recognizes the METTL3-catalyzed m6A modification of L1 retrotransposons and degrades L1 mRNA through autophagy, thereby blocking L1 retrotransposition. Moreover, the study confirmed that m6A modification in human fetal germ cells promotes the degradation of L1 retrotransposon RNA, preventing the insertion of new L1 retrotransposons into the genome. Interestingly, L1 retrotransposon RNA was highly expressed while METTL3 was significantly downregulated in the seminal plasma of azoospermic patients with meiotic arrest compared to males with normal fertility. Additionally, we identified some potentially pathogenic variants in m6A-related genes in azoospermic men with meiotic arrest. In summary, our study suggests that m6A modification serves as a guardian of genome stability during human germline development and provides novel insights into the function and regulatory mechanisms of m6A modification in restricting L1 retrotransposition.
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Affiliation(s)
- Zili Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China
- Wuhan Huake Reproductive Hospital, 128 Sanyang Road, Wuhan, 430013, China
| | - Fang Fang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Mohammad Ishraq Zafar
- Center of Reproductive Medicine, Fourth Affiliated Hospital, Zhejiang University School of Medicine, N1 Shangcheng Avenue, Yiwu, China
| | - Xunwei Wu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China
| | - Xinyu Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China
| | - Xia Tan
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jingwen Luo
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhen Ye
- Wuhan Huake Reproductive Hospital, 128 Sanyang Road, Wuhan, 430013, China
| | - Chengliang Xiong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China.
- Wuhan Huake Reproductive Hospital, 128 Sanyang Road, Wuhan, 430013, China.
- Hubei Engineering Research Center for Preparation, Application and Preservation of Human Stem Cells, Wuhan, 430013, China.
| | - Honggang Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China.
- Wuhan Huake Reproductive Hospital, 128 Sanyang Road, Wuhan, 430013, China.
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15
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Tao X, Wang G, Wei W, Su J, Chen X, Shi M, Liao Y, Qin T, Wu Y, Lu B, Liang H, Ye L, Jiang J. A bibliometric analysis of m6A methylation in viral infection from 2000 to 2022. Virol J 2024; 21:20. [PMID: 38238848 PMCID: PMC10797797 DOI: 10.1186/s12985-024-02294-1] [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: 10/08/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) methylation has become an active research area in viral infection, while little bibliometric analysis has been performed. In this study, we aim to visualize hotspots and trends using bibliometric analysis to provide a comprehensive and objective overview of the current research dynamics in this field. METHODS The data related to m6A methylation in viral infection were obtained through the Web of Science Core Collection form 2000 to 2022. To reduce bias, the literature search was conducted on December 1, 2022. Bibliometric and visual analyzes were performed using CiteSpace and Bibliometrix package. After screening, 319 qualified records were retrieved. RESULTS These publications mainly came from 28 countries led by China and the United States (the US), with the US ranking highest in terms of total link strength.The most common keywords were m6A, COVID-19, epitranscriptomics, METTL3, hepatitis B virus, innate immunity and human immunodeficiency virus 1. The thematic map showed that METTL3, plant viruses, cancer progression and type I interferon (IFN-I) reflected a good development trend and might become a research hotspot in the future, while post-transcriptional modification, as an emerging or declining theme, might not develop well. CONCLUSIONS In conclusion, m6A methylation in viral infection is an increasingly important topic in articles. METTL3, plant viruses, cancer progression and IFN-I may still be research hotspots and trends in the future.
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Affiliation(s)
- Xing Tao
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Gang Wang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Wudi Wei
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Jinming Su
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiu Chen
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Minjuan Shi
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Yinlu Liao
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Tongxue Qin
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Yuting Wu
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Beibei Lu
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China.
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China.
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China.
| | - Junjun Jiang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- China (Guangxi) - ASEAN Joint Laboratory of Emerging Infectious Diseases, Guangxi Medical University, Nanning, Guangxi, China.
- Biosafety Level -3 Laboratory, Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China.
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16
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Lu X. Regulation of endogenous retroviruses in murine embryonic stem cells and early embryos. J Mol Cell Biol 2024; 15:mjad052. [PMID: 37604781 PMCID: PMC10794949 DOI: 10.1093/jmcb/mjad052] [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: 06/08/2022] [Revised: 11/24/2022] [Accepted: 08/19/2023] [Indexed: 08/23/2023] Open
Abstract
Endogenous retroviruses (ERVs) are important components of transposable elements that constitute ∼40% of the mouse genome. ERVs exhibit dynamic expression patterns during early embryonic development and are engaged in numerous biological processes. Therefore, ERV expression must be closely monitored in cells. Most studies have focused on the regulation of ERV expression in mouse embryonic stem cells (ESCs) and during early embryonic development. This review touches on the classification, expression, and functions of ERVs in mouse ESCs and early embryos and mainly discusses ERV modulation strategies from the perspectives of transcription, epigenetic modification, nucleosome/chromatin assembly, and post-transcriptional control.
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Affiliation(s)
- Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China
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17
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Spradling AC. The Ancient Origin and Function of Germline Cysts. Results Probl Cell Differ 2024; 71:3-21. [PMID: 37996670 DOI: 10.1007/978-3-031-37936-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Gamete production in most animal species is initiated within an evolutionarily ancient multicellular germline structure, the germline cyst, whose interconnected premeiotic cells synchronously develop from a single progenitor arising just downstream from a stem cell. Cysts in mice, Drosophila, and many other animals protect developing sperm, while in females, cysts generate nurse cells that guard sister oocytes from transposons (TEs) and help them grow and build a Balbiani body. However, the origin and extreme evolutionary conservation of germline cysts remains a mystery. We suggest that cysts arose in ancestral animals like Hydra and Planaria whose multipotent somatic and germline stem cells (neoblasts) express genes conserved in all animal germ cells and frequently begin differentiation in cysts. A syncytial state is proposed to help multipotent stem cell chromatin transition to an epigenetic state with heterochromatic domains suitable for TE repression and specialized function. Most modern animals now lack neoblasts but have retained stem cells and cysts in their early germlines, which continue to function using this ancient epigenetic strategy.
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Affiliation(s)
- Allan C Spradling
- Carnegie Institution for Science/Howard Hughes Medical Institute, Baltimore, MD, USA.
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18
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Tong B, Sun Y. Activation of Young LINE-1 Elements by CRISPRa. Int J Mol Sci 2023; 25:424. [PMID: 38203595 PMCID: PMC10778729 DOI: 10.3390/ijms25010424] [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: 10/31/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Long interspersed element-1 (LINE-1; L1s) are mobile genetic elements that comprise nearly 20% of the human genome. L1s have been shown to have important functions in various biological processes, and their dysfunction is thought to be linked with diseases and cancers. However, the roles of the repetitive elements are largely not understood. While the CRISPR activation (CRISPRa) system based on catalytically deadCas9 (dCas9) is widely used for genome-wide interrogation of gene function and genetic interaction, few studies have been conducted on L1s. Here, we report using the CRISPRa method to efficiently activate L1s in human L02 cells, a derivative of the HeLa cancer cell line. After CRISPRa, the young L1 subfamilies such as L1HS/L1PA1 and L1PA2 are found to be expressed at higher levels than the older L1s. The L1s with high levels of transcription are closer to full-length and are more densely occupied by the YY1 transcription factor. The activated L1s can either be mis-spliced to form chimeric transcripts or act as alternative promoters or enhancers to facilitate the expression of neighboring genes. The method described here can be used for studying the functional roles of young L1s in cultured cells of interest.
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Affiliation(s)
- Bei Tong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yuhua Sun
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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19
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Yuan S, Xi S, Weng H, Guo MM, Zhang JH, Yu ZP, Zhang H, Yu Z, Xing Z, Liu MY, Ming DJ, Sah RK, Zhou Y, Li G, Zeng T, Hong X, Li Y, Zeng XT, Hu H. YTHDC1 as a tumor progression suppressor through modulating FSP1-dependent ferroptosis suppression in lung cancer. Cell Death Differ 2023; 30:2477-2490. [PMID: 37903990 PMCID: PMC10733405 DOI: 10.1038/s41418-023-01234-w] [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: 01/09/2023] [Revised: 10/08/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Ferroptosis is a regulated cell death process initiated by iron-dependent phospholipid peroxidation and is mainly suppressed by GPX4-dependent and FSP1-dependent surveillance mechanisms. However, how the ferroptosis surveillance system is regulated during cancer development remains largely unknown. Here, we report that the YTHDC1-mediated m6A epigenetic regulation of FSP1 alleviates the FSP1-dependent ferroptosis suppression that partially contributes to the tumor suppressive role of YTHDC1 in lung cancer progression. YTHDC1 knockdown promoted the lung tumor progression and upregulated FSP1 protein level that resulted in ferroptosis resistance of lung cancer cells. Silencing FSP1 abrogated YTHDC1 knockdown-induced proliferation increase and ferroptosis resistance. Mechanistically, YTHDC1 binding to the m6A sites in the FSP1 3'-UTR recruited the alternative polyadenylation regulator CSTF3 to generate a less stable shorter 3'-UTR contained FSP1 mRNA, whereas YTHDC1 downregulation generated the longer 3'-UTR contained FSP1 mRNA that is stabilized by RNA binding protein HuR and thus led to the enhanced FSP1 protein level. Therefore, our findings identify YTHDC1 as a tumor progression suppressor in lung cancer and a ferroptosis regulator through modulating the FSP1 mRNA stability and thus suggest a ferroptosis-related therapeutic option for YTHDC1high lung cancer.
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Affiliation(s)
- Shuai Yuan
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shu Xi
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hong Weng
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Meng-Meng Guo
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jin-Hui Zhang
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhi-Ping Yu
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Haozhe Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zhaojun Yu
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zengzhen Xing
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Meng-Yang Liu
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Dao-Jing Ming
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Rajiv Kumar Sah
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yi Zhou
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Gang Li
- Cancer Center, Faculty of Health Sciences, MoE Frontier Science Center for Precision Oncology, University of Macau, Taipa, Macau, SAR, China
| | - Tao Zeng
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xin Hong
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China
| | - Yafei Li
- Department of Epidemiology, College of Preventive Medicine, Army Medical University, Chongqing, China.
| | - Xian-Tao Zeng
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Hailiang Hu
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China.
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20
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Bai L, Xiang Y, Tang M, Liu S, Chen Q, Chen Q, Zhang M, Wan S, Sang Y, Li Q, Wang S, Li Z, Song Y, Hu X, Mao L, Feng G, Cui L, Ye Y, Zhu Y. ALKBH5 controls the meiosis-coupled mRNA clearance in oocytes by removing the N 6-methyladenosine methylation. Nat Commun 2023; 14:6532. [PMID: 37848452 PMCID: PMC10582257 DOI: 10.1038/s41467-023-42302-6] [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: 04/15/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023] Open
Abstract
N6-methyladenosine (m6A) maintains maternal RNA stability in oocytes. One regulator of m6A, ALKBH5, reverses m6A deposition and is essential in RNA metabolism. However, the specific role of ALKBH5 in oocyte maturation remains elusive. Here, we show that Alkbh5 depletion causes a wide range of defects in oocyte meiosis and results in female infertility. Temporal profiling of the maternal transcriptomes revealed striking RNA accumulation in Alkbh5-/- oocytes during meiotic maturation. Analysis of m6A dynamics demonstrated that ALKBH5-mediated m6A demethylation ensures the timely degradation of maternal RNAs, which is severely disrupted following Alkbh5-/- depletion. A distinct subset of transcripts with persistent m6A peaks are recognized by the m6A reader IGF2BP2 and thus remain stabilized, resulting in impaired RNA clearance. Additionally, reducing IGF2BP2 in Alkbh5-depleted oocytes partially rescued these defects. Overall, this work identifies ALKBH5 as a key determinant of oocyte quality and unveil the facilitating role of ALKBH5-mediated m6A removal in maternal RNA decay.
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Affiliation(s)
- Long Bai
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China.
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China.
| | - Yu Xiang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Minyue Tang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Shuangying Liu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Qingqing Chen
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Qichao Chen
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Min Zhang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Shan Wan
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Yimiao Sang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Qingfang Li
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Sisi Wang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Zhekun Li
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Yang Song
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Xiaoling Hu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Luna Mao
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Guofang Feng
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Long Cui
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Yinghui Ye
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China
| | - Yimin Zhu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310006, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China.
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China.
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21
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Dai Z, Asgari S. ALKBH8 as a potential N 6 -methyladenosine (m 6 A) eraser in insects. INSECT MOLECULAR BIOLOGY 2023; 32:461-468. [PMID: 37119026 DOI: 10.1111/imb.12843] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
The N6 -methyladenosine (m6 A) machinery functions through three groups of proteins in eukaryotic cells, including m6 A writers, erasers and readers. The m6 A cellular machinery has mostly been characterised in mammalian species, and the relevant literature on insects is currently scant. While homologues of m6 A writers and readers have been reported from insects, no erasers have been described so far. Here, using BLAST search, we searched for potential erasers in insects. While we found homologues of human m6 A eraser ALKBH5 in termites, beetles and true bugs, they could not be found in representative dipteran and lepidopteran species. However, a potential m6 A eraser, ALKBH8, was identified and experimentally investigated. Our results showed that ALKBH8 can reduce the m6 A levels of Aedes aegypti and Drosophila melanogaster RNAs, suggesting that AeALKBH8 could be a candidate m6 A eraser in insects.
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Affiliation(s)
- Zhenkai Dai
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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22
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Shi K, Sa R, Dou L, Wu Y, Dong Z, Fu X, Yu H. METTL3 exerts synergistic effects on m6A methylation and histone modification to regulate the function of VGF in lung adenocarcinoma. Clin Epigenetics 2023; 15:153. [PMID: 37742030 PMCID: PMC10517543 DOI: 10.1186/s13148-023-01568-9] [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: 07/14/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND Multiple genetic and epigenetic regulatory mechanisms play a vital role in tumorigenesis and development. Understanding the interplay between different epigenetic modifications and its contribution to transcriptional regulation in cancer is essential for precision medicine. Here, we aimed to investigate the interplay between N6-methyladenosine (m6A) modifications and histone modifications in lung adenocarcinoma (LUAD). RESULTS Based on the data from public databases, including chromatin property data (ATAC-seq, DNase-seq), methylated RNA immunoprecipitation sequencing (MeRIP-seq), and gene expression data (RNA-seq), a m6A-related differentially expressed gene nerve growth factor inducible (VGF) was identified between LUAD tissues and normal lung tissues. VGF was significantly highly expressed in LUAD tissues and cells, and was associated with a worse prognosis for LUAD, silencing of VGF inhibited the malignant phenotype of LUAD cells by inactivating the PI3K/AKT/mTOR pathway. Through the weighted correlation network analysis (WGCNA) and integration of TCGA-LUAD RNA-seq and m6A methyltransferase METTL3-knockdown RNA-seq data, a significant positive correlation between METTL3 and VGF was observed. By using the MeRIP-qPCR and dual-luciferase reporter assays, we demonstrated that METTL3 knockdown decreased m6A modification level of VGF coding sequences in LUAD cells, the colorimetric m6A quantification assay also showed that METTL3 knockdown significantly decreased global m6A modification level in LUAD cells. Interestingly, we found that METTL3 knockdown also reduced VGF expression by increasing H3K36me3 modification at the VGF promoter. Further research revealed that METTL3 knockdown upregulated the expression of histone methylase SETD2, the major H3K36me3 methyltransferase, by methylating the m6A site in the 3'UTR of SETD2 mRNA in LUAD cells. CONCLUSIONS Overall, our results reveal that the expression of VGF in LUAD cells is regulated spatio-temporally by METTL3 through both transcriptional (via histone modifications) and post-transcriptional (via m6A modifications) mechanisms. The synergistic effect of these multiple epigenetic mechanisms provides new opportunities for the diagnosis and precision treatment of tumors.
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Affiliation(s)
- Kesong Shi
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Rula Sa
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Le Dou
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Yuan Wu
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Zhiqiang Dong
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Xinyao Fu
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China
| | - Haiquan Yu
- State Key Laboratory of Reproductive Regulation a Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, Inner Mongolia, China.
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23
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Zou Z, Wei J, He C. New horizons of regulatory RNA. FUNDAMENTAL RESEARCH 2023; 3:760-762. [PMID: 38933289 PMCID: PMC11197478 DOI: 10.1016/j.fmre.2022.12.001] [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: 10/24/2022] [Revised: 11/23/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022] Open
Abstract
Genetic information flows from DNA to protein through RNA in the central dogma. Different RNA species are known to accomplish essential tasks of protein encoding (mRNAs), amino acid loading (tRNAs), and translation machinery assembly (rRNAs). However, on top of these well-known roles, RNAs are central to various cellular regulatory pathways. Here we summarize newly emerging regulatory functions of RNA, specifically focusing on regulations through RNA modifications, RNP granules, and chromatin-associated regulatory RNA. In addition to being an essential building block of the central dogma, RNA can be critical to the regulation of many cellular processes.
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Affiliation(s)
- Zhongyu Zou
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, United States
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, United States
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, United States
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, United States
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24
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Zhang J, Qiu T, Yao X, Sun X. Insights into the role of N6-methyladenosine in ferroptosis. Biomed Pharmacother 2023; 165:115192. [PMID: 37487443 DOI: 10.1016/j.biopha.2023.115192] [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: 04/22/2023] [Revised: 07/03/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023] Open
Abstract
N6-methyladenosine (m6A) methylation modification is one of the most prevalent epigenetic modifications of eukaryotic RNA. m6A methylation is widely associated with many biological processes through the modification of RNA metabolism and is associated with multiple disease states. As a newly discovered regulatory cell death in recent years, ferroptosis is an iron-dependent cell death characterized by excessive lipid peroxidation. Emerging evidence supports that ferroptosis has a significant role in the progression of diverse diseases. Besides, the key regulators of ferroptosis exhibit aberrant m6A levels under different pathological conditions. However, the correlation between m6A-modified ferroptosis and multiple diseases has not been well elucidated. In this review, we summarized the functions of m6A in ferroptosis, which are associated with the initiation and progression of multiple diseases. Investigating the role of m6A in ferroptosis might both facilitate a better understanding of the pathogenesis of these diseases and provide new opportunities for targeted treatment.
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Affiliation(s)
- Jingyuan Zhang
- Occupational and Environmental Health Department, School of Public Health, Dalian Medical University, No. 9 West Section Lvshun South Road, Dalian 116044, PR China.
| | - Tianming Qiu
- Occupational and Environmental Health Department, School of Public Health, Dalian Medical University, No. 9 West Section Lvshun South Road, Dalian 116044, PR China.
| | - Xiaofeng Yao
- Occupational and Environmental Health Department, School of Public Health, Dalian Medical University, No. 9 West Section Lvshun South Road, Dalian 116044, PR China.
| | - Xiance Sun
- Occupational and Environmental Health Department, School of Public Health, Dalian Medical University, No. 9 West Section Lvshun South Road, Dalian 116044, PR China; Global Health Research Center, Dalian Medical University, No. 9 West Section Lvshun South Road, Dalian, 116044, PR China.
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25
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Huang J, Chen P, Jia L, Li T, Yang X, Liang Q, Zeng Y, Liu J, Wu T, Hu W, Kee K, Zeng H, Liang X, Zhou C. Multi-Omics Analysis Reveals Translational Landscapes and Regulations in Mouse and Human Oocyte Aging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301538. [PMID: 37401155 PMCID: PMC10502832 DOI: 10.1002/advs.202301538] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/28/2023] [Indexed: 07/05/2023]
Abstract
Abnormal resumption of meiosis and decreased oocyte quality are hallmarks of maternal aging. Transcriptional silencing makes translational control an urgent task during meiosis resumption in maternal aging. However, insights into aging-related translational characteristics and underlying mechanisms are limited. Here, using multi-omics analysis of oocytes, it is found that translatomics during aging is related to changes in the proteome and reveals decreased translational efficiency with aging phenotypes in mouse oocytes. Translational efficiency decrease is associated with the N6-methyladenosine (m6A) modification of transcripts. It is further clarified that m6A reader YTHDF3 is significantly decreased in aged oocytes, inhibiting oocyte meiotic maturation. YTHDF3 intervention perturbs the translatome of oocytes and suppress the translational efficiency of aging-associated maternal factors, such as Hells, to affect the oocyte maturation. Moreover, the translational landscape is profiled in human oocyte aging, and the similar translational changes of epigenetic modifications regulators between human and mice oocyte aging are observed. In particular, due to the translational silence of YTHDF3 in human oocytes, translation activity is not associated with m6A modification, but alternative splicing factor SRSF6. Together, the findings profile the specific translational landscapes during oocyte aging in mice and humans, and uncover non-conservative regulators on translation control in meiosis resumption and maternal aging.
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Affiliation(s)
- Jiana Huang
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Peigen Chen
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Lei Jia
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Tingting Li
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Xing Yang
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Qiqi Liang
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Yanyan Zeng
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Jiawen Liu
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Taibao Wu
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Wenqi Hu
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of MedicineTsinghua UniversityBeijing100084China
| | - Kehkooi Kee
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of MedicineTsinghua UniversityBeijing100084China
| | - Haitao Zeng
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Xiaoyan Liang
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Chuanchuan Zhou
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
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Hamashima K, Wong KW, Sam TW, Teo JHJ, Taneja R, Le MTN, Li QJ, Hanna JH, Li H, Loh YH. Single-nucleus multiomic mapping of m 6A methylomes and transcriptomes in native populations of cells with sn-m6A-CT. Mol Cell 2023; 83:S1097-2765(23)00649-4. [PMID: 37657444 PMCID: PMC10895704 DOI: 10.1016/j.molcel.2023.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/21/2023] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
N6-methyladenosine (m6A) RNA modification plays important roles in the governance of gene expression and is temporally regulated in different cell states. In contrast to global m6A profiling in bulk sequencing, single-cell technologies for analyzing m6A heterogeneity are not extensively established. Here, we developed single-nucleus m6A-CUT&Tag (sn-m6A-CT) for simultaneous profiling of m6A methylomes and transcriptomes within a single nucleus using mouse embryonic stem cells (mESCs). m6A-CT is capable of enriching m6A-marked RNA molecules in situ, without isolating RNAs from cells. We adapted m6A-CT to the droplet-based single-cell omics platform and demonstrated high-throughput performance in analyzing nuclei isolated from thousands of cells from various cell types. We show that sn-m6A-CT profiling is sufficient to determine cell identity and allows the generation of cell-type-specific m6A methylome landscapes from heterogeneous populations. These indicate that sn-m6A-CT provides additional dimensions to multimodal datasets and insights into epitranscriptomic landscape in defining cell fate identity and states.
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Affiliation(s)
- Kiyofumi Hamashima
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.
| | - Ka Wai Wong
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Tsz Wing Sam
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore, Singapore
| | - Jia Hao Jackie Teo
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Reshma Taneja
- Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore, Singapore
| | - Minh T N Le
- Department of Pharmacology and Institute for Digital Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore; Department of Surgery, Immunology Program, Cancer Program, and Nanomedicine Translational Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Qi-Jing Li
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore; Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Physiology, NUS Yong Loo Lin School of Medicine, 2 Medical Drive, MD9, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore; NUS Graduate School's Integrative Sciences and Engineering Programme, National University of Singapore, 28 Medical Drive, Singapore, Singapore.
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27
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Wang Y, Liu J, Wang Y. Role of TNF-α-induced m6A RNA methylation in diseases: a comprehensive review. Front Cell Dev Biol 2023; 11:1166308. [PMID: 37554306 PMCID: PMC10406503 DOI: 10.3389/fcell.2023.1166308] [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: 02/15/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023] Open
Abstract
Tumor Necrosis Factor-alpha (TNF-α) is ubiquitous in the human body and plays a significant role in various physiological and pathological processes. However, TNF-α-induced diseases remain poorly understood with limited efficacy due to the intricate nature of their mechanisms. N6-methyladenosine (m6A) methylation, a prevalent type of epigenetic modification of mRNA, primarily occurs at the post-transcriptional level and is involved in intranuclear and extranuclear mRNA metabolism. Evidence suggests that m6A methylation participates in TNF-α-induced diseases and signaling pathways associated with TNF-α. This review summarizes the involvement of TNF-α and m6A methylation regulators in various diseases, investigates the impact of m6A methylation on TNF-α-induced diseases, and puts forth potential therapeutic targets for treating TNF-α-induced diseases.
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Affiliation(s)
- Youlin Wang
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jing Liu
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yongchen Wang
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- General Practice Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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28
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Mu M, Li X, Dong L, Wang J, Cai Q, Hu Y, Wang D, Zhao P, Zhang L, Zhang D, Cheng S, Tan L, Wu F, Shi YG, Xu W, Shi Y, Shen H. METTL14 regulates chromatin bivalent domains in mouse embryonic stem cells. Cell Rep 2023; 42:112650. [PMID: 37314930 DOI: 10.1016/j.celrep.2023.112650] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 04/11/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
METTL14 (methyltransferase-like 14) is an RNA-binding protein that partners with METTL3 to mediate N6-methyladenosine (m6A) methylation. Recent studies identified a function for METTL3 in heterochromatin in mouse embryonic stem cells (mESCs), but the molecular function of METTL14 on chromatin in mESCs remains unclear. Here, we show that METTL14 specifically binds and regulates bivalent domains, which are marked by trimethylation of histone H3 lysine 27 (H3K27me3) and lysine 4 (H3K4me3). Knockout of Mettl14 results in decreased H3K27me3 but increased H3K4me3 levels, leading to increased transcription. We find that bivalent domain regulation by METTL14 is independent of METTL3 or m6A modification. METTL14 enhances H3K27me3 and reduces H3K4me3 by interacting with and probably recruiting the H3K27 methyltransferase polycomb repressive complex 2 (PRC2) and H3K4 demethylase KDM5B to chromatin. Our findings identify an METTL3-independent role of METTL14 in maintaining the integrity of bivalent domains in mESCs, thus indicating a mechanism of bivalent domain regulation in mammals.
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Affiliation(s)
- Mandi Mu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinze Li
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Dong
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jin Wang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qingqing Cai
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yajun Hu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Duanduan Wang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peng Zhao
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lei Zhang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Daixuan Zhang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Siyi Cheng
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Tan
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China
| | - Feizhen Wu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yujiang Geno Shi
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenqi Xu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.
| | - Yang Shi
- Ludwig Institute for Cancer Research, Oxford Branch, Oxford University, Oxford, UK.
| | - Hongjie Shen
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.
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29
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You M, Liu J, Li J, Ji C, Ni H, Guo W, Zhang J, Jia W, Wang Z, Zhang Y, Yao Y, Yu G, Ji H, Wang X, Han D, Du X, Xu MM, Yu S. Mettl3-m 6A-Creb1 forms an intrinsic regulatory axis in maintaining iNKT cell pool and functional differentiation. Cell Rep 2023; 42:112584. [PMID: 37267102 DOI: 10.1016/j.celrep.2023.112584] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/07/2023] [Accepted: 05/15/2023] [Indexed: 06/04/2023] Open
Abstract
N6-methyladenosine (m6A) methyltransferase Mettl3 is involved in conventional T cell immunity; however, its role in innate immune cells remains largely unknown. Here, we show that Mettl3 intrinsically regulates invariant natural killer T (iNKT) cell development and function in an m6A-dependent manner. Conditional ablation of Mettl3 in CD4+CD8+ double-positive (DP) thymocytes impairs iNKT cell proliferation, differentiation, and cytokine secretion, which synergistically causes defects in B16F10 melanoma resistance. Transcriptomic and epi-transcriptomic analyses reveal that Mettl3 deficiency disturbs the expression of iNKT cell-related genes with altered m6A modification. Strikingly, Mettl3 modulates the stability of the Creb1 transcript, which in turn controls the protein and phosphorylation levels of Creb1. Furthermore, conditional targeting of Creb1 in DP thymocytes results in similar phenotypes of iNKT cells lacking Mettl3. Importantly, ectopic expression of Creb1 largely rectifies such developmental defects in Mettl3-deficient iNKT cells. These findings reveal that the Mettl3-m6A-Creb1 axis plays critical roles in regulating iNKT cells at the post-transcriptional layer.
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Affiliation(s)
- Menghao You
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jingjing Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jie Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China; Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ce Ji
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Haochen Ni
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenhui Guo
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiarui Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Weiwei Jia
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhao Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yajiao Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yingpeng Yao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Guotao Yu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Huanyu Ji
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaohu Wang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dali Han
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuguang Du
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Meng Michelle Xu
- Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Shuyang Yu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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30
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Liang Y, Wang H, Wu B, Peng N, Yu D, Wu X, Zhong X. The emerging role of N 6-methyladenine RNA methylation in metal ion metabolism and metal-induced carcinogenesis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023:121897. [PMID: 37244530 DOI: 10.1016/j.envpol.2023.121897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
Abstract
N6-methyladenine (m6A) is the most common and abundant internal modification in eukaryotic mRNAs, which can regulate gene expression and perform important biological tasks. Metal ions participate in nucleotide biosynthesis and repair, signal transduction, energy generation, immune defense, and other important metabolic processes. However, long-term environmental and occupational exposure to metals through food, air, soil, water, and industry can result in toxicity, serious health problems, and cancer. Recent evidence indicates dynamic and reversible m6A modification modulates various metal ion metabolism, such as iron absorption, calcium uptake and transport. In turn, environmental heavy metal can alter m6A modification by directly affecting catalytic activity and expression level of methyltransferases and demethylases, or through reactive oxygen species, eventually disrupting normal biological function and leading to diseases. Therefore, m6A RNA methylation may play a bridging role in heavy metal pollution-induced carcinogenesis. This review discusses interaction among heavy metal, m6A, and metal ions metabolism, and their regulatory mechanism, focuses on the role of m6A methylation and heavy metal pollution in cancer. Finally, the role of nutritional therapy that targeting m6A methylation to prevent metal ion metabolism disorder-induced cancer is summarized.
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Affiliation(s)
- Yaxu Liang
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Huan Wang
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Bencheng Wu
- Anyou Biotechnology Group Co., LTD., Taicang, 215437, China
| | - Ning Peng
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Dongming Yu
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Xin Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiang Zhong
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China.
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31
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Abouhashem AS, Singh K, Srivastava R, Liu S, Mathew-Steiner SS, Gu X, Kacar S, Hagar A, Sandusky GE, Roy S, Wan J, Sen CK. The Prolonged Terminal Phase of Human Life Induces Survival Response in the Skin Transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540715. [PMID: 37292819 PMCID: PMC10245562 DOI: 10.1101/2023.05.15.540715] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Human death marks the end of organismal life under conditions such that the components of the human body continue to be alive. Such postmortem cellular survival depends on the nature (Hardy scale of slow-fast death) of human death. Slow and expected death typically results from terminal illnesses and includes a prolonged terminal phase of life. As such organismal death process unfolds, do cells of the human body adapt for postmortem cellular survival? Organs with low energy cost-of-living, such as the skin, are better suited for postmortem cellular survival. In this work, the effect of different durations of terminal phase of human life on postmortem changes in cellular gene expression was investigated using RNA sequencing data of 701 human skin samples from the Genotype-Tissue Expression (GTEx) database. Longer terminal phase (slow-death) was associated with a more robust induction of survival pathways (PI3K-Akt signaling) in postmortem skin. Such cellular survival response was associated with the upregulation of embryonic developmental transcription factors such as FOXO1 , FOXO3 , ATF4 and CEBPD . Upregulation of PI3K-Akt signaling was independent of sex or duration of death-related tissue ischemia. Analysis of single nucleus RNA-seq of post-mortem skin tissue specifically identified the dermal fibroblast compartment to be most resilient as marked by adaptive induction of PI3K-Akt signaling. In addition, slow death also induced angiogenic pathways in the dermal endothelial cell compartment of postmortem human skin. In contrast, specific pathways supporting functional properties of the skin as an organ were downregulated following slow death. Such pathways included melanogenesis and those representing the skin extracellular matrix (collagen expression and metabolism). Efforts to understand the significance of death as a biological variable (DABV) in influencing the transcriptomic composition of surviving component tissues has far-reaching implications including rigorous interpretation of experimental data collected from the dead and mechanisms involved in transplant-tissue obtained from dead donors.
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32
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Wang Y, Li Y, Skuland T, Zhou C, Li A, Hashim A, Jermstad I, Khan S, Dalen KT, Greggains GD, Klungland A, Dahl JA, Au KF. The RNA m 6A landscape of mouse oocytes and preimplantation embryos. Nat Struct Mol Biol 2023; 30:703-709. [PMID: 37081317 DOI: 10.1038/s41594-023-00969-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/16/2023] [Indexed: 04/22/2023]
Abstract
Despite the significance of N6-methyladenosine (m6A) in gene regulation, the requirement for large amounts of RNA has hindered m6A profiling in mammalian early embryos. Here we apply low-input methyl RNA immunoprecipitation and sequencing to map m6A in mouse oocytes and preimplantation embryos. We define the landscape of m6A during the maternal-to-zygotic transition, including stage-specifically expressed transcription factors essential for cell fate determination. Both the maternally inherited transcripts to be degraded post fertilization and the zygotically activated genes during zygotic genome activation are widely marked by m6A. In contrast to m6A-marked zygotic ally-activated genes, m6A-marked maternally inherited transcripts have a higher tendency to be targeted by microRNAs. Moreover, RNAs derived from retrotransposons, such as MTA that is maternally expressed and MERVL that is transcriptionally activated at the two-cell stage, are largely marked by m6A. Our results provide a foundation for future studies exploring the regulatory roles of m6A in mammalian early embryonic development.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yanjiao Li
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trine Skuland
- Department of Reproductive Medicine, Oslo University Hospital, Oslo, Norway
- Division of Gynaecology and Obstetrics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Chengjie Zhou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Aifu Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Adnan Hashim
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ingunn Jermstad
- Norwegian Transgenic Centre, Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Shaista Khan
- Norwegian Transgenic Centre, Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Knut Tomas Dalen
- Norwegian Transgenic Centre, Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gareth D Greggains
- Department of Reproductive Medicine, Oslo University Hospital, Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
| | - John Arne Dahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
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Zhu W, Ding Y, Meng J, Gu L, Liu W, Li L, Chen H, Wang Y, Li Z, Li C, Sun Y, Liu Z. Reading and writing of mRNA m 6A modification orchestrate maternal-to-zygotic transition in mice. Genome Biol 2023; 24:67. [PMID: 37024923 PMCID: PMC10080794 DOI: 10.1186/s13059-023-02918-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
N6-methyladenosine (m6A) modification has been shown to regulate RNA metabolism. Here, we investigate m6A dynamics during maternal-to-zygotic transition (MZT) in mice through multi-omic analysis. Our results show that m6A can be maternally inherited or de novo gained after fertilization. Interestingly, m6A modification on maternal mRNAs not only correlates with mRNA degradation, but also maintains the stability of a small group of mRNAs thereby promoting their translation after fertilization. We identify Ythdc1 and Ythdf2 as key m6A readers for mouse preimplantation development. Our study reveals a key role of m6A mediated RNA metabolism during MZT in mammals.
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Affiliation(s)
- Wencheng Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Yufeng Ding
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Juan Meng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Gu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjun Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Hongyu Chen
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Yining Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China
| | - Ziyi Li
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, China
| | - Chen Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
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Chen J, Xiao L, Chen Y, Li W, Liu Y, Zhou Y, Tan H. YT521-B homology domain containing 1 ameliorates mitochondrial damage and ferroptosis in sleep deprivation by activating the sirtuin 1/nuclear factor erythroid-derived 2-like 2/heme oxygenase 1 pathway. Brain Res Bull 2023; 197:1-12. [PMID: 36935054 DOI: 10.1016/j.brainresbull.2023.03.008] [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: 11/09/2022] [Revised: 03/01/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
In sleep deprivation (SD) models, ferroptosis is increased. SIRT1 alleviates cognitive impairment in SD, and SIRT1/NRF2/HO1 pathway depresses ferroptosis in different diseases. Moreover, YTHDC1 can regulate SIRT1 mRNA stability. Therefore, our study explored effects of the YTHDC1/SIRT1/NRF2/HO1 axis on neuronal damage and ferroptosis in SD. The SD mouse model was established through a modified multi-platform water environment method and a cell model of ferroptosis was constructed with Erastin, followed by gain- and loss-of-function assays. In mice, the cognitive impairment and CLOCK and BMAL1 levels in hippocampal tissues were assessed. In cells, viability was measured. In mice and cells, mitochondrial ultrastructure, the content of reactive oxygen species (ROS), malondialdehyde (MDA), glutathione (GSH), and iron, and the expression of GPX4 and ACSL4 were detected. The potential relationships among YTHDC1, SIRT1, and NRF2 were analyzed. SD mice had downregulated YTHDC1, SIRT1, NRF2, and HO1 protein expression in hippocampal tissues and increased ferroptosis. Mechanically, SIRT1 activated the NRF2/HO1 pathway through deacetylation, and YTHDC1 increased SIRT1 mRNA stability. YTHDC1 overexpression diminished mitochondrial damage, the content of ROS, iron, and MDA, and the expression of ACSL4 while enhancing GSH contents and GPX4 expression in hippocampal tissues of SD mice and Erastin-induced HT22 cells. Additionally, YTHDC1 overexpression elevated viability in Erastin-induced HT22 cells. SIRT1 or NRF2 overexpression ameliorated Erastin-induced mitochondrial damage and ferroptosis in HT22 cells. Silencing SIRT1 abolished the impact of YTHDC1 overexpression on SD mice and Erastin-induced HT22 cells. Collectively, YTHDC1 ameliorates mitochondrial damage and ferroptosis after SD by activating the SIRT1/NRF2/HO1 pathway.
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Affiliation(s)
- Juan Chen
- Department of Neurology, the First Hospital of Changsha, Changsha, Hunan 410005, P.R. China.
| | - Lijun Xiao
- Department of Neurology, the First Hospital of Changsha, Changsha, Hunan 410005, P.R. China
| | - Ying Chen
- Department of Neurology, the First Hospital of Changsha, Changsha, Hunan 410005, P.R. China
| | - Wei Li
- Department of Neurology, the First Hospital of Changsha, Changsha, Hunan 410005, P.R. China
| | - Yinan Liu
- Department of Neurology, the First Hospital of Changsha, Changsha, Hunan 410005, P.R. China
| | - Ying Zhou
- Department of Neurology, the First Hospital of Changsha, Changsha, Hunan 410005, P.R. China
| | - Hong Tan
- Department of Neurology, the First Hospital of Changsha, Changsha, Hunan 410005, P.R. China
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35
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Stamidis N, Żylicz JJ. RNA-mediated heterochromatin formation at repetitive elements in mammals. EMBO J 2023; 42:e111717. [PMID: 36847618 PMCID: PMC10106986 DOI: 10.15252/embj.2022111717] [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: 05/20/2022] [Revised: 12/12/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
The failure to repress transcription of repetitive genomic elements can lead to catastrophic genome instability and is associated with various human diseases. As such, multiple parallel mechanisms cooperate to ensure repression and heterochromatinization of these elements, especially during germline development and early embryogenesis. A vital question in the field is how specificity in establishing heterochromatin at repetitive elements is achieved. Apart from trans-acting protein factors, recent evidence points to a role of different RNA species in targeting repressive histone marks and DNA methylation to these sites in mammals. Here, we review recent discoveries on this topic and predominantly focus on the role of RNA methylation, piRNAs, and other localized satellite RNAs.
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Affiliation(s)
- Nikolaos Stamidis
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Jan Jakub Żylicz
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
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36
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Yi Y, Zeng Y, Sam TW, Hamashima K, Tan RJR, Warrier T, Phua JX, Taneja R, Liou YC, Li H, Xu J, Loh YH. Ribosomal proteins regulate 2-cell-stage transcriptome in mouse embryonic stem cells. Stem Cell Reports 2023; 18:463-474. [PMID: 36638791 PMCID: PMC9968990 DOI: 10.1016/j.stemcr.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/14/2023] Open
Abstract
A rare sub-population of mouse embryonic stem cells (mESCs), the 2-cell-like cell, is defined by the expression of MERVL and 2-cell-stage-specific transcript (2C transcript). Here, we report that the ribosomal proteins (RPs) RPL14, RPL18, and RPL23 maintain the identity of mESCs and regulate the expression of 2C transcripts. Disregulation of the RPs induces DUX-dependent expression of 2C transcripts and alters the chromatin landscape. Mechanically, knockdown (KD) of RPs triggers the binding of RPL11 to MDM2, an interaction known to prevent P53 protein degradation. Increased P53 protein upon RP KD further activates its downstream pathways, including DUX. Our study delineates the critical roles of RPs in 2C transcript activation, ascribing a novel function to these essential proteins.
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Affiliation(s)
- Yao Yi
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Yingying Zeng
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Tsz Wing Sam
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Kiyofumi Hamashima
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Rachel Jun Rou Tan
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Tushar Warrier
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Jun Xiang Phua
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Reshma Taneja
- Department of Physiology, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Xu
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore; Joint Center for Single Cell Biology, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Laboratory, Division of Cell Biology and Therapies, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, Singapore 119077, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore.
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37
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Li H, Sun J, Dong Y, Huang Y, Wu L, Xi C, Su Z, Xiao Y, Zhang C, Liang Y, Li Y, Lin Z, Shen L, Zuo Y, Abudureheman A, Yin J, Wang H, Kong X, Le R, Gao S, Zhang Y. Remodeling of H3K9me3 during the pluripotent to totipotent-like state transition. Stem Cell Reports 2023; 18:449-462. [PMID: 36638787 PMCID: PMC9968986 DOI: 10.1016/j.stemcr.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 01/14/2023] Open
Abstract
Multiple chromatin modifiers associated with H3K9me3 play important roles in the transition from embryonic stem cells to 2-cell (2C)-like cells. However, it remains elusive how H3K9me3 is remodeled and its association with totipotency. Here, we integrated transcriptome and H3K9me3 profiles to conduct a detailed comparison of 2C embryos and 2C-like cells. Globally, H3K9me3 is highly preserved and H3K9me3 dynamics within the gene locus is not associated with gene expression change during 2C-like transition. Promoter-deposited H3K9me3 plays non-repressive roles in the activation of genes during 2C-like transition. In contrast, transposable elements, residing in the nearby regions of up-regulated genes, undergo extensive elimination of H3K9me3 and are tended to be induced in 2C-like transitions. Furthermore, a large fraction of trophoblast stem cell-specific enhancers undergo loss of H3K9me3 exclusively in MERVL+/Zscan4+ cells. Our study therefore reveals the unique H3K9me3 profiles of 2C-like cells, facilitating the further exploration of totipotency.
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Affiliation(s)
- Hu Li
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, China
| | - Jiatong Sun
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yu Dong
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yixin Huang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Li Wu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chenxiang Xi
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhongqu Su
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Yihan Xiao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chuyu Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yuwei Liang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yujun Li
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiyi Lin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lu Shen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yixing Zuo
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Abuduwaili Abudureheman
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiqing Yin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiangyin Kong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Yanping Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
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38
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Tang J, Wang X, Xiao D, Liu S, Tao Y. The chromatin-associated RNAs in gene regulation and cancer. Mol Cancer 2023; 22:27. [PMID: 36750826 PMCID: PMC9903551 DOI: 10.1186/s12943-023-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Eukaryotic genomes are prevalently transcribed into many types of RNAs that translate into proteins or execute gene regulatory functions. Many RNAs associate with chromatin directly or indirectly and are called chromatin-associated RNAs (caRNAs). To date, caRNAs have been found to be involved in gene and transcriptional regulation through multiple mechanisms and have important roles in different types of cancers. In this review, we first present different categories of caRNAs and the modes of interaction between caRNAs and chromatin. We then detail the mechanisms of chromatin-associated nascent RNAs, chromatin-associated noncoding RNAs and emerging m6A on caRNAs in transcription and gene regulation. Finally, we discuss the roles of caRNAs in cancer as well as epigenetic and epitranscriptomic mechanisms contributing to cancer, which could provide insights into the relationship between different caRNAs and cancer, as well as tumor treatment and intervention.
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Affiliation(s)
- Jun Tang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078 Hunan China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078 Hunan China
| | - Xiang Wang
- grid.216417.70000 0001 0379 7164Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongguang Tao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China. .,Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China. .,Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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39
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Sendinc E, Shi Y. RNA m6A methylation across the transcriptome. Mol Cell 2023; 83:428-441. [PMID: 36736310 DOI: 10.1016/j.molcel.2023.01.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/05/2023]
Abstract
Since the early days of foundational studies of nucleic acids, many chemical moieties have been discovered to decorate RNA and DNA in diverse organisms. In mammalian cells, one of these chemical modifications, N6-methyl adenosine (m6A), is unique in a way that it is highly abundant not only on RNA polymerase II (RNAPII) transcribed, protein-coding transcripts but also on non-coding RNAs, such as ribosomal RNAs and snRNAs, mediated by distinct, evolutionarily conserved enzymes. Here, we review RNA m6A modification in the light of the recent appreciation of nuclear roles for m6A in regulating chromatin states and gene expression, as well as the recent discoveries of the evolutionarily conserved methyltransferases, which catalyze methylation of adenosine on diverse sets of RNAs. Considering that the substrates of these enzymes are involved in many important biological processes, this modification warrants further research to understand the molecular mechanisms and functions of m6A in health and disease.
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Affiliation(s)
- Erdem Sendinc
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yang Shi
- Ludwig Institute for Cancer Research, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7DQ, UK.
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40
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Warkocki Z. An update on post-transcriptional regulation of retrotransposons. FEBS Lett 2023; 597:380-406. [PMID: 36460901 DOI: 10.1002/1873-3468.14551] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/04/2022]
Abstract
Retrotransposons, including LINE-1, Alu, SVA, and endogenous retroviruses, are one of the major constituents of human genomic repetitive sequences. Through the process of retrotransposition, some of them occasionally insert into new genomic locations by a copy-paste mechanism involving RNA intermediates. Irrespective of de novo genomic insertions, retrotransposon expression can lead to DNA double-strand breaks and stimulate cellular innate immunity through endogenous patterns. As a result, retrotransposons are tightly regulated by multi-layered regulatory processes to prevent the dangerous effects of their expression. In recent years, significant progress was made in revealing how retrotransposon biology intertwines with general post-transcriptional RNA metabolism. Here, I summarize current knowledge on the involvement of post-transcriptional factors in the biology of retrotransposons, focusing on LINE-1. I emphasize general RNA metabolisms such as methylation of adenine (m6 A), RNA 3'-end polyadenylation and uridylation, RNA decay and translation regulation. I discuss the effects of retrotransposon RNP sequestration in cytoplasmic bodies and autophagy. Finally, I summarize how innate immunity restricts retrotransposons and how retrotransposons make use of cellular enzymes, including the DNA repair machinery, to complete their replication cycles.
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Affiliation(s)
- Zbigniew Warkocki
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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41
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Koo KM, Go YH, Kim SM, Kim CD, Do JT, Kim TH, Cha HJ. Label-free and non-destructive identification of naïve and primed embryonic stem cells based on differences in cellular metabolism. Biomaterials 2023; 293:121939. [PMID: 36521427 DOI: 10.1016/j.biomaterials.2022.121939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/25/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022]
Abstract
Pluripotent stem cells (PSCs) exist in naïve or primed states based on their origin. For in vitro culture, these PSCs require different supplements and growth factors. However, owing to their similar phenotypic features, identifying both cell types without harming cellular functions is challenging. This study reports an electrochemical method that enables simple, label-free, and non-destructive detection of naïve embryonic stem cells (ESCs) derived from mouse ESCs, based on the differences in cellular metabolism. Two major metabolic pathways to generate adenosine triphosphate (ATP)-glycolysis and oxidative phosphorylation (OXPHOS)-were blocked, and it was found that mitochondrial energy generation is the origin of the strong electrochemical signals of naïve ESCs. The number of ESCs is quantified when mixed with primed ESCs or converted from naïve-primed switchable metastable ESCs. The mouse PSCs derived from doxycycline-inducible mouse embryonic fibroblasts (MEFs) are also sensitively identified among other cell types such as unconverted MEFs and primed PSCs. The developed sensing platform operates in a non-invasive and label-free manner. Thus, it can be useful in the development of stem cell-derived therapeutics.
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Affiliation(s)
- Kyeong-Mo Koo
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Young-Hyun Go
- Research Institute of Pharmaceutical Science, Seoul National University, Seoul, 08826, Republic of Korea; College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seong-Min Kim
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang-Dae Kim
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biology, College of Animal Bioscience and Technology, Konkuk University, Seoul, Republic of Korea
| | - Tae-Hyung Kim
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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Zhu Y, Li J, Yang H, Yang X, Zhang Y, Yu X, Li Y, Chen G, Yang Z. The potential role of m6A reader YTHDF1 as diagnostic biomarker and the signaling pathways in tumorigenesis and metastasis in pan-cancer. Cell Death Dis 2023; 9:34. [PMID: 36707507 PMCID: PMC9883452 DOI: 10.1038/s41420-023-01321-4] [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: 11/26/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/29/2023]
Abstract
m6A is an important RNA methylation in progression of various human cancers. As the m6A reader protein, YTHDF1 is reported to accelerate m6A-modified mRNAs translation in cytoplasm. It is highly expressed in various human cancers and contributes to the progression and metastasis of cancers. YTHDF1 was closely associated with poor prognosis and also used as a molecular marker for clinical diagnosis or therapy in human cancers. It has been reported to promote chemoresistance to Adriamycin, Cisplatin and Olaparib by increasing mRNA stability of its target molecule. Moreover, it contributes to CSC-like characteristic of tumor cells and inducing the antitumor immune microenvironment. Here, we reviewed the clinical diagnostic and prognostic values of YTHDF1, as well as the molecular mechanisms of YTHDF1 in progression and metastasis of human cancers.
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Affiliation(s)
- Yanan Zhu
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Jing Li
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Hang Yang
- grid.415444.40000 0004 1800 0367Department of Rehabilitation Medicine, The Second Affiliated Hospital of Kunming Medical University, 650106 Kunming, Yunnan China
| | - Xinyi Yang
- grid.413458.f0000 0000 9330 9891Guizhou Medical University, 550004 Guiyang, Guizhou China
| | - Ya Zhang
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Xinchao Yu
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Ying Li
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Gangxian Chen
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Zuozhang Yang
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
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Uzonyi A, Dierks D, Nir R, Kwon OS, Toth U, Barbosa I, Burel C, Brandis A, Rossmanith W, Le Hir H, Slobodin B, Schwartz S. Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability. Mol Cell 2023; 83:237-251.e7. [PMID: 36599352 DOI: 10.1016/j.molcel.2022.12.026] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023]
Abstract
N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-uniformly distributed across the transcriptome, yet the basis for its selective deposition is unknown. Here, we propose that m6A deposition is not selective. Instead, it is exclusion based: m6A consensus motifs are methylated by default, unless they are within a window of ∼100 nt from a splice junction. A simple model which we extensively validate, relying exclusively on presence of m6A motifs and exon-intron architecture, allows in silico recapitulation of experimentally measured m6A profiles. We provide evidence that exclusion from splice junctions is mediated by the exon junction complex (EJC), potentially via physical occlusion, and that previously observed associations between exon-intron architecture and mRNA decay are mechanistically mediated via m6A. Our findings establish a mechanism coupling nuclear mRNA splicing and packaging with the covalent installation of m6A, in turn controlling cytoplasmic decay.
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Affiliation(s)
- Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - David Dierks
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Oh Sung Kwon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Ursula Toth
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Cindy Burel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Boris Slobodin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel; Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel.
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel.
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44
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Deng M, Wang X, Xiong Z, Tang P. Control of RNA degradation in cell fate decision. Front Cell Dev Biol 2023; 11:1164546. [PMID: 37025171 PMCID: PMC10070868 DOI: 10.3389/fcell.2023.1164546] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Cell fate is shaped by a unique gene expression program, which reflects the concerted action of multilayered precise regulation. Substantial research attention has been paid to the contribution of RNA biogenesis to cell fate decisions. However, increasing evidence shows that RNA degradation, well known for its function in RNA processing and the surveillance of aberrant transcripts, is broadly engaged in cell fate decisions, such as maternal-to-zygotic transition (MZT), stem cell differentiation, or somatic cell reprogramming. In this review, we first look at the diverse RNA degradation pathways in the cytoplasm and nucleus. Then, we summarize how selective transcript clearance is regulated and integrated into the gene expression regulation network for the establishment, maintenance, and exit from a special cellular state.
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Affiliation(s)
- Mingqiang Deng
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiwei Wang
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Zhi Xiong
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou, China
| | - Peng Tang
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Peng Tang,
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Weng H, Huang H, Chen J. N 6-Methyladenosine RNA Modification in Normal and Malignant Hematopoiesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:105-123. [PMID: 38228961 DOI: 10.1007/978-981-99-7471-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Over 170 nucleotide variants have been discovered in messenger RNAs (mRNAs) and non-coding RNAs so far. However, only a few of them, including N6-methyladenosine (m6A), 5-methylcytidine (m5C), and N1-methyladenosine (m1A), could be mapped in the transcriptome. These RNA modifications appear to be dynamically regulated, with writer, eraser, and reader proteins being identified for each modification. As a result, there is a growing interest in studying their biological impacts on normal bioprocesses and tumorigenesis over the past few years. As the most abundant internal modification in eukaryotic mRNAs, m6A plays a vital role in the post-transcriptional regulation of mRNA fate via regulating almost all aspects of mRNA metabolism, including RNA splicing, nuclear export, RNA stability, and translation. Studies on mRNA m6A modification serve as a great example for exploring other modifications on mRNA. In this chapter, we will review recent advances in the study of biological functions and regulation of mRNA modifications, specifically m6A, in both normal hematopoiesis and malignant hematopoiesis. We will also discuss the potential of targeting mRNA modifications as a treatment for hematopoietic disorders.
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Affiliation(s)
- Hengyou Weng
- The First Affiliated Hospital, The Fifth Affiliated Hospital, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China.
- Bioland Laboratory, Guangzhou, China.
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- Gehr Family Center for Leukemia Research and City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
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YTHDC1 Promotes Stemness Maintenance and Malignant Progression in Head and Neck Squamous Cell Carcinoma. Stem Cells Int 2022; 2022:7494354. [DOI: 10.1155/2022/7494354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/27/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background. YTH domain containing 1 (YTHDC1), an N6-methyladenosine (m6A) modification reading protein, plays a key role in regulating RNA translation and degradation. However, the role of YTHDC1 in head and neck squamous cell carcinoma (HNSCC) cancer stem cells remains largely unknown. This study is aimed at investigating the role of YTHDC1 in HNSCC and exploring its role in regulating cancer stem cells. Methods. RNA sequencing was used to detect differentially expressed genes (DEGs) between SCC9 spheres and SCC9 cells and to uncover molecular pathways and target molecules associated with CSCs. We detected YTHDC1 expression in The Cancer Genome Atlas (TCGA) database data and clinical samples. Subsequently, YTHDC1 gene suppression assays were performed in HNSCC cell lines to investigate the effect of YTHDC1 on tumor cell stemness maintenance, proliferation, and migration capacity. To further confirm the role of YTHDC1 in regulating cancer stem cells in HNSCC, we analyzed online HNSCC single-cell transcriptomic data to investigate YTHDC1 expression patterns at the single-cell level and the correlation of these levels with the expression of stem cell markers. Results. YTHDC1 expression levels were significantly upregulated in SCC9 spheres, and YTHDC1 was aberrantly expressed in HNSCC tumor tissues. The increased YTHDC1 expression was closely correlated with the clinical characteristics of HNSCC patients. YTHDC1 regulates the malignant phenotype of HNSCC in both in vivo and in vitro studies. Further single-cell transcriptomic data analysis revealed that YTHDC1 positively correlated with malignant epithelial cell stemness capacity at the single-cell level, and that YTHDC1 was involved in regulating stemness maintenance in HNSCC. Conclusions. These findings suggest that YTHDC1 may serve as a biomarker for stem maintenance and malignant progression in HNSCC, providing new insights into the treatment of cancer.
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Zhang L, Yuan M, Huang X, Cao Q, Huang S, Sun R, Lei L. Inhibition of METTL5 improves preimplantation development of mouse somatic cell nuclear transfer embryos. Reproduction 2022; 164:221-230. [PMID: 36111643 DOI: 10.1530/rep-22-0169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022]
Abstract
In brief Several factors affect the reprogramming efficiency of nuclear transfer embryos. This study shows that inhibiting 18S rRNA m6A methyltransferase METTL5 during nuclear transfer can improve the developmental rate of nuclear transfer embryos. Abstract N6-methyladenosine (m6A) is one of the most important epigenetic modifications in eukaryotic RNAs, which regulates development and diseases. It is identified by several proteins. Methyltransferase-like 5 (METTL5), an enzyme that methylates 18S rRNA m6A, controls the translation of proteins and regulates pluripotency in embryonic stem cells. However, the functions of METTL5 in embryonic development have not been explored. Here, we found that Mettl5 was upregulated in somatic cell nuclear transfer (SCNT) embryos compared with normal fertilized embryos. Therefore, we hypothesized that METTL5 knockdown during the early stage of SCNT would improve the developmental rate of SCNT embryos. Notably, injection of Mettl5 siRNA (si-Mettl5) into enucleated oocytes during nuclear transfer increased the rate of development and the number of cells in blastocysts. Moreover, inhibition of METTL5 reduced the activity of phosphorylated ribosomal protein S6, decreased the levels of the repressive histone modification H3K27me3 and increased the expression of activating histone modifications H3K27ac and H3K4me3 and mRNA levels of some 2-cell-specific genes. These results expand our understanding of the role of METTL5 in early embryonic development and provide a novel idea for improving the efficiency of nuclear transfer cloning.
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Affiliation(s)
- Luchun Zhang
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Meng Yuan
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xingwei Huang
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Qianzi Cao
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Shaogang Huang
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Ruizhen Sun
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang, China
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48
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Begik O, Mattick JS, Novoa EM. Exploring the epitranscriptome by native RNA sequencing. RNA (NEW YORK, N.Y.) 2022; 28:1430-1439. [PMID: 36104106 PMCID: PMC9745831 DOI: 10.1261/rna.079404.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Chemical RNA modifications, collectively referred to as the "epitranscriptome," are essential players in fine-tuning gene expression. Our ability to analyze RNA modifications has improved rapidly in recent years, largely due to the advent of high-throughput sequencing methodologies, which typically consist of coupling modification-specific reagents, such as antibodies or enzymes, to next-generation sequencing. Recently, it also became possible to map RNA modifications directly by sequencing native RNAs using nanopore technologies, which has been applied for the detection of a number of RNA modifications, such as N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). However, the signal modulations caused by most RNA modifications are yet to be determined. A global effort is needed to determine the signatures of the full range of RNA modifications to avoid the technical biases that have so far limited our understanding of the epitranscriptome.
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Affiliation(s)
- Oguzhan Begik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra, Barcelona 08002, Spain
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49
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Liu XM, Mao Y, Wang S, Zhou J, Qian SB. METTL3 modulates chromatin and transcription dynamics during cell fate transition. Cell Mol Life Sci 2022; 79:559. [PMID: 36266520 DOI: 10.1007/s00018-022-04590-x] [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: 03/30/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/26/2022]
Abstract
Transcriptional programming plays a key role in determining the cell state. Timely reconfiguration of chromatin structure and attenuation of pluripotent genes are required for efficient embryonic stem cell (ESC) differentiation. Here, we identify METTL3, a core N6-methyladenosine (m6A) catalyzing enzyme, as a crucial modulator of dynamic transcription and chromatin accessibility upon ESC-derived cardiac differentiation. Genome-wide analysis of chromatin-associated RNAs revealed that depletion of METTL3 failed to dramatically attenuate the transcription of pluripotent genes, as well as activate nascent cardiomyocyte-specific transcripts upon differentiation. Consistently, ATAC-seq analysis showed that loss of METTL3 markedly attenuated the dynamic alteration of chromatin accessibility at both promoters and gene bodies, resulting in reduced sensitivity of ESC chromatin structure to cardiac differentiation signal. Furthermore, we found that METTL3 negatively regulated the histone modifications H3K4me3 and H3K36me3, which are involved in METTL3-modulated dynamic chromatin architecture during cell state transition. Unexpectedly, using chromatin-associated m6A sequencing, we found that nuclear m6A underwent a dramatic increase upon differentiation, which correlates with the decrease of chromatin accessibility. Collectively, our findings reveal that METTL3 and nuclear m6A epitranscriptome couple with chromatin state to ensure transcriptional regulation of cell fate transition.
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Affiliation(s)
- Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China.
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Shen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China
| | - Jun Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA.
- Field of Genetics, Genomics, and Development, Cornell University, Ithaca, NY, 14853, USA.
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50
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Xu W, Shen H. When RNA methylation meets DNA methylation. Nat Genet 2022; 54:1261-1262. [PMID: 36071174 DOI: 10.1038/s41588-022-01166-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wenqi Xu
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hongjie Shen
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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