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Geens B, Goossens S, Li J, Van de Peer Y, Vanden Broeck J. Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects. Mol Cell Endocrinol 2024; 585:112178. [PMID: 38342134 DOI: 10.1016/j.mce.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.
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Affiliation(s)
- Bart Geens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Stijn Goossens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
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2
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Guarnacci M, Preiss T. The je ne sais quoi of 5-methylcytosine in messenger RNA. RNA 2024; 30:560-569. [PMID: 38531644 PMCID: PMC11019750 DOI: 10.1261/rna.079982.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
The potential presence of 5-methylcytosine as a sparse internal modification of mRNA was first raised in 1975, and a first map of the modification was also part of the epitranscriptomics "big bang" in 2012. Since then, the evidence for its presence in mRNA has firmed up, and initial insights have been gained into the molecular function and broader biological relevance of 5-methylcytosine when present in mRNA. Here, we summarize the status quo of the field, outline some of its current challenges, and suggest how to address them in future work.
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Affiliation(s)
- Marco Guarnacci
- Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia
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3
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Tu R, Ping Z, Liu J, Tsoi ML, Song X, Liu W, Xie T. Niche Tet maintains germline stem cells independently of dioxygenase activity. EMBO J 2024; 43:1570-1590. [PMID: 38499787 PMCID: PMC11021519 DOI: 10.1038/s44318-024-00074-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Ten-eleven translocation (TET) proteins are dioxygenases that convert 5-methylcytosine (5mC) into 5-hydroxylmethylcytosine (5hmC) in DNA and RNA. However, their involvement in adult stem cell regulation remains unclear. Here, we identify a novel enzymatic activity-independent function of Tet in the Drosophila germline stem cell (GSC) niche. Tet activates the expression of Dpp, the fly homologue of BMP, in the ovary stem cell niche, thereby controlling GSC self-renewal. Depletion of Tet disrupts Dpp production, leading to premature GSC loss. Strikingly, both wild-type and enzyme-dead mutant Tet proteins rescue defective BMP signaling and GSC loss when expressed in the niche. Mechanistically, Tet interacts directly with Bap55 and Stat92E, facilitating recruitment of the Polybromo Brahma associated protein (PBAP) complex to the dpp enhancer and activating Dpp expression. Furthermore, human TET3 can effectively substitute for Drosophila Tet in the niche to support BMP signaling and GSC self-renewal. Our findings highlight a conserved novel catalytic activity-independent role of Tet as a scaffold protein in supporting niche signaling for adult stem cell self-renewal.
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Affiliation(s)
- Renjun Tu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
| | - Zhaohua Ping
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO, USA
| | - Jian Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Centre, Shenzhen, Guangdong, China
| | - Man Lung Tsoi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, New Territories, Hong Kong Special Administrative Region, China
| | - Xiaoqing Song
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO, USA
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Centre, Shenzhen, Guangdong, China
| | - Ting Xie
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China.
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO, USA.
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4
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Liu WW, Zheng SQ, Li T, Fei YF, Wang C, Zhang S, Wang F, Jiang GM, Wang H. RNA modifications in cellular metabolism: implications for metabolism-targeted therapy and immunotherapy. Signal Transduct Target Ther 2024; 9:70. [PMID: 38531882 DOI: 10.1038/s41392-024-01777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
Cellular metabolism is an intricate network satisfying bioenergetic and biosynthesis requirements of cells. Relevant studies have been constantly making inroads in our understanding of pathophysiology, and inspiring development of therapeutics. As a crucial component of epigenetics at post-transcription level, RNA modification significantly determines RNA fates, further affecting various biological processes and cellular phenotypes. To be noted, immunometabolism defines the metabolic alterations occur on immune cells in different stages and immunological contexts. In this review, we characterize the distribution features, modifying mechanisms and biological functions of 8 RNA modifications, including N6-methyladenosine (m6A), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N4-acetylcytosine (ac4C), N7-methylguanosine (m7G), Pseudouridine (Ψ), adenosine-to-inosine (A-to-I) editing, which are relatively the most studied types. Then regulatory roles of these RNA modification on metabolism in diverse health and disease contexts are comprehensively described, categorized as glucose, lipid, amino acid, and mitochondrial metabolism. And we highlight the regulation of RNA modifications on immunometabolism, further influencing immune responses. Above all, we provide a thorough discussion about clinical implications of RNA modification in metabolism-targeted therapy and immunotherapy, progression of RNA modification-targeted agents, and its potential in RNA-targeted therapeutics. Eventually, we give legitimate perspectives for future researches in this field from methodological requirements, mechanistic insights, to therapeutic applications.
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Affiliation(s)
- Wei-Wei Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- School of Clinical Medicine, Shandong University, Jinan, China
| | - Si-Qing Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Tian Li
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Yun-Fei Fei
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Chen Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Shuang Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Fei Wang
- Neurosurgical Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Guan-Min Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
| | - Hao Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China.
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Liu X, Wei Q, Yang C, Zhao H, Xu J, Mobet Y, Luo Q, Yang D, Zuo X, Chen N, Yang Y, Li L, Wang W, Yu J, Xu J, Liu T, Yi P. RNA m 5C modification upregulates E2F1 expression in a manner dependent on YBX1 phase separation and promotes tumor progression in ovarian cancer. Exp Mol Med 2024; 56:600-615. [PMID: 38424195 PMCID: PMC10984993 DOI: 10.1038/s12276-024-01184-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/01/2023] [Accepted: 12/26/2023] [Indexed: 03/02/2024] Open
Abstract
5-Methylcytosine (m5C) is a common RNA modification that modulates gene expression at the posttranscriptional level, but the crosstalk between m5C RNA modification and biomolecule condensation, as well as transcription factor-mediated transcriptional regulation, in ovarian cancer, is poorly understood. In this study, we revealed that the RNA methyltransferase NSUN2 facilitates mRNA m5C modification and forms a positive feedback regulatory loop with the transcription factor E2F1 in ovarian cancer. Specifically, NSUN2 promotes m5C modification of E2F1 mRNA and increases its stability, and E2F1 binds to the NSUN2 promoter, subsequently reciprocally activating NSUN2 transcription. The RNA binding protein YBX1 functions as the m5C reader and is involved in NSUN2-mediated E2F1 regulation. m5C modification promotes YBX1 phase separation, which upregulates E2F1 expression. In ovarian cancer, NSUN2 and YBX1 are amplified and upregulated, and higher expression of NSUN2 and YBX1 predicts a worse prognosis for ovarian cancer patients. Moreover, E2F1 transcriptionally regulates the expression of the oncogenes MYBL2 and RAD54L, driving ovarian cancer progression. Thus, our study delineates a NSUN2-E2F1-NSUN2 loop regulated by m5C modification in a manner dependent on YBX1 phase separation, and this previously unidentified pathway could be a promising target for ovarian cancer treatment.
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Affiliation(s)
- Xiaoyi Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Qinglv Wei
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Chenyue Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Hongyan Zhao
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Jie Xu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Youchaou Mobet
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Qingya Luo
- Department of Pathology, Southwest Hospital, Army Medical University, Chongqing, 400038, China
| | - Dan Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Xinzhao Zuo
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Ningxuan Chen
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Yu Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Li Li
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Wei Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Jing Xu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Tao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China.
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China.
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6
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Wei H, Xu Y, Lin L, Li Y, Zhu X. A review on the role of RNA methylation in aging-related diseases. Int J Biol Macromol 2024; 254:127769. [PMID: 38287578 DOI: 10.1016/j.ijbiomac.2023.127769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
Senescence is the underlying mechanism of organism aging and is robustly regulated at the post-transcriptional level. This regulation involves the chemical modifications, of which the RNA methylation is the most common. Recently, a rapidly growing number of studies have demonstrated that methylation is relevant to aging and aging-associated diseases. Owing to the rapid development of detection methods, the understanding on RNA methylation has gone deeper. In this review, we summarize the current understanding on the influence of RNA modification on cellular senescence, with a focus on mRNA methylation in aging-related diseases, and discuss the emerging potential of RNA modification in diagnosis and therapy.
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Affiliation(s)
- Hong Wei
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Department of Neurology, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuhao Xu
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Li Lin
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuefeng Li
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China.
| | - Xiaolan Zhu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China.
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7
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Wang MK, Gao CC, Yang YG. Emerging Roles of RNA Methylation in Development. Acc Chem Res 2023; 56:3417-3427. [PMID: 37965760 DOI: 10.1021/acs.accounts.3c00448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
ConspectusMore than 170 different types of chemical modifications have been identified on diverse types of RNA, collectively known as the epitranscriptome. Among them, N6-methyladenine (m6A), 5-methylcytosine (m5C), N1-methyladenine (m1A), and N7-methylguanosine (m7G) as the ubiquitous post-transcriptional modification are widely involved in regulating the metabolic processes such as RNA degradation, translation, stability, and export, mediating important physiological and pathological processes such as stress regulation, immune response, development, and tumorigenesis. Recently, the regulatory role of RNA modification during developmental processes is getting more attention. Therefore, the development of low-input even single-cell and high-resolution sequencing technologies is crucial for the exploration of the regulatory roles of RNA modifications in these important biological events of trace samples.This account focuses on the roles of RNA modifications in various developmental processes. We describe the distribution characteristics of various RNA modifications, catalytic enzymes, binding proteins, and the development of sequencing technologies. RNA modification is dynamically reversible, which can be catalyzed by methyltransferases and eliminated by demethylases. RNA m6A is the most abundant post-transcriptional modification on eukaryote mRNA, which is mainly concentrated near the stop codon, and involves in RNA metabolism regulation. RNA m5C, another most studied RNA modification, has been identified in a various of organisms and RNA species, mainly enriched in the regions downstream of translation initiation sites and broadly distributes across the whole coding sequence (CDS) in mammalian mRNAs. RNA m1A, with a lower abundance than m6A, is widely distributed in various RNA types, mainly locates in the 5' untranslated region (5'UTR) of mRNA and regulates translation. RNA m7G, one of the most common RNA modifications in eukaryotes, has been identified at cap regions and internal positions of RNAs and recently gained considerable attention.Thanks to the development of sequencing technology, m6A has been found to regulate the tumorigenic process, including tumor proliferation, invasion, and metastasis by modulating oncogenes and tumor suppressor genes, and affect oocyte maturation and embryonic development through regulating maternal and zygotic genes. m5C related proteins have been identified to participate in embryonic development, plant growth, and neural stem cell differentiation in a m5C dependent manner. m1A also has been revealed to be involved in these developmental processes. m7G dysregulation mainly involves in neurodevelopmental disorders and neurodegenerative diseases.Collectively, we summarized the gradually exhibited roles of RNA methylation during development, and discussed the possibility of RNA modifications as candidate biomarkers and potential therapeutic targets. The technological development is anticipated as the major driving force to expand our knowledge in this field.
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Affiliation(s)
- Meng-Ke Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, P. R. China
| | - Chun-Chun Gao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, P. R. China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, P. R. China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, P. R. China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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8
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Wang H, Feng J, Zeng C, Liu J, Fu Z, Wang D, Wang Y, Zhang L, Li J, Jiang A, He M, Cao Y, Yan K, Tang H, Guo D, Xu K, Zhou X, Zhou L, Lan K, Zhou Y, Chen Y. NSUN2-mediated M 5c methylation of IRF3 mRNA negatively regulates type I interferon responses during various viral infections. Emerg Microbes Infect 2023; 12:2178238. [PMID: 36748584 PMCID: PMC9946332 DOI: 10.1080/22221751.2023.2178238] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
5-Methylcytosine (m5C) is a widespread post-transcriptional RNA modification and is reported to be involved in manifold cellular responses and biological processes through regulating RNA metabolism. However, its regulatory role in antiviral innate immunity has not yet been elucidated. Here, we report that NSUN2, a typical m5C methyltransferase, negatively regulates type I interferon responses during various viral infections, including SARS-CoV-2. NSUN2 specifically mediates m5C methylation of IRF3 mRNA and accelerates its degradation, resulting in low levels of IRF3 and downstream IFN-β production. Knockout or knockdown of NSUN2 enhanced type I interferon and downstream ISGs during various viral infection in vitro. And in vivo, the antiviral innate response is more dramatically enhanced in Nsun2+/- mice than in Nsun2+/+ mice. The highly m5C methylated cytosines in IRF3 mRNA were identified, and their mutation enhanced cellular IRF3 mRNA levels. Moreover, infection with Sendai virus (SeV), vesicular stomatitis virus (VSV), herpes simplex virus 1 (HSV-1), or Zika virus (ZIKV) resulted in a reduction of endogenous NSUN2 levels. Especially, SARS-CoV-2 infection (WT strain and BA.1 omicron variant) also decreased endogenous levels of NSUN2 in COVID-19 patients and K18-hACE2 KI mice, further increasing type I interferon and downstream ISGs. Together, our findings reveal that NSUN2 serves as a negative regulator of interferon response by accelerating the fast turnover of IRF3 mRNA, while endogenous NSUN2 levels decrease during SARS-CoV-2 and various viral infections to boost antiviral responses for effective elimination of viruses.
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Affiliation(s)
- Hongyun Wang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Jiangpeng Feng
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Cong Zeng
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China,College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jiejie Liu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Zhiying Fu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Dehe Wang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yafen Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Lu Zhang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Jiali Li
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Ao Jiang
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Miao He
- School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yuanyuan Cao
- Department of Microbiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, People’s Republic of China
| | - Kun Yan
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Hao Tang
- Heart Center of Henan Provincial People’s Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Deyin Guo
- School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Ke Xu
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Li Zhou
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China,Animal Bio-Safety Level III Laboratory at Center for Animal Experiment, Wuhan University, Wuhan, People’s Republic of China
| | - Ke Lan
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yu Zhou
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yu Chen
- State Key Laboratory of Virology, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China, Yu Chen State Key Laboratory of Virology, Modern Virology Research Center, RNA Institute, College of Life Sciences, Wuhan University, Wuhan430072, People’s Republic of China
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9
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Abstract
Nucleobase modifications are prevalent in eukaryotic mRNA and their discovery has resulted in the emergence of epitranscriptomics as a research field. The most abundant internal (non-cap) mRNA modification is N6-methyladenosine (m6A), the study of which has revolutionized our understanding of post-transcriptional gene regulation. In addition, numerous other mRNA modifications are gaining great attention because of their major roles in RNA metabolism, immunity, development and disease. In this Review, we focus on the regulation and function of non-m6A modifications in eukaryotic mRNA, including pseudouridine (Ψ), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), inosine, 5-methylcytidine (m5C), N4-acetylcytidine (ac4C), 2'-O-methylated nucleotide (Nm) and internal N7-methylguanosine (m7G). We highlight their regulation, distribution, stoichiometry and known roles in mRNA metabolism, such as mRNA stability, translation, splicing and export. We also discuss their biological consequences in physiological and pathological processes. In addition, we cover research techniques to further study the non-m6A mRNA modifications and discuss their potential future applications.
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Affiliation(s)
- Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Kai Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Cong Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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10
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Li N, Zhang T, Zhu L, Sun L, Shao G, Gao J. Recent Advances of Using Exosomes as Diagnostic Markers and Targeting Carriers for Cardiovascular Disease. Mol Pharm 2023; 20:4354-4372. [PMID: 37566627 DOI: 10.1021/acs.molpharmaceut.3c00268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of human death worldwide. Exosomes act as endogenous biological vectors; they possess advantages of low immunogenicity and low safety risks, also providing tissue selectivity, including the inherent targeting the to heart. Therefore, exosomes not only have been applied as biomarkers for diagnosis and therapeutic outcome confirmation but also showed potential as drug carriers for cardiovascular targeting delivery. This review aims to summarize the progress and challenges of exosomes as novel biomarkers, especially many novel exosomal noncoding RNAs (ncRNAs), and also provides an overview of the improved targeting functions of exosomes by unique engineered approaches, the latest developed administration methods, and the therapeutic effects of exosomes used as the biocarriers of medications for cardiovascular disease treatment. Also, the possible therapeutic mechanisms and the potentials for transferring exosomes to the clinic for CVD treatment are discussed. The advances, in vivo and in vitro applications, modifications, mechanisms, and challenges summarized in this review will provide a general understanding of this promising strategy for CVD treatment.
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Affiliation(s)
- Ni Li
- Department of Cardiothoracic Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, China
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tianyuan Zhang
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Linwen Zhu
- Department of Cardiothoracic Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, China
| | - Lebo Sun
- Department of Cardiothoracic Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, China
| | - Guofeng Shao
- Department of Cardiothoracic Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, China
| | - Jianqing Gao
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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11
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Tu R, Tang XA, Xu R, Ping Z, Yu Z, Xie T. Gap junction-transported cAMP from the niche controls stem cell progeny differentiation. Proc Natl Acad Sci U S A 2023; 120:e2304168120. [PMID: 37603749 PMCID: PMC10468610 DOI: 10.1073/pnas.2304168120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/22/2023] [Indexed: 08/23/2023] Open
Abstract
The niche has been shown to control stem cell self-renewal in different tissue types and organisms. Recently, a separate niche has been proposed to control stem cell progeny differentiation, called the differentiation niche. However, it remains poorly understood whether and how the differentiation niche directly signals to stem cell progeny to control their differentiation. In the Drosophila ovary, inner germarial sheath (IGS) cells contribute to two separate niche compartments for controlling both germline stem cell (GSC) self-renewal and progeny differentiation. In this study, we show that IGS cells express Inx2 protein, which forms gap junctions (GJs) with germline-specific Zpg protein to control stepwise GSC lineage development, including GSC self-renewal, germline cyst formation, meiotic double-strand DNA break formation, and oocyte specification. Germline-specific Zpg and IGS-specific Inx2 knockdowns cause similar defects in stepwise GSC development. Additionally, secondary messenger cAMP is transported from IGS cells to GSCs and their progeny via GJs to activate PKA signaling for controlling stepwise GSC development. Therefore, this study demonstrates that the niche directly controls GSC progeny differentiation via the GJ-cAMP-PKA signaling axis, which provides important insights into niche control of stem cell differentiation and highlights the importance of GJ-transported cAMP in tissue regeneration. This may represent a general strategy for the niche to control adult stem cell development in various tissue types and organisms since GJs and cAMP are widely distributed.
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Affiliation(s)
- Renjun Tu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong Special Administrative Region (SAR), China
| | - Xiaohan Alex Tang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong Special Administrative Region (SAR), China
| | - Rui Xu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong Special Administrative Region (SAR), China
| | - Zhaohua Ping
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Ting Xie
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong Special Administrative Region (SAR), China
- Stowers Institute for Medical Research, Kansas City, MO64110
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12
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Zhang H, Yang Y, Liu Z, Xu H, Zhu H, Wang P, Liang G. Significance of methylation-related genes in diagnosis and subtype classification of renal interstitial fibrosis. Hereditas 2023; 160:32. [PMID: 37496082 PMCID: PMC10373342 DOI: 10.1186/s41065-023-00295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND RNA methylation modifications, such as N1-methyladenosine/N6-methyladenosine /N5-methylcytosine (m1A/m6A/m5C), are the most common RNA modifications and are crucial for a number of biological processes. Nonetheless, the role of RNA methylation modifications of m1A/m6A/m5C in the pathogenesis of renal interstitial fibrosis (RIF) remains incompletely understood. METHODS Firstly, we downloaded 2 expression datasets from the GEO database, namely GSE22459 and GSE76882. In a differential analysis of these datasets between patients with and without RIF, we selected 33 methylation-related genes (MRGs). We then applied a PPI network, LASSO analysis, SVM-RFE algorithm, and RF algorithm to identify key MRGs. RESULTS We eventually obtained five candidate MRGs (WTAP, ALKBH5, YTHDF2, RBMX, and ELAVL1) to forecast the risk of RIF. We created a nomogram model derived from five key MRGs, which revealed that the nomogram model may be advantageous to patients. Based on the selected five significant MRGs, patients with RIF were classified into two MRG patterns using consensus clustering, and the correlation between the five MRGs, the two MRG patterns, and the genetic pattern with immune cell infiltration was shown. Moreover, we conducted GO and KEGG analyses on 768 DEGs between MRG clusters A and B to look into their different involvement in RIF. To measure the MRG patterns, a PCA algorithm was developed to determine MRG scores for each sample. The MRG scores of the patients in cluster B were higher than those in cluster A. CONCLUSIONS Ultimately, we concluded that cluster A in the two MRG patterns identified on these five key m1A/m6A/m5C regulators may be associated with RIF.
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Affiliation(s)
- Hanchao Zhang
- Department of Urology, The Affilated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China
- Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Yue Yang
- Department of Urology, The Affilated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China
- Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zhengdao Liu
- Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Hong Xu
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Han Zhu
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Peirui Wang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Guobiao Liang
- Medical College of Soochow University, Suzhou, Jiangsu, China.
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China.
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13
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Kong Y, Yu J, Ge S, Fan X. Novel insight into RNA modifications in tumor immunity: Promising targets to prevent tumor immune escape. Innovation (N Y) 2023; 4:100452. [PMID: 37485079 PMCID: PMC10362524 DOI: 10.1016/j.xinn.2023.100452] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/23/2023] [Indexed: 07/25/2023] Open
Abstract
An immunosuppressive state is a typical feature of the tumor microenvironment. Despite the dramatic success of immune checkpoint inhibitor (ICI) therapy in preventing tumor cell escape from immune surveillance, primary and acquired resistance have limited its clinical use. Notably, recent clinical trials have shown that epigenetic drugs can significantly improve the outcome of ICI therapy in various cancers, indicating the importance of epigenetic modifications in immune regulation of tumors. Recently, RNA modifications (N6-methyladenosine [m6A], N1-methyladenosine [m1A], 5-methylcytosine [m5C], etc.), novel hotspot areas of epigenetic research, have been shown to play crucial roles in protumor and antitumor immunity. In this review, we provide a comprehensive understanding of how m6A, m1A, and m5C function in tumor immunity by directly regulating different immune cells as well as indirectly regulating tumor cells through different mechanisms, including modulating the expression of immune checkpoints, inducing metabolic reprogramming, and affecting the secretion of immune-related factors. Finally, we discuss the current status of strategies targeting RNA modifications to prevent tumor immune escape, highlighting their potential.
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Affiliation(s)
- Yuxin Kong
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200001, China
| | - Jie Yu
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200001, China
| | - Shengfang Ge
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200001, China
| | - Xianqun Fan
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200001, China
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14
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Ni P, Zhou C, Liang S, Jiang Y, Liu D, Shao Z, Noh H, Zhao L, Tian Y, Zhang C, Wei J, Li X, Yu H, Ni R, Yu X, Qi X, Zhang Y, Ma X, Deng W, Guo W, Wang Q, Sham PC, Chung S, Li T. YBX1-Mediated DNA Methylation-Dependent SHANK3 Expression in PBMCs and Developing Cortical Interneurons in Schizophrenia. Adv Sci (Weinh) 2023; 10:e2300455. [PMID: 37211699 PMCID: PMC10369273 DOI: 10.1002/advs.202300455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/05/2023] [Indexed: 05/23/2023]
Abstract
Schizophrenia (SCZ) is a severe psychiatric and neurodevelopmental disorder. The pathological process of SCZ starts early during development, way before the first onset of psychotic symptoms. DNA methylation plays an important role in regulating gene expression and dysregulated DNA methylation is involved in the pathogenesis of various diseases. The methylated DNA immunoprecipitation-chip (MeDIP-chip) is performed to investigate genome-wide DNA methylation dysregulation in peripheral blood mononuclear cells (PBMCs) of patients with first-episode SCZ (FES). Results show that the SHANK3 promoter is hypermethylated, and this hypermethylation (HyperM) is negatively correlated with the cortical surface area in the left inferior temporal cortex and positively correlated with the negative symptom subscores in FES. The transcription factor YBX1 is further found to bind to the HyperM region of SHANK3 promoter in induced pluripotent stem cells (iPSCs)-derived cortical interneurons (cINs) but not glutamatergic neurons. Furthermore, a direct and positive regulatory effect of YBX1 on the expression of SHANK3 is confirmed in cINs using shRNAs. In summary, the dysregulated SHANK3 expression in cINs suggests the potential role of DNA methylation in the neuropathological mechanism underlying SCZ. The results also suggest that HyperM of SHANK3 in PBMCs can serve as a potential peripheral biomarker of SCZ.
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Affiliation(s)
- Peiyan Ni
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Chuqing Zhou
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Sugai Liang
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Youhui Jiang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Dongxin Liu
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Zhicheng Shao
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
| | - Haneul Noh
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Liansheng Zhao
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Yang Tian
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Chengcheng Zhang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Jinxue Wei
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Xiaojing Li
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Hua Yu
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Rongjun Ni
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Xueli Yu
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Xueyu Qi
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Yamin Zhang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Xiaohong Ma
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Wei Deng
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Wanjun Guo
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Qiang Wang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Pak C. Sham
- Department of PsychiatryLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong, SAR999077China
- Centre for PanorOmic SciencesThe University of Hong KongHong Kong, SAR999077China
| | - Sangmi Chung
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Tao Li
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
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15
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Lirussi L, Nilsen HL. DNA Glycosylases Define the Outcome of Endogenous Base Modifications. Int J Mol Sci 2023; 24:10307. [PMID: 37373453 DOI: 10.3390/ijms241210307] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Chemically modified nucleic acid bases are sources of genomic instability and mutations but may also regulate gene expression as epigenetic or epitranscriptomic modifications. Depending on the cellular context, they can have vastly diverse impacts on cells, from mutagenesis or cytotoxicity to changing cell fate by regulating chromatin organisation and gene expression. Identical chemical modifications exerting different functions pose a challenge for the cell's DNA repair machinery, as it needs to accurately distinguish between epigenetic marks and DNA damage to ensure proper repair and maintenance of (epi)genomic integrity. The specificity and selectivity of the recognition of these modified bases relies on DNA glycosylases, which acts as DNA damage, or more correctly, as modified bases sensors for the base excision repair (BER) pathway. Here, we will illustrate this duality by summarizing the role of uracil-DNA glycosylases, with particular attention to SMUG1, in the regulation of the epigenetic landscape as active regulators of gene expression and chromatin remodelling. We will also describe how epigenetic marks, with a special focus on 5-hydroxymethyluracil, can affect the damage susceptibility of nucleic acids and conversely how DNA damage can induce changes in the epigenetic landscape by altering the pattern of DNA methylation and chromatin structure.
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Affiliation(s)
- Lisa Lirussi
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Hilde Loge Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
- Unit for Precision Medicine, Akershus University Hospital, 1478 Lørenskog, Norway
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16
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Zhang L, Xu X, Su X. Modifications of noncoding RNAs in cancer and their therapeutic implications. Cell Signal 2023:110726. [PMID: 37230201 DOI: 10.1016/j.cellsig.2023.110726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/06/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
In the last 50 years, over 150 various chemical modifications on RNA molecules, including mRNAs, rRNAs, tRNAs, and other noncoding RNAs (ncRNAs), have been identified and characterized. These RNA modifications regulate RNA biogenesis and biological functions and are widely involved in various physiological processes and diseases, including cancer. In recent decades, broad interest has arisen in the epigenetic modification of ncRNAs due to the increased knowledge of the critical roles of ncRNAs in cancer. In this review, we summarize the various modifications of ncRNAs and highlight their roles in cancer initiation and progression. In particular, we discuss the potential of RNA modifications as novel biomarkers and therapeutic targets in cancer.
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Affiliation(s)
- Le Zhang
- Center for Reproductive Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China
| | - Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612-9497, USA
| | - Xiulan Su
- Clinical Medical Research Center, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China.
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17
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Huang E, Chen L. RNA N 6-methyladenosine modification in female reproductive biology and pathophysiology. Cell Commun Signal 2023; 21:53. [PMID: 36894952 PMCID: PMC9996912 DOI: 10.1186/s12964-023-01078-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 02/12/2023] [Indexed: 03/11/2023] Open
Abstract
Gene expression and posttranscriptional regulation can be strongly influenced by epigenetic modifications. N6-methyladenosine, the most extensive RNA modification, has been revealed to participate in many human diseases. Recently, the role of RNA epigenetic modifications in the pathophysiological mechanism of female reproductive diseases has been intensively studied. RNA m6A modification is involved in oogenesis, embryonic growth, and foetal development, as well as preeclampsia, miscarriage, endometriosis and adenomyosis, polycystic ovary syndrome, premature ovarian failure, and common gynaecological tumours such as cervical cancer, endometrial cancer, and ovarian cancer. In this review, we provide a summary of the research results of m6A on the female reproductive biology and pathophysiology in recent years and aim to discuss future research directions and clinical applications of m6A-related targets. Hopefully, this review will add to our understanding of the cellular mechanisms, diagnostic biomarkers, and underlying therapeutic strategies of female reproductive system diseases. Video Abstract.
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Affiliation(s)
- Erqing Huang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lijuan Chen
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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18
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Lu J, Wang H, Cao W, Chen D, He Z, Xu J. Construction of a m5C-related long non-coding RNA signature for the prognosis of hepatocellular carcinoma. Hum Cell 2023; 36:712-24. [PMID: 36520346 DOI: 10.1007/s13577-022-00845-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022]
Abstract
RNA modification serves as a kind of posttranscriptional modification. Besides N6-methyladenosine (m6A), 5-methylcytosine(m5C) is also an important RNA modification. Long non-coding RNAs (lncRNAs) play an important role in tumor progression. Thus, we performed bioinformatic analysis to establish a m5C-related lncRNA signature(m5ClncSig) for hepatocellular carcinoma (HCC). The RNA sequencing data and clinical data were obtained from The Cancer Genome Atlas (TCGA) database. Pearson correlation coefficient analysis was applied to conduct m5C-related genes and m5C-related lncRNAs co-expressing network. Univariate Cox regression was used to screen the m5C-related lncRNAs with prognosis value. LASSO regression was applied to establish m5ClncSig. Functional analysis including KEGG and GO were performed. The relation between m5ClncSig and immunity was assessed by CIBERSORT and ESTIMATE. RP11-498C9.15 was selected for in vitro validation. A m5ClncSig was established containing 8 lncRNAs with significantly prognosis value. According to risk score calculated by m5ClncSig, high-risk group had worse clinical outcomes than low-risk group. The risk score was validated as an independent prognosis factor. Moreover, the abundances of 11 types of immune cells were significantly different between high-risk group and low-risk group while 8 immune-related genes expressed differently between these two groups. RP11-498C9.15 was validated as a risk factor in HCC progression.
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19
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Hollmann NM, Jagtap PKA, Linse JB, Ullmann P, Payr M, Murciano B, Simon B, Hub JS, Hennig J. Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein. Nucleic Acids Res 2023; 51:1895-1913. [PMID: 36688322 PMCID: PMC9976900 DOI: 10.1093/nar/gkac1277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/24/2023] Open
Abstract
RNA binding proteins (RBPs) often engage multiple RNA binding domains (RBDs) to increase target specificity and affinity. However, the complexity of target recognition of multiple RBDs remains largely unexplored. Here we use Upstream of N-Ras (Unr), a multidomain RBP, to demonstrate how multiple RBDs orchestrate target specificity. A crystal structure of the three C-terminal RNA binding cold-shock domains (CSD) of Unr bound to a poly(A) sequence exemplifies how recognition goes beyond the classical ππ-stacking in CSDs. Further structural studies reveal several interaction surfaces between the N-terminal and C-terminal part of Unr with the poly(A)-binding protein (pAbp). All interactions are validated by mutational analyses and the high-resolution structures presented here will guide further studies to understand how both proteins act together in cellular processes.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Johanna-Barbara Linse
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Philip Ullmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marco Payr
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jochen S Hub
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany.,Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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20
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Gong W, Zhang S. YB1 participated in regulating mitochondrial activity through RNA replacement. Front Oncol 2023; 13:1145379. [PMID: 37035211 PMCID: PMC10076880 DOI: 10.3389/fonc.2023.1145379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
As a relic of ancient bacterial endosymbionts, mitochondria play a central role in cell metabolism, apoptosis, autophagy, and other processes. However, the function of mitochondria-derived nucleic acids in cellular signal transduction has not been fully elucidated. Here, our work has found that Y-box binding protein 1 (YB1) maintained cellular autophagy at a moderate level to inhibit mitochondrial oxidative phosphorylation. In addition, mitochondrial RNA was leaked into cytosol under starvation, accompanied by YB1 mitochondrial relocation, resulting in YB1-bound RNA replacement. The mRNAs encoded by oxidative phosphorylation (OXPHOS)-associated genes and oncogene HMGA1 (high-mobility group AT-hook 1) were competitively replaced by mitochondria-derived tRNAs. The increase of free OXPHOS mRNAs released from the YB1 complex enhanced mitochondrial activity through facilitating translation, but the stability of HMGA1 mRNA was impaired without the protection of YB1, both contributing to breast cancer cell apoptosis and reactive oxygen species production. Our finding not only provided a new potential target for breast cancer therapy but also shed new light on understanding the global landscape of cellular interactions between RNA-binding proteins and different RNA species.
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Affiliation(s)
- Weipeng Gong
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Song Zhang
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, Shandong, China
- *Correspondence: Song Zhang,
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21
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Hamar R, Varga M. The role of post-transcriptional modifications during development. Biol Futur 2022. [PMID: 36481986 DOI: 10.1007/s42977-022-00142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
AbstractWhile the existence of post-transcriptional modifications of RNA nucleotides has been known for decades, in most RNA species the exact positions of these modifications and their physiological function have been elusive until recently. Technological advances, such as high-throughput next-generation sequencing (NGS) methods and nanopore-based mapping technologies, have made it possible to map the position of these modifications with single nucleotide accuracy, and genetic screens have uncovered the “writer”, “reader” and “eraser” proteins that help to install, interpret and remove such modifications, respectively. These discoveries led to intensive research programmes with the aim of uncovering the roles of these modifications during diverse biological processes. In this review, we assess novel discoveries related to the role of post-transcriptional modifications during animal development, highlighting how these discoveries can affect multiple aspects of development from fertilization to differentiation in many species.
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22
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Tian Y, Zhang Y, Dong PY, Sun YH, Zhao AH, Shen W, Zhang XF. Single-cell transcriptomic profiling to evaluate the effects of Di(2-ethylhexyl)phthalate exposure on early meiosis of female mouse germ cells. Chemosphere 2022; 307:135698. [PMID: 35842051 DOI: 10.1016/j.chemosphere.2022.135698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Di(2-ethylhexyl)phthalate (DEHP) has proven characteristics of an endocrine-disrupting compound (EDC), which can threaten the reproductive health of humans and other animals. In mammals, a series of chromosomal events occur during the meiotic stage of oocytes. External toxins may enter the body and cause infertility and other related diseases. Therefore, it is crucial to explore the influence of DEHP exposure on the molecular mechanism of germ cell meiosis. We used single-cell RNA sequencing (scRNA-seq) to analyse the ovaries of foetal mice at embryonic day 12.5 (E12.5) and E14.5 after maternal DEHP exposure. DEHP exposure further activated the pathways related to DNA repair in germ cells, increased the expression of genes related to DNA damage and changed the developmental trajectory of germ cells. DEHP exposure may affect the proliferation of pregranulosa (PG) cells. Moreover, DEHP exposure altered the signal transduction between PG cells and germ cells. We showed that DEHP affects meiosis by causing DNA damage in oocytes and disrupting the signal transduction between PG cells and germ cells. These results provide a strong theoretical basis for the prevention and treatment of DEHP-mediated female reproductive health problems.
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Affiliation(s)
- Yu Tian
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China; College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ye Zhang
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China; Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, China; National Research Center for Assisted Reproductive Technology and Reproductive Genetic, Shandong University, Jinan, Shandong, 250012, China
| | - Pei-Yu Dong
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yong-Hong Sun
- Qingdao Academy of Agricultural Sciences, Qingdao, 266100, China
| | - Ai-Hong Zhao
- Qingdao Academy of Agricultural Sciences, Qingdao, 266100, China
| | - Wei Shen
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xi-Feng Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
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23
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Zhang Y, Zhang LS, Dai Q, Chen P, Lu M, Kairis EL, Murugaiah V, Xu J, Shukla RK, Liang X, Zou Z, Cormet-Boyaka E, Qiu J, Peeples ME, Sharma A, He C, Li J. 5-methylcytosine (m 5C) RNA modification controls the innate immune response to virus infection by regulating type I interferons. Proc Natl Acad Sci U S A 2022; 119:e2123338119. [PMID: 36240321 PMCID: PMC9586267 DOI: 10.1073/pnas.2123338119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
5-methylcytosine (m5C) is one of the most prevalent modifications of RNA, playing important roles in RNA metabolism, nuclear export, and translation. However, the potential role of RNA m5C methylation in innate immunity remains elusive. Here, we show that depletion of NSUN2, an m5C methyltransferase, significantly inhibits the replication and gene expression of a wide range of RNA and DNA viruses. Notably, we found that this antiviral effect is largely driven by an enhanced type I interferon (IFN) response. The antiviral signaling pathway is dependent on the cytosolic RNA sensor RIG-I but not MDA5. Transcriptome-wide mapping of m5C following NSUN2 depletion in human A549 cells revealed a marked reduction in the m5C methylation of several abundant noncoding RNAs (ncRNAs). However, m5C methylation of viral RNA was not noticeably altered by NSUN2 depletion. In NSUN2-depleted cells, the host RNA polymerase (Pol) III transcribed ncRNAs, in particular RPPH1 and 7SL RNAs, were substantially up-regulated, leading to an increase of unshielded 7SL RNA in cytoplasm, which served as a direct ligand for the RIG-I-mediated IFN response. In NSUN2-depleted cells, inhibition of Pol III transcription or silencing of RPPH1 and 7SL RNA dampened IFN signaling, partially rescuing viral replication and gene expression. Finally, depletion of NSUN2 in an ex vivo human lung model and a mouse model inhibits viral replication and reduces pathogenesis, which is accompanied by enhanced type I IFN responses. Collectively, our data demonstrate that RNA m5C methylation controls antiviral innate immunity through modulating the m5C methylome of ncRNAs and their expression.
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Affiliation(s)
- Yuexiu Zhang
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Li-Sheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
| | - Phylip Chen
- Center for Vaccines and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43205
| | - Mijia Lu
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Elizabeth L. Kairis
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Valarmathy Murugaiah
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Jiayu Xu
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Rajni Kant Shukla
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Xueya Liang
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Zhongyu Zou
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
| | - Estelle Cormet-Boyaka
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Mark E. Peeples
- Center for Vaccines and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43205
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43205
| | - Amit Sharma
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637
| | - Jianrong Li
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
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Chaudhary A, Chaurasia PK, Kushwaha S, Chauhan P, Chawade A, Mani A. Correlating multi-functional role of cold shock domain proteins with intrinsically disordered regions. Int J Biol Macromol 2022; 220:743-753. [PMID: 35987358 DOI: 10.1016/j.ijbiomac.2022.08.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/26/2022] [Accepted: 08/14/2022] [Indexed: 11/05/2022]
Abstract
Cold shock proteins (CSPs) are an ancient and conserved family of proteins. They are renowned for their role in response to low-temperature stress in bacteria and nucleic acid binding activities. In prokaryotes, cold and non-cold inducible CSPs are involved in various cellular and metabolic processes such as growth and development, osmotic oxidation, starvation, stress tolerance, and host cell invasion. In prokaryotes, cold shock condition reduces cell transcription and translation efficiency. Eukaryotic cold shock domain (CSD) proteins are evolved form of prokaryotic CSPs where CSD is flanked by N- and C-terminal domains. Eukaryotic CSPs are multi-functional proteins. CSPs also act as nucleic acid chaperons by preventing the formation of secondary structures in mRNA at low temperatures. In human, CSD proteins play a crucial role in the progression of breast cancer, colon cancer, lung cancer, and Alzheimer's disease. A well-defined three-dimensional structure of intrinsically disordered regions of CSPs family members is still undetermined. In this article, intrinsic disorder regions of CSPs have been explored systematically to understand the pleiotropic role of the cold shock family of proteins.
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Affiliation(s)
- Amit Chaudhary
- Department of Metallurgical Engineering & Materials Science, Indian Institute of Technology Bombay
| | - Pankaj Kumar Chaurasia
- PG Department of Chemistry, L.S. College, Babasaheb Bhimrao Ambedkar Bihar University, Muzaffarpur, Bihar 842001, India
| | - Sandeep Kushwaha
- National Institute of Animal Biotechnology, Hyderabad 500032, India.
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53 Alnarp, Sweden.
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, India.
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25
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Dome A, Dymova M, Richter V, Stepanov G. Post-Transcriptional Modifications of RNA as Regulators of Apoptosis in Glioblastoma. Int J Mol Sci 2022; 23:9272. [PMID: 36012529 PMCID: PMC9408889 DOI: 10.3390/ijms23169272] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
This review is devoted to changes in the post-transcriptional maturation of RNA in human glioblastoma cells, which leads to disruption of the normal course of apoptosis in them. The review thoroughly highlights the latest information on both post-transcriptional modifications of certain regulatory RNAs, associated with the process of apoptosis, presents data on the features of apoptosis in glioblastoma cells, and shows the relationship between regulatory RNAs and the apoptosis in tumor cells. In conclusion, potential target candidates are presented that are necessary for the development of new drugs for the treatment of glioblastoma.
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26
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Liu Y, Yang Y, Wu R, Gao CC, Liao X, Han X, Zeng B, Huang C, Luo Y, Liu Y, Chen Y, Chen W, Liu J, Jiang Q, Zhao Y, Bi Z, Guo G, Yao Y, Xiang Y, Zhang X, Valencak TG, Wang Y, Wang X. mRNA m 5C inhibits adipogenesis and promotes myogenesis by respectively facilitating YBX2 and SMO mRNA export in ALYREF-m 5C manner. Cell Mol Life Sci 2022; 79:481. [PMID: 35962235 PMCID: PMC11072269 DOI: 10.1007/s00018-022-04474-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022]
Abstract
Although 5-methylcytosine (m5C) has been identified as a novel and abundant mRNA modification and associated with energy metabolism, its regulation function in adipose tissue and skeletal muscle is still limited. This study aimed at investigating the effect of mRNA m5C on adipogenesis and myogenesis using Jinhua pigs (J), Yorkshire pigs (Y) and their hybrids Yorkshire-Jinhua pigs (YJ). We found that Y grow faster than J and YJ, while fatness-related characteristics observed in Y were lower than those of J and YJ. Besides, total mRNA m5C levels and expression rates of NSUN2 were higher both in backfat layer (BL) and longissimus dorsi muscle (LDM) of Y compared to J and YJ, suggesting that higher mRNA m5C levels positively correlate with lower fat and higher muscle mass. RNA bisulfite sequencing profiling of m5C revealed tissue-specific and dynamic features in pigs. Functionally, hyper-methylated m5C-containing genes were enriched in pathways linked to impaired adipogenesis and enhanced myogenesis. In in vitro, m5C inhibited lipid accumulation and promoted myogenic differentiation. Furthermore, YBX2 and SMO were identified as m5C targets. Mechanistically, YBX2 and SMO mRNAs with m5C modification were recognized and exported into the cytoplasm from the nucleus by ALYREF, thus leading to increased YBX2 and SMO protein expression and thereby inhibiting adipogenesis and promoting myogenesis, respectively. Our work uncovered the critical role of mRNA m5C in regulating adipogenesis and myogenesis via ALYREF-m5C-YBX2 and ALYREF-m5C-SMO manners, providing a potential therapeutic target in the prevention and treatment of obesity, skeletal muscle dysfunction and metabolic disorder diseases.
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Affiliation(s)
- Youhua Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Hangzhou, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Ruifan Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Chun-Chun Gao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Hangzhou, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xing Liao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xiao Han
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Hangzhou, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Botao Zeng
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Chaoqun Huang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yaojun Luo
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yuxi Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yushi Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Wei Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jiaqi Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Qin Jiang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yuanling Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Zhen Bi
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Guanqun Guo
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yongxi Yao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yun Xiang
- Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Xiaojun Zhang
- Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Teresa G Valencak
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xinxia Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
- Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Hangzhou, China.
- Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China.
- Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Hangzhou, Zhejiang, China.
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27
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Wang S, Li H, Lian Z, Deng S. The Role of RNA Modification in HIV-1 Infection. Int J Mol Sci 2022; 23:7571. [PMID: 35886919 PMCID: PMC9317671 DOI: 10.3390/ijms23147571] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 01/25/2023] Open
Abstract
RNA plays an important role in biology, and more than 170 RNA modifications have been identified so far. Post-transcriptional modification of RNA in cells plays a crucial role in the regulation of its stability, transport, processing, and gene expression. So far, the research on RNA modification and the exact role of its enzymes is becoming more and more comprehensive. Human immunodeficiency virus 1 (HIV-1) is an RNA virus and the causative agent of acquired immunodeficiency syndrome (AIDS), which is one of the most devastating viral pandemics in history. More and more studies have shown that HIV has RNA modifications and regulation of its gene expression during infection and replication. This review focuses on several RNA modifications and their regulatory roles as well as the roles that different RNA modifications play during HIV-1 infection, in order to find new approaches for the development of anti-HIV-1 therapeutics.
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28
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Xu X, Johnson Z, Xie H. Neuronal Depolarization Induced RNA m5C Methylation Changes in Mouse Cortical Neurons. Biology 2022; 11:biology11070988. [PMID: 36101370 PMCID: PMC9311806 DOI: 10.3390/biology11070988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022]
Abstract
Neuronal activity is accomplished via substantial changes in gene expression, which may be accompanied by post-transcriptional modifications including RNA cytosine-5 methylation (m5C). Despite several reports on the transcriptome profiling of activated neurons, the dynamics of neuronal mRNA m5C modification in response to environmental stimuli has not been explored. Here, we provide transcriptome-wide maps of m5C modification, together with gene expression profiles, for mouse cortical neurons at 0 h, 2 h, and 6 h upon membrane depolarization. Thousands of differentially expressed genes (DEGs) were identified during the neuronal depolarization process. In stimulated neurons, the majority of early response genes were found to serve as expression regulators of late response genes, which are involved in signaling pathways and diverse synaptic functions. With RNA bisulfite sequencing data, a union set of 439 m5C sites was identified with high confidence, and approximately 30% of them were shared by neurons at all three time points. Interestingly, over 41% of the m5C sites showed increased methylation upon neuronal activation and were enriched in transcripts coding for proteins with synaptic functions. In addition, a modest negative correlation was observed between RNA expression and methylation. In summary, our study provided dynamic transcriptome-wide landscapes of RNA m5C methylation in neurons, and revealed that mRNA m5C methylation is associated with the regulation of gene expression.
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Affiliation(s)
- Xiguang Xu
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA; (X.X.); (Z.J.)
- Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Zachary Johnson
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA; (X.X.); (Z.J.)
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA
| | - Hehuang Xie
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA; (X.X.); (Z.J.)
- Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA 24061, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
- Translational Biology, Medicine and Health Program, Virginia Tech, Blacksburg, VA 24061, USA
- Correspondence:
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Johnson Z, Xu X, Pacholec C, Xie H. Systematic evaluation of parameters in RNA bisulfite sequencing data generation and analysis. NAR Genom Bioinform 2022; 4:lqac045. [PMID: 35669236 PMCID: PMC9164272 DOI: 10.1093/nargab/lqac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/05/2022] [Accepted: 05/23/2022] [Indexed: 12/26/2022] Open
Abstract
The presence of 5-methylcytosine (m5C) in RNA molecules has been known for decades and its importance in regulating RNA metabolism has gradually become appreciated. Despite recent advances made in the functional and mechanistic understanding of RNA m5C modifications, the detection and quantification of methylated RNA remains a challenge. In this study, we compared four library construction procedures for RNA bisulfite sequencing and implemented an analytical pipeline to assess the key parameters in the process of m5C calling. We found that RNA fragmentation after bisulfite conversion increased the yield significantly, and an additional high temperature treatment improved bisulfite conversion efficiency especially for sequence reads mapped to the mitochondrial transcriptome. Using Unique Molecular Identifiers (UMIs), we observed that PCR favors the amplification of unmethylated templates. The low sequencing quality of bisulfite-converted bases is a major contributor to the methylation artifacts. In addition, we found that mitochondrial transcripts are frequently resistant to bisulfite conversion and no p-m5C sites with high confidence could be identified on mitochondrial mRNAs. Taken together, this study reveals the various sources of artifacts in RNA bisulfite sequencing data and provides an improved experimental procedure together with analytical methodology.
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Affiliation(s)
- Zachary Johnson
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA
| | - Xiguang Xu
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine; Virginia Tech, Blacksburg, VA 24061, USA
| | - Christina Pacholec
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine; Virginia Tech, Blacksburg, VA 24061, USA
| | - Hehuang Xie
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine; Virginia Tech, Blacksburg, VA 24061, USA
- Translational Biology, Medicine and Health Program, Virginia Tech, Blacksburg, VA 24061, USA
- School of Neuroscience, Virginia Tech, Blacksburg, VA 24061, USA
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30
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Jiang D, Qiu T, Peng J, Li S, Tala, Ren W, Yang C, Wen Y, Chen CH, Sun J, Wu Y, Liu R, Zhou J, Wu K, Liu W, Mao X, Zhou Z, Chen C. YB-1 is a positive regulator of KLF5 transcription factor in basal-like breast cancer. Cell Death Differ 2022; 29:1283-1295. [PMID: 35022570 PMCID: PMC9177637 DOI: 10.1038/s41418-021-00920-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/25/2022] Open
Abstract
Y-box binding protein 1 (YB-1) is a well-known oncogene highly expressed in various cancers, including basal-like breast cancer (BLBC). Beyond its role as a transcription factor, YB-1 is newly defined as an epigenetic regulator involving RNA 5-methylcytosine. However, its specific targets and pro-cancer functions are poorly defined. Here, based on clinical database, we demonstrate a positive correlation between Kruppel-like factor 5 (KLF5) and YB-1 expression in breast cancer patients, but a negative correlation with that of Dachshund homolog 1 (DACH1). Mechanistically, YB-1 enhances KLF5 expression not only through transcriptional activation that can be inhibited by DACH1, but also by stabilizing KLF5 mRNA in a RNA 5-methylcytosine modification-dependent manner. Additionally, ribosomal S6 kinase 2 (RSK2) mediated YB-1 phosphorylation at Ser102 promotes YB-1/KLF5 transcriptional complex formation, which co-regulates the expression of BLBC specific genes, Keratin 16 (KRT16) and lymphocyte antigen 6 family member D (Ly6D), to promote cancer cell proliferation. The RSK inhibitor, LJH685, suppressed BLBC cell tumourigenesis in vivo by disturbing YB-1-KLF5 axis. Our data suggest that YB-1 positively regulates KLF5 at multiple levels to promote BLBC progression. The novel RSK2-YB-1-KLF5-KRT16/Ly6D axis provides candidate diagnostic markers and therapeutic targets for BLBC.
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Affiliation(s)
- Dewei Jiang
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China ,grid.410726.60000 0004 1797 8419Kunming College of Lifesciences, University of Chinese Academy Sciences, Kunming, China
| | - Ting Qiu
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China ,grid.410726.60000 0004 1797 8419Kunming College of Lifesciences, University of Chinese Academy Sciences, Kunming, China
| | - Junjiang Peng
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Siyuan Li
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Tala
- grid.216938.70000 0000 9878 7032State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenlong Ren
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China ,grid.59053.3a0000000121679639College of Life Sciences, China University of Science and Technology, Hefei, Anhui China
| | - Chuanyu Yang
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yi Wen
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chuan-Huizi Chen
- grid.440773.30000 0000 9342 2456School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Jian Sun
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China ,grid.410726.60000 0004 1797 8419Kunming College of Lifesciences, University of Chinese Academy Sciences, Kunming, China
| | - Yingying Wu
- grid.285847.40000 0000 9588 0960The First Affiliated Hospital, Kunming Medical University, Kunming, China
| | - Rong Liu
- grid.11135.370000 0001 2256 9319The First Affiliated Hospital, Peking University, Beijing, China
| | - Jun Zhou
- grid.216938.70000 0000 9878 7032State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Kongming Wu
- grid.412793.a0000 0004 1799 5032Department of Oncology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Wen Liu
- grid.12955.3a0000 0001 2264 7233School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China
| | - Xiaoyun Mao
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China.
| | - Zhongmei Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Lifesciences, University of Chinese Academy Sciences, Kunming, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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31
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Yin Q, Zheng M, Luo Q, Jiang D, Zhang H, Chen C. YB-1 as an Oncoprotein: Functions, Regulation, Post-Translational Modifications, and Targeted Therapy. Cells 2022; 11:1217. [PMID: 35406781 DOI: 10.3390/cells11071217] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/26/2022] [Accepted: 04/02/2022] [Indexed: 02/04/2023] Open
Abstract
Y box binding protein 1 (YB-1) is a protein with a highly conserved cold shock domain (CSD) that also belongs to the family of DNA- and RNA-binding proteins. YB-1 is present in both the nucleus and cytoplasm and plays versatile roles in gene transcription, RNA splicing, DNA damage repair, cell cycle progression, and immunity. Cumulative evidence suggests that YB-1 promotes the progression of multiple tumor types and serves as a potential tumor biomarker and therapeutic target. This review comprehensively summarizes the emerging functions, mechanisms, and regulation of YB-1 in cancers, and further discusses targeted strategies.
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32
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Song H, Zhang J, Liu B, Xu J, Cai B, Yang H, Straube J, Yu X, Ma T. Biological roles of RNA m 5C modification and its implications in Cancer immunotherapy. Biomark Res 2022; 10:15. [PMID: 35365216 DOI: 10.1186/s40364-022-00362-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 01/08/2023] Open
Abstract
Epigenetics including DNA and RNA modifications have always been the hotspot field of life sciences in the post-genome era. Since the first mapping of N6-methyladenosine (m6A) and the discovery of its widespread presence in mRNA, there are at least 160-170 RNA modifications have been discovered. These methylations occur in different RNA types, and their distribution is species-specific. 5-methylcytosine (m5C) has been found in mRNA, rRNA and tRNA of representative organisms from all kinds of species. As reversible epigenetic modifications, m5C modifications of RNA affect the fate of the modified RNA molecules and play important roles in various biological processes including RNA stability control, protein synthesis, and transcriptional regulation. Furthermore, accumulative evidence also implicates the role of RNA m5C in tumorigenesis. Here, we review the latest progresses in the biological roles of m5C modifications and how it is regulated by corresponding “writers”, “readers” and “erasers” proteins, as well as the potential molecular mechanism in tumorigenesis and cancer immunotherapy.
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33
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Xu J, Gao Z, Liu K, Fan Y, Zhang Z, Xue H, Guo X, Zhang P, Deng L, Wang S, Wang H, Wang Q, Zhao R, Li G. The Non-N 6-Methyladenosine Epitranscriptome Patterns and Characteristics of Tumor Microenvironment Infiltration and Mesenchymal Transition in Glioblastoma. Front Immunol 2022; 12:809808. [PMID: 35154083 PMCID: PMC8825368 DOI: 10.3389/fimmu.2021.809808] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/29/2021] [Indexed: 12/13/2022] Open
Abstract
Background An increasing number of RNA modification types other than N6-methyladenosine (m6A) modification have been detected. Nonetheless, the probable functions of RNA modifications beyond m6A in the tumor microenvironment (TME), mesenchymal (MES) transition, immunotherapy, and drug sensitivity remain unclear. Methods We analyzed the characteristics of 32 non-m6A RNA modification regulators in 539 glioblastoma (GBM) patients and the TME cell infiltration and MES transition patterns. Using principal component analysis, a non-m6A epitranscriptome regulator score (RM score) model was established. We estimated the association between RM score and clinical characteristics, TME status, GBM subtypes, and drug and immunotherapy response. Results Three definite non-m6A RNA modification patterns associated with diverse biological pathways and clinical characteristics were identified. The high RM score group was characterized by a poor prognosis, enhanced immune infiltration, and MES subtype. Further analysis indicated that the high RM score group had a lower tumor mutation burden as well as a weaker response to immunotherapy. The higher RM score group may benefit more from drugs targeting the EGFR and WNT signaling pathways. Conclusion Our study exposed the potential relationship of non-m6A RNA modification regulators with clinical features, TME status, and GBM subtype and clarified its therapeutic value.
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Affiliation(s)
- Jianye Xu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Zijie Gao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Kaining Liu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Yang Fan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Zongpu Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Hao Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Xing Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Ping Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Lin Deng
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Shaobo Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Huizhi Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Qingtong Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Rongrong Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
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34
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Zhao Y, Yang M, Wang S, Abbas SJ, Zhang J, Li Y, Shao R, Liu Y. An Overview of Epigenetic Methylation in Pancreatic Cancer Progression. Front Oncol 2022; 12:854773. [PMID: 35296007 PMCID: PMC8918690 DOI: 10.3389/fonc.2022.854773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Over the past decades, the aberrant epigenetic modification, apart from genetic alteration, has emerged as dispensable events mediating the transformation of pancreatic cancer (PC). However, the understanding of molecular mechanisms of methylation modifications, the most abundant epigenetic modifications, remains superficial. In this review, we focused on the mechanistic insights of DNA, histone, and RNA methylation that regulate the progression of PC. The methylation regulators including writer, eraser and reader participate in the modification of gene expression associated with cell proliferation, invasion and apoptosis. Some of recent clinical trials on methylation drug targeting were also discussed. Understanding the novel regulatory mechanisms in the methylation modification may offer alternative opportunities to improve therapeutic efficacy to fight against this dismal disease.
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Affiliation(s)
- Yuhao Zhao
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
| | - Mao Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
| | - Shijia Wang
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
| | - Sk Jahir Abbas
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, China
| | - Junzhe Zhang
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
| | - Yongsheng Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
| | - Rong Shao
- Department of Pharmacology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Yingbin Liu, ; Rong Shao,
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
- *Correspondence: Yingbin Liu, ; Rong Shao,
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35
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Jiang ZY, Fan HY. Five questions toward mRNA degradation in oocytes and preimplantation embryos: When, who, to whom, how, and why? Biol Reprod 2022; 107:62-75. [DOI: 10.1093/biolre/ioac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
RNA, the primary product of the genome, is subject to various biological events during its lifetime. During mammalian gametogenesis and early embryogenesis, germ cells and preimplantation embryos undergo marked changes in the transcriptome, including mRNA turnover. Various factors, including specialized proteins, RNAs, and organelles, function in an intricate degradation system, and the degradation selectivity is determined by effectors and their target mRNAs. RNA homeostasis regulators and surveillance factors function in the global transcriptome of oocytes and somatic cells. Other factors, including BTG4, PABPN1L, the CCR4-NOT subunits, CNOT6L and CNOT7, and TUTs, are responsible for two maternal mRNA avalanches: M- and Z-decay. In this review, we discuss recent advances in mRNA degradation mechanisms in mammalian oocytes and preimplantation embryos. We focused on the studies in mice, as a model mammalian species, and on RNA turnover effectors and the cis-elements in targeting RNAs.
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Affiliation(s)
- Zhi-Yan Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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Mai H, Xie H, Luo M, Hou J, Chen J, Hou J, Jiang D. Implications of Stemness Features in 1059 Hepatocellular Carcinoma Patients from Five Cohorts: Prognosis, Treatment Response, and Identification of Potential Compounds. Cancers (Basel) 2022; 14:563. [PMID: 35158838 PMCID: PMC8833508 DOI: 10.3390/cancers14030563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Cancer stemness has been reported to drive hepatocellular carcinoma (HCC) tumorigenesis and treatment resistance. However, comprehensive interpretations of transcriptomic stemness features in HCC patients have not been conducted in multiple cohorts. Our aim was to interpret clinical and therapeutic implications of transcriptional stemness features and explore potential compounds for HCC treatment. We found that transcriptional stemness indexes (mRNAsi) were independently associated with worse HCC prognosis. The HCC stemness risk model (HSRM) developed in this study significantly predicted prognosis and treatment response in various HCC cohorts. Analysis of two stemness subtypes suggested several liver-specific metabolic pathways, and mutations of TP53 and RB1 were associated with HCC transcriptional stemness. Moreover, we also identified potential compounds that target HCC transcriptional stemness. Our findings comprehensively characterized transcriptional stemness as a risk factor in HCC progression and treatment. Abstract Cancer stemness has been reported to drive hepatocellular carcinoma (HCC) tumorigenesis and treatment resistance. In this study, five HCC cohorts with 1059 patients were collected to calculate transcriptional stemness indexes (mRNAsi) by the one-class logistic regression machine learning algorithm. In the TCGA-LIHC cohort, we found mRNAsi was an independent prognostic factor, and 626 mRNAsi-related genes were identified by Spearman correlation analysis. The HCC stemness risk model (HSRM) was trained in the TCGA-LIHC cohort and significantly discriminated overall survival in four independent cohorts. HSRM was also significantly associated with transarterial chemoembolization treatment response and rapid tumor growth in HCC patients. Consensus clustering was conducted based on mRNAsi-related genes to divide 1059 patients into two stemness subtypes. On gene set variation analysis, samples of subtype I were found enriched with pathways such as DNA replication and cell cycle, while several liver-specific metabolic pathways were inhibited in these samples. Somatic mutation analysis revealed more frequent mutations of TP53 and RB1 in the subtype I samples. In silico analysis suggested topoisomerase, cyclin-dependent kinase, and histone deacetylase as potential targets to inhibit HCC stemness. In vitro assay showed two predicted compounds, Aminopurvalanol-a and NCH-51, effectively suppressed oncosphere formation and impaired viability of HCC cell lines, which may shed new light on HCC treatment.
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Sun Y, Li Z, Wang W, Zhang X, Li W, Du G, Yin J, Xiao W, Yang H. Identification and verification of YBX3 and its regulatory gene HEIH as an oncogenic system: A multidimensional analysis in colon cancer. Front Immunol 2022; 13:957865. [PMID: 36059530 PMCID: PMC9433931 DOI: 10.3389/fimmu.2022.957865] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/21/2022] [Indexed: 02/05/2023] Open
Abstract
The novel gene YBX3 is important for regulating translation and RNA catabolism and encodes a protein with a highly conserved cold-shock domain. However, its pathogenic roles across cancers (e.g., colon cancer) and its regulation remain unclear. We identified the pathogenic roles of YBX3 and its regulatory lncRNA HEIH in various cancers and investigated their effects on tumor progression in colon cancer. Methods including RNA pull-down, MS, and TMA of 93 patients, qPCR of 12 patients with diverse clinicopathologic stages, and western blotting were performed. The pancancer analysis showed that YBX3 expression varies significantly among not only cancer types but also molecular and immune subtypes of the same cancer. Furthermore, its expression in colon cancer is clinically significant, and there is an obvious negative regulatory association between HEIH and YBX3. Among various cancers, especially colon cancer, YBX3 is more related than HEIH expression to the clinical features and prognosis of subgroups. The receiver operating characteristic analysis showed that HEIH and YBX3 have similar predictive capacity in various cancers. The analysis of differentially expressed genes in colon cancer revealed that they have similar hub gene networks, indicating an oncogenic system with a strong overlap. The results also suggest that YBX3 is associated with tumor immune evasion via different mechanisms involving T-cell exclusion in different cancer types and by the tumor infiltration of immune cells. Interestingly, scRNA-seq revealed that HEIH inhibits this phenomenon. Our results also suggest that YBX3 expression is associated with immune or chemotherapeutic outcomes in various cancers, and YBX3 exhibited a higher predictive power than two of seven standardized biomarkers for response outcomes and overall survival of immune checkpoint blockade subcohorts. In colon cancer cell lines, lncRNA-HEIH and YBX3 associate. MS confirmed that YBX3 was pulled down with HEIH, and western blot showed that HEIH knockdown disinhibited YBX3. This study strongly suggests that lncRNA-HEIH/YBX3 is a pancancer immune-oncogenic system and could serve as a biomarker for diagnosis and prognosis and as a therapeutic target, especially in colon cancer.
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Affiliation(s)
- Yiming Sun
- Department of General Surgery, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Zhixi Li
- Department of General Surgery, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Wensheng Wang
- Department of General Surgery, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | | | - Wenjing Li
- Department of Stem Cell and Regenerative Medicine, The Southwest Hospital of Army Medical University, Chongqing, China
| | - Guangsheng Du
- Department of General Surgery, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Jiuheng Yin
- Department of General Surgery, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Weidong Xiao
- Department of General Surgery, The Second Affiliated Hospital of Army Medical University, Chongqing, China
- *Correspondence: Hua Yang, ; Weidong Xiao,
| | - Hua Yang
- Department of General Surgery, The Second Affiliated Hospital of Army Medical University, Chongqing, China
- Department of General Surgery, Chongqing General Hospital, Chongqing, China
- *Correspondence: Hua Yang, ; Weidong Xiao,
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38
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Motorin Y, Helm M. RNA nucleotide methylation: 2021 update. Wiley Interdiscip Rev RNA 2022; 13:e1691. [PMID: 34913259 DOI: 10.1002/wrna.1691] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022]
Abstract
Among RNA modifications, transfer of methylgroups from the typical cofactor S-adenosyl-l-methionine by methyltransferases (MTases) to RNA is by far the most common reaction. Since our last review about a decade ago, the field has witnessed the re-emergence of mRNA methylation as an important mechanism in gene regulation. Attention has then spread to many other RNA species; all being included into the newly coined concept of the "epitranscriptome." The focus moved from prokaryotes and single cell eukaryotes as model organisms to higher eukaryotes, in particular to mammals. The perception of the field has dramatically changed over the past decade. A previous lack of phenotypes in knockouts in single cell organisms has been replaced by the apparition of MTases in numerous disease models and clinical investigations. Major driving forces of the field include methylation mapping techniques, as well as the characterization of the various MTases, termed "writers." The latter term has spilled over from DNA modification in the neighboring epigenetics field, along with the designations "readers," applied to mediators of biological effects upon specific binding to a methylated RNA. Furthermore "eraser" enzymes effect the newly discovered oxidative removal of methylgroups. A sense of reversibility and dynamics has replaced the older perception of RNA modification as a concrete-cast, irreversible part of RNA maturation. A related concept concerns incompletely methylated residues, which, through permutation of each site, lead to inhomogeneous populations of numerous modivariants. This review recapitulates the major developments of the past decade outlined above, and attempts a prediction of upcoming trends. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Mainz, Germany
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39
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Kretov DA. Role of Y-Box Binding Proteins in Ontogenesis. Biochemistry (Mosc) 2022; 87:S71-S74. [PMID: 35501987 DOI: 10.1134/s0006297922140061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding proteins (YB proteins) are multifunctional DNA/RNA-binding proteins capable of regulating gene expression at multiple levels. At present, the most studied function of these proteins is the regulation of protein synthesis. Special attention in this review has been paid to the role of YB proteins in the control of mRNA translation and stability at the earliest stages of organism formation, from fertilization to gastrulation. Furthermore, the functions of YB proteins in the formation of germ cells, in which they accumulate in large amounts, are summarized. The review then discusses the contribution of YB proteins to the regulation of gene expression during the differentiation of various types of somatic cells. Finally, future directions in the study of YB proteins and their role in ontogenesis are considered.
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Affiliation(s)
- Dmitry A Kretov
- Department of Biochemistry, School of Medicine, Boston University, Boston, USA, 02218.
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40
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Guo G, Pan K, Fang S, Ye L, Tong X, Wang Z, Xue X, Zhang H. Advances in mRNA 5-methylcytosine modifications: Detection, effectors, biological functions, and clinical relevance. Mol Ther Nucleic Acids 2021; 26:575-593. [PMID: 34631286 PMCID: PMC8479277 DOI: 10.1016/j.omtn.2021.08.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
5-methylcytosine (m5C) post-transcriptional modifications affect the maturation, stability, and translation of the mRNA molecule. These modifications play an important role in many physiological and pathological processes, including stress response, tumorigenesis, tumor cell migration, embryogenesis, and viral replication. Recently, there has been a better understanding of the biological implications of m5C modification owing to the rapid development and optimization of detection technologies, including liquid chromatography-tandem mass spectrometry (LC-MS/MS) and RNA-BisSeq. Further, predictive models (such as PEA-m5C, m5C-PseDNC, and DeepMRMP) for the identification of potential m5C modification sites have also emerged. In this review, we summarize the current experimental detection methods and predictive models for mRNA m5C modifications, focusing on their advantages and limitations. We systematically surveyed the latest research on the effectors related to mRNA m5C modifications and their biological functions in multiple species. Finally, we discuss the physiological effects and pathological significance of m5C modifications in multiple diseases, as well as their therapeutic potential, thereby providing new perspectives for disease treatment and prognosis.
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Affiliation(s)
- Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Su Fang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhibin Wang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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Bataglia L, Simões ZLP, Nunes FMF. Active genic machinery for epigenetic RNA modifications in bees. Insect Mol Biol 2021; 30:566-579. [PMID: 34291855 DOI: 10.1111/imb.12726] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Epitranscriptomics is an emerging field of investigation dedicated to the study of post-transcriptional RNA modifications. RNA methylations regulate RNA metabolism and processing, including changes in response to environmental cues. Although RNA modifications are conserved from bacteria to eukaryotes, there is little evidence of an epitranscriptomic pathway in insects. Here we identified genes related to RNA m6 A (N6-methyladenine) and m5 C (5-methylcytosine) methylation machinery in seven bee genomes (Apis mellifera, Melipona quadrifasciata, Frieseomelitta varia, Eufriesea mexicana, Bombus terrestris, Megachile rotundata and Dufourea novaeangliae). In A. mellifera, we validated the expression of methyltransferase genes and found that the global levels of m6 A and m5 C measured in the fat body and brain of adult workers differ significantly. Also, m6 A levels were differed significantly mainly between the fourth larval instar of queens and workers. Moreover, we found a conserved m5 C site in the honeybee 28S rRNA. Taken together, we confirm the existence of epitranscriptomic machinery acting in bees and open avenues for future investigations on RNA epigenetics in a wide spectrum of hymenopteran species.
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Affiliation(s)
- L Bataglia
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Z L P Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - F M F Nunes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
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Abner JJ, Franklin JL, Clement MA, Hinger SA, Allen RM, Liu X, Kellner S, Wu J, Karijolich J, Liu Q, Vickers KC, Dedon P, Weaver AM, Coffey RJ, Patton JG. Depletion of METTL3 alters cellular and extracellular levels of miRNAs containing m 6A consensus sequences. Heliyon 2021; 7:e08519. [PMID: 34934837 PMCID: PMC8654799 DOI: 10.1016/j.heliyon.2021.e08519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/29/2021] [Indexed: 12/21/2022] Open
Abstract
Extracellular vesicles (EVs) are capable of transferring cargo from donor to recipient cells, but precisely how cargo content is regulated for export is mostly unknown. For miRNA cargo, we previously showed that when compared to isogenic colorectal cancer (CRC) cells expressing wild-type KRAS, a distinct subset of miRNAs are differentially enriched in EVs from KRAS mutant active CRC cells, with miR-100 being one of the most enriched. The mechanisms that could explain how miR-100 and other miRNAs are differentially exported into EVs have not been fully elucidated. Here, we tested the effect of N6-methyladenosine (m6A) modification on miRNA export into EVs by depletion of METTL3 and ALKBH5, a writer and eraser of m6A modification, respectively. While the effects of ALKBH5 knockdown were quite modest, decreased levels of METTL3 led to reduced cellular and extracellular levels of a subset of miRNAs that contain consensus sequences for m6A modification. Functional testing of EVs prepared from cells expressing shRNAs against METTL3 showed that they were less capable of conferring colony growth in 3D to wild-type KRAS cells and were also largely incapable of conferring the spread of cetuximab resistance. Our data support a role for METTL3 modification on cellular miRNA levels and export of specific miRNAs.
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Affiliation(s)
- Jessica J. Abner
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Jeffrey L. Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Margaret A. Clement
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Scott A. Hinger
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Ryan M. Allen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Xiao Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Junzhou Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Kasey C. Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Peter Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Alissa M. Weaver
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Robert J. Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - James G. Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
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Abstract
Small non-coding RNAs are short RNA molecules and involved in many biological processes, including cell proliferation and differentiation, immune response, cell death, epigenetic regulation, metabolic control. A diversity of RNA modifications have been identified in these small non-coding RNAs, including transfer RNAs (tRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nuclear RNA (snRNA), small nucleolar RNAs (snoRNAs), and tRNA-derived small RNAs (tsRNAs). These post-transcriptional modifications are involved in the biogenesis and function of these small non-coding RNAs. In this review, we will summarize the existence of RNA modifications in the small non-coding RNAs and the emerging roles of these epitranscriptomic marks.
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Affiliation(s)
- Xiaoyu Li
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.,Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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44
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Zhou W, Wang X, Chang J, Cheng C, Miao C. The molecular structure and biological functions of RNA methylation, with special emphasis on the roles of RNA methylation in autoimmune diseases. Crit Rev Clin Lab Sci 2021; 59:203-218. [PMID: 34775884 DOI: 10.1080/10408363.2021.2002256] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and systemic vasculitis are caused by the body's immune response to autoantigens. The pathogenesis of autoimmune diseases is complex. RNA methylation is known to play a key role in disease progression as it regulates almost all aspects of RNA processing, including RNA nuclear export, translation, splicing, and noncoding RNA processing. This review summarizes the mechanisms, molecular structures of RNA methylations and their roles in biological functions. Similar to the roles of RNA methylation in cancers, RNA methylation in RA and SLE involves "writers" that deposit methyl groups to form N6-methyladenosine (m6A) and 5-methylcytosine (m5C), "erasers" that remove these modifications, and "readers" that further affect mRNA splicing, export, translation, and degradation. Recent advances in detection methods have identified N1-methyladenosine (m1A), N6,2-O-dimethyladenosine (m6Am), and 7-methylguanosine (m7G) RNA modifications, and their roles in RA and SLE need to be further studied. The relationship between RNA methylation and other autoimmune diseases has not been reported, and the roles and mechanisms of RNA modifications in these diseases need to be explored in the future.
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Affiliation(s)
- Wanwan Zhou
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xiao Wang
- Department of Clinical Nursing, School of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jun Chang
- Department of Orthopaedics, Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Chenglong Cheng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Institute of Prevention and Treatment of Rheumatoid Arthritis, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Department of Pharmacy, School of Life and Health Sciences, Anhui University of Science and Technology, Fengyang, Anhui Province, China
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45
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Liu Y, Zhao Y, Wu R, Chen Y, Chen W, Liu Y, Luo Y, Huang C, Zeng B, Liao X, Guo G, Wang Y, Wang X. mRNA m5C controls adipogenesis by promoting CDKN1A mRNA export and translation. RNA Biol 2021; 18:711-721. [PMID: 34570675 DOI: 10.1080/15476286.2021.1980694] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
5-Methylcytosine (m5C) is a type of RNA modification that exists in tRNAs and rRNAs and was recently found in mRNA. Although mRNA m5C modification has been reported to regulate diverse biological process, its function in adipogenesis remains unknown. Here, we demonstrated that knockdown of NOL1/NOP2/Sun domain family member 2 (NSUN2), a m5C methyltransferase, increased lipid accumulation of 3T3-L1 preadipocytes through accelerating cell cycle progression during mitotic clonal expansion (MCE) at the early stage of adipogenesis. Mechanistically, we proved that NSUN2 directly targeted cyclin-dependent kinase inhibitor 1A (CDKN1A) mRNA, a key inhibitory regulator of cell cycle progression, and upregulated its protein expression in an m5C-dependent manner. Further study identified that CDKN1A was the target of Aly/REF export factor (ALYREF), a reader of m5C modified mRNA. Upon NSUN2 deficiency, the recognition of CDKN1A mRNA by ALYREF was suppressed, resulting in the decrease of CDKN1A mRNA shuttling from nucleus to cytoplasm. Thereby, the translation of CDKN1A was reduced, leading to the acceleration of cell cycle and the promotion of adipogenesis. Together, these findings unveiled an important function and mechanism of the m5C modification on adipogenesis by controlling cell cycle progression, providing a potential therapeutic target to prevent obesity.
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Affiliation(s)
- Youhua Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Yuanling Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Ruifan Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Yushi Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Wei Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Yuxi Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Yaojun Luo
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Chaoqun Huang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Botao Zeng
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Xing Liao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Guanqun Guo
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
| | - Xinxia Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, China.,Laboratory of Molecular Animal Nutrition, Zhejiang University, Ministry of Education, Hangzhou, Zhejiang, China
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Lyu H, Xu G, Peng X, Gong C, Peng Y, Song Q, Feng Q, Zheng S. Interacting C/EBPg and YBP regulate DNA methyltransferase 1 expression in Bombyx mori embryos and ovaries. Insect Biochem Mol Biol 2021; 134:103583. [PMID: 34010702 DOI: 10.1016/j.ibmb.2021.103583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/05/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
DNA methylation is an important epigenetic modification. DNA methyltransferases (Dnmts), which catalyze the formation of 5-methylcytosine, play a role in ovarian and embryonic development in some insects. However, the underlying mechanism of Dnmt in mediating ovarian and embryonic development remains unclear. In this study, the regulation and function of Bombyx mori Dnmt1 were investigated. By progressively deleting the sequence upstream of Dnmt1, a region located between -580 and -560 region from the transcription initiation site was found to have the most transcriptional activity. Electrophoretic mobility shift assay and chromatin immunoprecipitation demonstrated that transcription factor Y box binding protein (YBP), a homolog of human Y box binding protein 1 (YBX1), bound to the -580 to -560 region. YBP knockdown and overexpression in a Bombyx cell line indicated that YBP activates Dnmt1 expression. Furthermore, GST-pulldown and co-immunoprecipitation demonstrated that YBP and ovarian CCAAT/enhancer binding protein (C/EBPg) could bind each other. Simultaneous knockdown of C/EBPg and YBP was more effective than single-gene RNAi in inhibiting Dnmt1 expression and reducing the hatching rate. These results demonstrated that the interaction of C/EBPg and YBP activated Dnmt1 expression. Correlated with the expression profiles of the studies genes, our results suggest that high-level expression and interaction of C/EBPg and YBP in ovaries and embryos enhance the expression of Dnmt1, thus ensuring high reproduction rate in B. mori.
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Affiliation(s)
- Hao Lyu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Guanfeng Xu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xuezhen Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chengcheng Gong
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yuling Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, 65211, USA
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sichun Zheng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China; Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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Schauerte M, Pozhydaieva N, Höfer K. Shaping the Bacterial Epitranscriptome-5'-Terminal and Internal RNA Modifications. Adv Biol (Weinh) 2021; 5:e2100834. [PMID: 34121369 DOI: 10.1002/adbi.202100834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/07/2021] [Indexed: 11/11/2022]
Abstract
All domains of life utilize a diverse set of modified ribonucleotides that can impact the sequence, structure, function, stability, and the fate of RNAs, as well as their interactions with other molecules. Today, more than 160 different RNA modifications are known that decorate the RNA at the 5'-terminus or internal RNA positions. The boost of next-generation sequencing technologies sets the foundation to identify and study the functional role of RNA modifications. The recent advances in the field of RNA modifications reveal a novel regulatory layer between RNA modifications and proteins, which is central to developing a novel concept called "epitranscriptomics." The majority of RNA modifications studies focus on the eukaryotic epitranscriptome. In contrast, RNA modifications in prokaryotes are poorly characterized. This review outlines the current knowledge of the prokaryotic epitranscriptome focusing on mRNA modifications. Here, it is described that several internal and 5'-terminal RNA modifications either present or likely present in prokaryotic mRNA. Thereby, the individual techniques to identify these epitranscriptomic modifications, their writers, readers and erasers, and their proposed functions are explored. Besides that, still unanswered questions in the field of prokaryotic epitranscriptomics are pointed out, and its future perspectives in the dawn of next-generation sequencing technologies are outlined.
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Affiliation(s)
- Maik Schauerte
- Max-Planck-Institute for terrestrial Microbiology, Marburg, Hessen, 35043, Germany
| | - Nadiia Pozhydaieva
- Max-Planck-Institute for terrestrial Microbiology, Marburg, Hessen, 35043, Germany
| | - Katharina Höfer
- Max-Planck-Institute for terrestrial Microbiology, Marburg, Hessen, 35043, Germany
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Chen YS, Yang WL, Zhao YL, Yang YG. Dynamic transcriptomic m 5 C and its regulatory role in RNA processing. Wiley Interdiscip Rev RNA 2021; 12:e1639. [PMID: 33438329 DOI: 10.1002/wrna.1639] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
RNA 5-methylcytosine (m5 C) is a prevalent RNA modification in multiple RNA species, including messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), and noncoding RNAs (ncRNAs), and broadly distributed from archaea, prokaryotes to eukaryotes. The multiple detecting techniques of m5 C have been developed, such as m5 C-RIP-seq, miCLIP-seq, AZA-IP-seq, RNA-BisSeq, TAWO-seq, and Nanopore sequencing. These high-throughput techniques, combined with corresponding analysis pipeline, provide a precise m5 C landscape contributing to the deciphering of its biological functions. The m5 C modification is distributed along with mRNA and enriched around 5'UTR and 3'UTR, and conserved in tRNAs and rRNAs. It is dynamically regulated by its related enzymes, including methyltransferases (NSUN, DNMT, and TRDMT family members), demethylases (TET families and ALKBH1), and binding proteins (ALYREF and YBX1). So far, accumulative studies have revealed that m5 C participates in a variety of RNA metabolism, including mRNA export, RNA stability, and translation. Depletion of m5 C modification in the organism could cause dysfunction of mitochondria, drawback of stress response, frustration of gametogenesis and embryogenesis, abnormality of neuro and brain development, and has been implicated in cell migration and tumorigenesis. In this review, we provide a comprehensive summary of dynamic regulatory elements of RNA m5 C, including methyltransferases (writers), demethylases (erasers), and binding proteins (readers). We also summarized the related detecting technologies and biological functions of the RNA 5-methylcytosine, and provided future perspectives in m5 C research. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yu-Sheng Chen
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Lan Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Liang Zhao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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Heinemann U, Roske Y. Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding. Cancers (Basel) 2021; 13:cancers13020190. [PMID: 33430354 PMCID: PMC7825780 DOI: 10.3390/cancers13020190] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Proteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. The abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. Proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to DNA or RNA binding. These functions include the regulation of transcription, RNA splicing, translation, stability and sequestration. Cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. Because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between DNA and RNA. Many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains. Abstract The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.
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Abstract
Modified nucleotides in mRNA are an essential addition to the standard genetic code of four nucleotides in animals, plants, and their viruses. The emerging field of epitranscriptomics examines nucleotide modifications in mRNA and their impact on gene expression. The low abundance of nucleotide modifications and technical limitations, however, have hampered systematic analysis of their occurrence and functions. Selective chemical and immunological identification of modified nucleotides has revealed global candidate topology maps for many modifications in mRNA, but further technical advances to increase confidence will be necessary. Single-molecule sequencing introduced by Oxford Nanopore now promises to overcome such limitations, and we summarize current progress with a particular focus on the bioinformatic challenges of this novel sequencing technology.
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Affiliation(s)
- Ina Anreiter
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Quoseena Mir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Sarath C Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Computational Biology and Bioinformatics, 5021 Health Information and Translational Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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