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Xu XF, Chen J, Long LH, Zhang AM, Yang JW, Li YJ, Chen L, Zhong XL, Xu Y, Cao WY. Chronic social isolation leads to abnormal behavior in male mice through the hippocampal METTL14 mediated epitranscriptomic RNA m6A modifications. J Affect Disord 2024; 366:262-272. [PMID: 39209273 DOI: 10.1016/j.jad.2024.08.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/25/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Social isolation not only increases the risk of mortality in later life but also causes depressive symptoms, cognitive and physical disabilities. Although RNA m6A modifications are suggested to play key roles in brain development, neuronal signaling and neurological disorders, both the roles of m6A and the enzymes that regulate RNA m6A modification in social isolation induced abnormal behavior is unknown. The present study aims to explore the possible epitranscriptomic role of RNA m6A modifications and its enzymes in social isolation induced impaired behavior. METHODS 3-4 weeks mice experiencing 8 weeks social isolation stress (SI) were used in the present study. We quantified m6A levels in brain regions related to mood and cognitive behavior. And the expression of hippocampal m6A enzymes was also determined. The role of hippocampal m6A and its enzymes in SI induced abnormal behavior was further verified by the virus tool. RESULTS SI led to not only depressive and anxiety-like behaviors but also cognitive impairment, with corresponding decreases in hippocampal m6A and METTL14. Hippocampal over-expression METTL14 with lentivirus not only rescued these behaviors but also enhanced the hippocampal m6A level. Hippocampal over-expression METTL14 resulted in increased synaptic related genes. CONCLUSIONS We provide the first evidence that post-weaning social isolation reduces hippocampal m6A level and causes altered expression of m6A enzyme in mice. Importantly, hippocampal METTL14 over-expression alleviated the SI-induced depression/anxiety-like and impaired cognitive behaviors and enhanced m6A level and synaptic related genes expression.
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Affiliation(s)
- Xiao Fan Xu
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Department of Neurosurgery, Liaocheng People's Hospital, Liaocheng 252000, Shandong, China
| | - Jie Chen
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Lu Hong Long
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Ao Mei Zhang
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Jing Wen Yang
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Yu Jia Li
- Institute of Neuroscience, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China
| | - Ling Chen
- Institute of Clinical Medicine, The First Affiliated Hospital of University of South China, 421001 Hengyang, Hunan, China
| | - Xiao Lin Zhong
- Institute of Clinical Medicine, The First Affiliated Hospital of University of South China, 421001 Hengyang, Hunan, China
| | - Yang Xu
- Institute of Neuroscience, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| | - Wen Yu Cao
- Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
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Wang L, Han H. Strategies for improving the genome-editing efficiency of class 2 CRISPR/Cas system. Heliyon 2024; 10:e38588. [PMID: 39397905 PMCID: PMC11471210 DOI: 10.1016/j.heliyon.2024.e38588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 09/26/2024] [Accepted: 09/26/2024] [Indexed: 10/15/2024] Open
Abstract
Since its advent, gene-editing technology has been widely used in microorganisms, animals, plants, and other species. This technology shows remarkable application prospects, giving rise to a new biotechnological industry. In particular, third-generation gene editing technology, represented by the CRISPR/Cas9 system, has become the mainstream gene editing technology owing to its advantages of high efficiency, simple operation, and low cost. These systems can be widely used because they have been modified and optimized, leading to notable improvements in the efficiency of gene editing. This review introduces the characteristics of popular CRISPR/Cas systems and optimization methods aimed at improving the editing efficiency of class 2 CRISPR/Cas systems, providing a reference for the development of superior gene editing systems. Additionally, the review discusses the development and optimization of base editors, primer editors, gene activation and repression tools, as well as the advancement and refinement of compact systems such as IscB, TnpB, Fanzor, and Cas12f.
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Affiliation(s)
- Linli Wang
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hongbing Han
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Xu T, Du T, Zhuang X, He X, Yan Y, Wu J, Zhou H, Li Y, Liao X, He J, Liu C, Dong Y, Ou J, Lin S, Chen D, Huang ZP. Loss of NAT10 Reduces the Translation of Kmt5a mRNA Through ac4C Modification in Cardiomyocytes and Induces Heart Failure. J Am Heart Assoc 2024; 13:e035714. [PMID: 39392166 DOI: 10.1161/jaha.124.035714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 09/06/2024] [Indexed: 10/12/2024]
Abstract
BACKGROUND In the past decade, the biological functions of various RNA modifications in mammals have been uncovered. N4-acetylcytidine (ac4C), a highly conserved RNA modification, has been implicated in human diseases. Despite this, the involvement of RNA ac4C modification in cardiac physiology and pathology remains incompletely understood. NAT10 (N-acetyltransferase 10) stands as the sole acetyltransferase known to catalyze RNA ac4C modification. This study aims to explore the role of NAT10 and ac4C modification in cardiac physiology and pathology. METHODS AND RESULTS Cardiac-specific knockout of NAT10, leading to reduced RNA ac4C modification, during both neonatal and adult stages resulted in severe heart failure. NAT10 deficiency induced cardiomyocyte apoptosis, a crucial step in heart failure pathogenesis, supported by in vitro data. Activation of the p53 signaling pathway was closely associated with enhanced apoptosis in NAT10-deficient cardiomyocytes. As ac4C modification on mRNA influences translational efficiency, we employed ribosome footprints coupled with RNA sequencing to explore genome-wide translational efficiency changes caused by NAT10 deficiency. We identified and validated that the translational efficiency of Kmt5a was suppressed in NAT10 knockout hearts due to reduced ac4C modification on its mRNA. This finding was consistent with the observation that Kmt5a protein levels were reduced in heart failure despite unchanged mRNA expression. Knockdown of Kmt5a in cardiomyocytes recapitulated the phenotype of NAT10 deficiency, including increased cardiomyocyte apoptosis and activated p53 signaling. Finally, overexpression of Kmt5a rescued cardiomyocyte apoptosis and p53 activation induced by NAT10 inhibition. CONCLUSIONS Our study highlights the significance of NAT10 in cardiomyocyte physiology, demonstrating that NAT10 loss is sufficient to induce cardiomyocyte apoptosis and heart failure. NAT10 regulates the translational efficiency of Kmt5a, a key mediator, through mRNA ac4C modification during heart failure.
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Affiliation(s)
- Ting Xu
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
| | - Tailai Du
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
| | - Xiaodong Zhuang
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
| | - Xin He
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
| | - Youchen Yan
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
| | - Jialing Wu
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
| | - Huimin Zhou
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
| | - Yan Li
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
- Division of Cardiac Surgery National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- Key Laboratory of Assisted Circulation and Vascular Diseases Chinese Academy of Medical Sciences, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
| | - Xinxue Liao
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
| | - Jiangui He
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
| | - Chen Liu
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
- Key Laboratory of Assisted Circulation and Vascular Diseases Chinese Academy of Medical Sciences, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
| | - Yugang Dong
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
| | - Jingsong Ou
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
- Division of Cardiac Surgery National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- Key Laboratory of Assisted Circulation and Vascular Diseases Chinese Academy of Medical Sciences, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
| | - Shuibin Lin
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
| | - Demeng Chen
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
| | - Zhan-Peng Huang
- Department of Cardiology, Center for Translational Medicine Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- NHC Key Laboratory of Assisted Circulation and Vascular Diseases (Sun Yat-sen University) Guangzhou China
- Division of Cardiac Surgery National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
- Key Laboratory of Assisted Circulation and Vascular Diseases Chinese Academy of Medical Sciences, The First Affiliated Hospital, Sun Yat-sen University Guangzhou China
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Khan FA, Nsengimana B, Awan UA, Ji XY, Ji S, Dong J. Regulatory roles of N6-methyladenosine (m 6A) methylation in RNA processing and non-communicable diseases. Cancer Gene Ther 2024; 31:1439-1453. [PMID: 38839892 DOI: 10.1038/s41417-024-00789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
Post-transcriptional RNA modification is an emerging epigenetic control mechanism in cells that is important in many different cellular and organismal processes. N6-methyladenosine (m6A) is one of the most prevalent, prolific, and ubiquitous internal transcriptional alterations in eukaryotic mRNAs, making it an important topic in the field of Epigenetics. m6A methylation acts as a dynamical regulatory process that regulates the activity of genes and participates in multiple physiological processes, by supporting multiple aspects of essential mRNA metabolic processes, including pre-mRNA splicing, nuclear export, translation, miRNA synthesis, and stability. Extensive research has linked aberrations in m6A modification and m6A-associated proteins to a wide range of human diseases. However, the impact of m6A on mRNA metabolism and its pathological connection between m6A and other non-communicable diseases, including cardiovascular disease, neurodegenerative disorders, liver diseases, and cancer remains in fragmentation. Here, we review the existing understanding of the overall role of mechanisms by which m6A exerts its activities and address new discoveries that highlight m6A's diverse involvement in gene expression regulation. We discuss m6A deposition on mRNA and its consequences on degradation, translation, and transcription, as well as m6A methylation of non-coding chromosomal-associated RNA species. This study could give new information about the molecular process, early detection, tailored treatment, and predictive evaluation of human non-communicable diseases like cancer. We also explore more about new data that suggests targeting m6A regulators in diseases may have therapeutic advantages.
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Affiliation(s)
- Faiz Ali Khan
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Integrative Medicine, Fudan University, Shanghai, China.
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan.
| | - Bernard Nsengimana
- Department of Hepatobiliary Surgery, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Usman Ayub Awan
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xin-Ying Ji
- Center for Molecular Medicine, Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou, Henan, China.
| | - Shaoping Ji
- Center for Molecular Medicine, Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou, Henan, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Jingcheng Dong
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Integrative Medicine, Fudan University, Shanghai, China.
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5
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Mehta SL, Arruri V, Vemuganti R. Role of transcription factors, noncoding RNAs, epitranscriptomics, and epigenetics in post-ischemic neuroinflammation. J Neurochem 2024; 168:3430-3448. [PMID: 38279529 PMCID: PMC11272908 DOI: 10.1111/jnc.16055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/28/2024]
Abstract
Post-stroke neuroinflammation is pivotal in brain repair, yet persistent inflammation can aggravate ischemic brain damage and hamper recovery. Following stroke, specific molecules released from brain cells attract and activate central and peripheral immune cells. These immune cells subsequently release diverse inflammatory molecules within the ischemic brain, initiating a sequence of events, including activation of transcription factors in different brain cell types that modulate gene expression and influence outcomes; the interactive action of various noncoding RNAs (ncRNAs) to regulate multiple biological processes including inflammation, epitranscriptomic RNA modification that controls RNA processing, stability, and translation; and epigenetic changes including DNA methylation, hydroxymethylation, and histone modifications crucial in managing the genic response to stroke. Interactions among these events further affect post-stroke inflammation and shape the depth of ischemic brain damage and functional outcomes. We highlighted these aspects of neuroinflammation in this review and postulate that deciphering these mechanisms is pivotal for identifying therapeutic targets to alleviate post-stroke dysfunction and enhance recovery.
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Affiliation(s)
- Suresh L. Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Vijay Arruri
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
- William S. Middleton Veterans Hospital, Madison, WI, USA
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Monroe J, Eyler DE, Mitchell L, Deb I, Bojanowski A, Srinivas P, Dunham CM, Roy B, Frank AT, Koutmou KS. N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation. Nat Commun 2024; 15:8119. [PMID: 39284850 PMCID: PMC11405884 DOI: 10.1038/s41467-024-51301-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/02/2024] [Indexed: 09/20/2024] Open
Abstract
The ribosome utilizes hydrogen bonding between mRNA codons and aminoacyl-tRNAs to ensure rapid and accurate protein production. Chemical modification of mRNA nucleobases can adjust the strength and pattern of this hydrogen bonding to alter protein synthesis. We investigate how the N1-methylpseudouridine (m1Ψ) modification, commonly incorporated into therapeutic and vaccine mRNA sequences, influences the speed and fidelity of translation. We find that m1Ψ does not substantially change the rate constants for amino acid addition by cognate tRNAs or termination by release factors. However, we also find that m1Ψ can subtly modulate the fidelity of amino acid incorporation in a codon-position and tRNA dependent manner in vitro and in human cells. Our computational modeling shows that altered energetics of mRNA:tRNA interactions largely account for the context dependence of the low levels of miscoding we observe on Ψ and m1Ψ containing codons. The outcome of translation on modified mRNA bases is thus governed by the sequence context in which they occur.
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Affiliation(s)
- Jeremy Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Daniel E Eyler
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Lili Mitchell
- RNA and Genome Editing, New England Biolabs Inc., Ipswich, MA, USA
| | - Indrajit Deb
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | | | - Pooja Srinivas
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | | | - Bijoyita Roy
- RNA and Genome Editing, New England Biolabs Inc., Ipswich, MA, USA
| | - Aaron T Frank
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Computational Chemistry, Arrakis Therapeutics, Waltham, MA, USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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7
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Hu Z, Liu W, Chen D, Gao K, Li Z. Direct quantification of N 6-methyladenosine fractions at specific site in RNA based on deoxyribozyme mediated CRISPR-Cas12a platform. Talanta 2024; 281:126806. [PMID: 39277937 DOI: 10.1016/j.talanta.2024.126806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/12/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024]
Abstract
As the most abundant modification in eukaryotic messenger RNA (mRNA) and long noncoding RNA (lncRA), N6-methyladenosine (m6A) has been shown to play essential roles in various significant biological processes and attracted growing attention in recent years. To investigate its functions and dynamics, there is a critical need to quantitatively determine the m6A modification fractions at a precise location. Here, we report a deoxyribozyme mediated CRISPR-Cas12a platform (termed "DCAS") that can directly quantify m6A fractions at single-base resolution. DCAS employs a deoxyribozyme (VMC10) to selectively cleave the unmodified adenine (A) in the RNA, allowing only m6A-modified RNA amplified by RT-PCR. Leveraging the CRISPR-Cas12a quantify the PCR amplification products, DCAS can directly determine the presence of m6A at target sites and its fractions. The combination of CRISPR-Cas12a with RT-PCR has greatly improved the sensitivity and accuracy, enabling the detection of m6A-modified RNA as low as 100 aM in 2 fM total target RNA. This robustly represents an improvement of 2-3 orders of magnitude of sensitivity and selectivity compared to traditional standard methods, such as SCARLET and primer extension methods. Therefore, this method can be successfully employed to accurately determine m6A fractions in real biological samples, even in low abundance RNA biomarkers.
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Affiliation(s)
- Zhian Hu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Weiliang Liu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China; Department of Chemistry, Tsinghua University, Beijing, 100084, PR China.
| | - Desheng Chen
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Kejian Gao
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China.
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8
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Wang N, Chen HQ, Zeng Y, Shi Y, Zhang Z, Li JY, Zhou SM, Li YW, Deng SW, Han X, Zhou ZY, Yao ML, Liu WB. Benzo(a)pyrene promotes the malignant progression of malignant-transformed BEAS-2B cells by regulating YTH N6-methyladenosine RNA binding protein 1 to inhibit ferroptosis. Toxicology 2024; 507:153886. [PMID: 39002880 DOI: 10.1016/j.tox.2024.153886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
Benzo[a]pyrene (BaP) is associated with the development of lung cancer, but the underlying mechanism has not been completely clarified. Here, we used 10 μM BaP to induce malignant transformation of human bronchial epithelial BEAS-2B cells, named BEAS-2B-T. Results indicated that BaP (6.25, 12.5 and 25 μM) treatment significantly promoted the migration and invasion of BEAS-2B-T cells. Meanwhile, BaP exposure inhibited ferroptosis in BEAS-2B-T, ferroptosis-related indexes Fe2+, malondialdehyde (MDA), lipid peroxidation (LPO) and reactive oxygen species (ROS) decreased significantly. The protein level of ferroptosis-related molecule transferrin receptor (TFRC) decreased significantly, while solute carrier family 7 membrane 11 (SLC7A11), ferritin heavy chain 1 (FTH1) and glutathione peroxidase 4 (GPX4) increased significantly. The intervention of ferroptosis dramatically effected the migration and invasion of BEAS-2B-T induced by BaP. Furthermore, the expression of YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) was markedly increased after BaP exposure. YTHDF1 knockdown inhibited BEAS-2B-T migration and invasion by promoting ferroptosis. In the meantime, the contents of Fe2+, MDA, LPO and ROS increased significantly, TFRC was markedly increased, and SLC7A11, FTH1, and GPX4 were markedly decreased. Moreover, overexpression of YTHDF1 promoted BEAS-2B-T migration and invasion by inhibiting ferroptosis. Importantly, knockdown of YTHDF1 promoted ferroptosis and reduced BEAS-2B-T migration and invasion during BaP exposure, and overexpression of YTHDF1 increased migration and invasion of BEAS-2B-T by inhibiting ferroptosis during BaP exposure. RNA immunoprecipitation assays indicated that the binding of YTHDF1 to SLC7A11 and FTH1 markedly increased after YTHDF1 overexpression. Therefore, we concluded that BaP promotes the malignant progression of BEAS-2B-T cells through YTHDF1 upregulating SLC7A11 and FTH1 to inhibit ferroptosis. This study reveals new epigenetic and ferroptosis markers for preventing and treating lung cancer induced by environmental carcinogens.
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Affiliation(s)
- Na Wang
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Hong-Qiang Chen
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yong Zeng
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yu Shi
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China; College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Zhe Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, China
| | - Jiang-Ying Li
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China; College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Shi-Meng Zhou
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Ya-Wen Li
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Shuang-Wu Deng
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xue Han
- Department of Traditional Chinese Medicine Health and Preventive Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou 510006, China
| | - Zi-Yuan Zhou
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Mao-Lin Yao
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China.
| | - Wen-Bin Liu
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China; Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China.
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9
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Zheng D, Wang J, Persyn L, Liu Y, Montoya FU, Cenik C, Agarwal V. Predicting the translation efficiency of messenger RNA in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.11.607362. [PMID: 39149337 PMCID: PMC11326250 DOI: 10.1101/2024.08.11.607362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The degree to which translational control is specified by mRNA sequence is poorly understood in mammalian cells. Here, we constructed and leveraged a compendium of 3,819 ribosomal profiling datasets, distilling them into a transcriptome-wide atlas of translation efficiency (TE) measurements encompassing >140 human and mouse cell types. We subsequently developed RiboNN, a multitask deep convolutional neural network, and classic machine learning models to predict TEs in hundreds of cell types from sequence-encoded mRNA features, achieving state-of-the-art performance (r=0.79 in human and r=0.78 in mouse for mean TE across cell types). While the majority of earlier models solely considered 5' UTR sequence, RiboNN integrates contributions from the full-length mRNA sequence, learning that the 5' UTR, CDS, and 3' UTR respectively possess ~67%, 31%, and 2% per-nucleotide information density in the specification of mammalian TEs. Interpretation of RiboNN revealed that the spatial positioning of low-level di- and tri-nucleotide features (i.e., including codons) largely explain model performance, capturing mechanistic principles such as how ribosomal processivity and tRNA abundance control translational output. RiboNN is predictive of the translational behavior of base-modified therapeutic RNA, and can explain evolutionary selection pressures in human 5' UTRs. Finally, it detects a common language governing mRNA regulatory control and highlights the interconnectedness of mRNA translation, stability, and localization in mammalian organisms.
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Affiliation(s)
- Dinghai Zheng
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Jun Wang
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Logan Persyn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yue Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | | | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Vikram Agarwal
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
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10
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He B, Chen Y, Yi C. Quantitative mapping of the mammalian epitranscriptome. Curr Opin Genet Dev 2024; 87:102212. [PMID: 38823337 DOI: 10.1016/j.gde.2024.102212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/04/2024] [Accepted: 05/17/2024] [Indexed: 06/03/2024]
Abstract
The epitranscriptome encompasses a diverse array of dynamic and reversible RNA modifications, affecting both coding and noncoding RNAs. Over 170 types of RNA chemical modifications have been identified, underscoring the need for innovative detection methods to deepen our understanding of RNA modification roles and mechanisms. In particular, the base resolution and quantitative information on RNA modifications are critical for understanding the regulation and functions of RNA modifications. Based on detection throughput and principles, existing quantitative RNA modification detection methods can be categorized into two groups, including next-generation sequencing and nanopore direct RNA sequencing. In this review, we focus on methodologies for elucidating the base resolution and stoichiometric information of RNA modifications. In addition, we further discuss the challenges and the potential prospects of the quantitative RNA modification detection methods.
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Affiliation(s)
- Bo He
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yuting Chen
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China
| | - Chengqi Yi
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China; State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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11
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Cao L, Wang L. Biospecific Chemistry for Covalent Linking of Biomacromolecules. Chem Rev 2024; 124:8516-8549. [PMID: 38913432 PMCID: PMC11240265 DOI: 10.1021/acs.chemrev.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Interactions among biomacromolecules, predominantly noncovalent, underpin biological processes. However, recent advancements in biospecific chemistry have enabled the creation of specific covalent bonds between biomolecules, both in vitro and in vivo. This Review traces the evolution of biospecific chemistry in proteins, emphasizing the role of genetically encoded latent bioreactive amino acids. These amino acids react selectively with adjacent natural groups through proximity-enabled bioreactivity, enabling targeted covalent linkages. We explore various latent bioreactive amino acids designed to target different protein residues, ribonucleic acids, and carbohydrates. We then discuss how these novel covalent linkages can drive challenging protein properties and capture transient protein-protein and protein-RNA interactions in vivo. Additionally, we examine the application of covalent peptides as potential therapeutic agents and site-specific conjugates for native antibodies, highlighting their capacity to form stable linkages with target molecules. A significant focus is placed on proximity-enabled reactive therapeutics (PERx), a pioneering technology in covalent protein therapeutics. We detail its wide-ranging applications in immunotherapy, viral neutralization, and targeted radionuclide therapy. Finally, we present a perspective on the existing challenges within biospecific chemistry and discuss the potential avenues for future exploration and advancement in this rapidly evolving field.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
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12
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Jalan A, Jayasree PJ, Karemore P, Narayan KP, Khandelia P. Decoding the 'Fifth' Nucleotide: Impact of RNA Pseudouridylation on Gene Expression and Human Disease. Mol Biotechnol 2024; 66:1581-1598. [PMID: 37341888 DOI: 10.1007/s12033-023-00792-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023]
Abstract
Cellular RNAs, both coding and noncoding are adorned by > 100 chemical modifications, which impact various facets of RNA metabolism and gene expression. Very often derailments in these modifications are associated with a plethora of human diseases. One of the most oldest of such modification is pseudouridylation of RNA, wherein uridine is converted to a pseudouridine (Ψ) via an isomerization reaction. When discovered, Ψ was referred to as the 'fifth nucleotide' and is chemically distinct from uridine and any other known nucleotides. Experimental evidence accumulated over the past six decades, coupled together with the recent technological advances in pseudouridine detection, suggest the presence of pseudouridine on messenger RNA, as well as on diverse classes of non-coding RNA in human cells. RNA pseudouridylation has widespread effects on cellular RNA metabolism and gene expression, primarily via stabilizing RNA conformations and destabilizing interactions with RNA-binding proteins. However, much remains to be understood about the RNA targets and their recognition by the pseudouridylation machinery, the regulation of RNA pseudouridylation, and its crosstalk with other RNA modifications and gene regulatory processes. In this review, we summarize the mechanism and molecular machinery involved in depositing pseudouridine on target RNAs, molecular functions of RNA pseudouridylation, tools to detect pseudouridines, the role of RNA pseudouridylation in human diseases like cancer, and finally, the potential of pseudouridine to serve as a biomarker and as an attractive therapeutic target.
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Affiliation(s)
- Abhishek Jalan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - P J Jayasree
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Pragati Karemore
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Kumar Pranav Narayan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India.
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13
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Dai Z, Yang X. The regulation of liquid-liquid phase separated condensates containing nucleic acids. FEBS J 2024; 291:2320-2331. [PMID: 37735903 DOI: 10.1111/febs.16959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023]
Abstract
Liquid-liquid phase separation (LLPS) has been recognized as a universal biological phenomenon. It plays an important role in life activities. LLPS is induced by weak interactions between intrinsically disordered regions or low complex domains. Nucleic acids are widely present in cells, and shown to be closely related to LLPS. Their structure and electronegativity provide the excellent platforms for the formation of phase-separated condensates. In this review, we summarize the interconnected regulation between nucleic acids and LLPS demonstrated in in vivo and in vitro studies. Beside homogeneous and single-phase condensates, complicated and multicompartment LLPS induced by nucleic acids is discussed as well. Recent advances about nucleic-acid-induced LLPS as a new pathogenic mechanism and drug design direction are highlighted, especially virus-mediated disease treatment and prevention.
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Affiliation(s)
- Zhuojun Dai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaorong Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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14
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Zhang XX, Sun YZ, Wang W, Gao Y, Wei XY, Sun HC, Wang CR, Ni HB, Yang X, Elsheikha HM, Guo HP. Altered landscape of total RNA, tRNA and sncRNA modifications in the liver and spleen of mice infected by Toxoplasma gondii. PLoS Negl Trop Dis 2024; 18:e0012281. [PMID: 38905319 PMCID: PMC11221703 DOI: 10.1371/journal.pntd.0012281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/03/2024] [Accepted: 06/07/2024] [Indexed: 06/23/2024] Open
Abstract
BACKGROUND Pathogens can impact host RNA modification machinery to establish a favorable cellular environment for their replication. In the present study, we investigated the effect of Toxoplasma gondii infection on host RNA modification profiles and explored how these modifications may influence the host-parasite interaction. METHODOLOGY/PRINCIPAL FINDINGS We analyzed the modification levels of ∼ 80 nt tRNA and 17-50 nt sncRNAs in mouse liver, spleen, and serum using liquid chromatography and tandem mass spectrometry analysis. The results revealed alterations in RNA modification profiles, particularly during acute infection. The liver exhibited more differentially abundant RNA modifications than the spleen. RNA modification levels in serum were mostly downregulated during acute infection compared to control mice. Correlations were detected between different RNA modifications in the liver and spleen during infection and between several RNA modifications and many cytokines. Alterations in RNA modifications affected tRNA stability and protein translation. CONCLUSIONS/SIGNIFICANCE These findings provide new insight into the role of RNA modifications in mediating the murine host response to T. gondii infection.
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Affiliation(s)
- Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, PR China
| | - Yu-Zhe Sun
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, PR China
| | - Wei Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, PR China
| | - Yang Gao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Xin-Yu Wei
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Hong-Chao Sun
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Science, Hangzhou, PR China
| | - Chun-Ren Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agriculture University, Daqing, PR China
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, PR China
| | - Xing Yang
- Department of Medical Microbiology and Immunology, School of Basic Medicine, Dali University, Dali, PR China
| | - Hany M. Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Huan-Ping Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, China
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15
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McCormick CA, Akeson S, Tavakoli S, Bloch D, Klink IN, Jain M, Rouhanifard SH. Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.06.535889. [PMID: 37066160 PMCID: PMC10104151 DOI: 10.1101/2023.04.06.535889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Nanopore direct RNA sequencing (DRS) enables measurements of RNA modifications. Modification-free transcripts are a practical and targeted control for DRS, providing a baseline measurement for canonical nucleotides within a matched and biologically derived sequence context. However, these controls can be challenging to generate and carry nanopore-specific nuances that can impact analysis. We produced DRS datasets using modification-free transcripts from in vitro transcription (IVT) of cDNA from six immortalized human cell lines. We characterized variation across cell lines and demonstrated how these may be interpreted. These data will serve as a versatile control and resource to the community for RNA modification analysis of human transcripts.
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Affiliation(s)
- Caroline A. McCormick
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Stuart Akeson
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Sepideh Tavakoli
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Dylan Bloch
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Isabel N. Klink
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Miten Jain
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
- Department of Physics, Northeastern University, Boston, MA, 02115, United States
| | - Sara H. Rouhanifard
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
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16
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Li Y, Zhou H, Chen S, Li Y, Guo Y, Chen X, Wang S, Wang L, Gan Y, Zhang S, Zheng Y, Sheng J, Zhou Z, Wang R. Bioorthogonal labeling and profiling of N6-isopentenyladenosine (i6A) modified RNA. Nucleic Acids Res 2024; 52:2808-2820. [PMID: 38426933 PMCID: PMC11014277 DOI: 10.1093/nar/gkae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Chemical modifications in RNAs play crucial roles in diversifying their structures and regulating numerous biochemical processes. Since the 1990s, several hydrophobic prenyl-modifications have been discovered in various RNAs. Prenyl groups serve as precursors for terpenes and many other biological molecules. The processes of prenylation in different macromolecules have been extensively studied. We introduce here a novel chemical biology toolkit that not only labels i6A, a prenyl-modified RNA residue, by leveraging the unique reactivity of the prenyl group, but also provides a general strategy to incorporate fluorescence functionalities into RNAs for molecular tracking purposes. Our findings revealed that iodine-mediated cyclization reactions of the prenyl group occur rapidly, transforming i6A from a hydrogen-bond acceptor to a donor. Based on this reactivity, we developed an Iodine-Mediated Cyclization and Reverse Transcription (IMCRT) tRNA-seq method, which can profile all nine endogenous tRNAs containing i6A residues in Saccharomyces cerevisiae with single-base resolution. Furthermore, under stress conditions, we observed a decline in i6A levels in budding yeast, accompanied by significant decrease of mutation rate at A37 position. Thus, the IMCRT tRNA-seq method not only permits semi-quantification of i6A levels in tRNAs but also holds potential for transcriptome-wide detection and analysis of various RNA species containing i6A modifications.
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Affiliation(s)
- Yuanyuan Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hongling Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Shasha Chen
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yinan Li
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuyang Guo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Xiaoqian Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Sheng Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Li Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Youfang Gan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Shusheng Zhang
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ya Ying Zheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Zhipeng Zhou
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518057, China
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17
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Shen W, Sun H, Liu C, Yi Y, Hou Y, Xiao Y, Hu Y, Lu B, Peng J, Wang J, Yi C. GLORI for absolute quantification of transcriptome-wide m 6A at single-base resolution. Nat Protoc 2024; 19:1252-1287. [PMID: 38253658 DOI: 10.1038/s41596-023-00937-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 10/20/2023] [Indexed: 01/24/2024]
Abstract
N6-methyladenosine (m6A) is the most abundant posttranscriptional chemical modification in mRNA, involved in regulating various physiological and pathological processes throughout mRNA metabolism. Recently, we developed GLORI, a sequencing method that enables the production of a globally absolute-quantitative m6A map at single-base resolution. Our technique utilizes the glyoxal- and nitrite-based chemical reaction, which selectively deaminates unmethylated adenosines while leaving m6A intact. The RNA library can then be prepared using a modified library construction protocol from enhanced UV crosslinking and immunoprecipitation (eCLIP) or commercial kits. Here we provide a detailed protocol for proper RNA sample handling and provide further guidelines for the use of a tailored bioinformatics pipeline (GLORI-tools) for subsequent data analysis. Compared with current methods, this new method is both exceptionally sensitive and robust, capable of identifying ~80,000 m6A sites with 50 Gb sequencing data in mammalian cells. It also provides a quantitative readout for m6A sites at single-base resolution. We hope the technique will provide a precise and unbiased tool for investigating m6A biology across various fields. Basic expertise in molecular biology and knowledge of bioinformatics are required for the protocol. The entire procedure can be completed within a week, with the library construction process taking ~4 d.
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Affiliation(s)
- Weiguo Shen
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of 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
| | - Yunpeng Yi
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan, China
| | - Yongkang Hou
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Ye Xiao
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yufei Hu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Bo Lu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical 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 and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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18
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Imani S, Tagit O, Pichon C. Neoantigen vaccine nanoformulations based on Chemically synthesized minimal mRNA (CmRNA): small molecules, big impact. NPJ Vaccines 2024; 9:14. [PMID: 38238340 PMCID: PMC10796345 DOI: 10.1038/s41541-024-00807-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Recently, chemically synthesized minimal mRNA (CmRNA) has emerged as a promising alternative to in vitro transcribed mRNA (IVT-mRNA) for cancer therapy and immunotherapy. CmRNA lacking the untranslated regions and polyadenylation exhibits enhanced stability and efficiency. Encapsulation of CmRNA within lipid-polymer hybrid nanoparticles (LPPs) offers an effective approach for personalized neoantigen mRNA vaccines with improved control over tumor growth. LPP-based delivery systems provide superior pharmacokinetics, stability, and lower toxicity compared to viral vectors, naked mRNA, or lipid nanoparticles that are commonly used for mRNA delivery. Precise customization of LPPs in terms of size, surface charge, and composition allows for optimized cellular uptake, target specificity, and immune stimulation. CmRNA-encoded neo-antigens demonstrate high translational efficiency, enabling immune recognition by CD8+ T cells upon processing and presentation. This perspective highlights the potential benefits, challenges, and future directions of CmRNA neoantigen vaccines in cancer therapy compared to Circular RNAs and IVT-mRNA. Further research is needed to optimize vaccine design, delivery, and safety assessment in clinical trials. Nevertheless, personalized LPP-CmRNA vaccines hold great potential for advancing cancer immunotherapy, paving the way for personalized medicine.
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Affiliation(s)
- Saber Imani
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China.
| | - Oya Tagit
- Institute of Chemistry and Bioanalytics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Chantal Pichon
- Center of Molecular Biophysics, CNRS, Orléans, France.
- ART-ARNm, National Institute of Health and Medical Research (Inserm) and University of Orléans, Orléans, France.
- Institut Universitaire de France, Paris, France.
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19
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Ding S, Liu H, Liu L, Ma L, Chen Z, Zhu M, Liu L, Zhang X, Hao H, Zuo L, Yang J, Wu X, Zhou P, Huang F, Zhu F, Guan W. Epigenetic addition of m 5C to HBV transcripts promotes viral replication and evasion of innate antiviral responses. Cell Death Dis 2024; 15:39. [PMID: 38216565 PMCID: PMC10786922 DOI: 10.1038/s41419-023-06412-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/14/2024]
Abstract
Eukaryotic five-methylcytosine (m5C) is an important regulator of viral RNA splicing, stability, and translation. However, its role in HBV replication remains largely unknown. In this study, functional m5C sites are identified in hepatitis B virus (HBV) mRNA. The m5C modification at nt 1291 is not only indispensable for Aly/REF export factor (ALYREF) recognition to promote viral mRNA export and HBx translation but also for the inhibition of RIG-I binding to suppress interferon-β (IFN-β) production. Moreover, NOP2/Sun RNA methyltransferase 2 (NSUN2) catalyzes the addition of m5C to HBV mRNA and is transcriptionally downregulated by the viral protein HBx, which suppresses the binding of EGR1 to the NSUN2 promoter. Additionally, NSUN2 expression correlates with m5C modification of type I IFN mRNA in host cells, thus, positively regulating IFN expression. Hence, the delicate regulation of NSUN2 expression induces m5C modification of HBV mRNA while decreasing the levels of m5C in host IFN mRNA, making it a vital component of the HBV life cycle. These findings provide new molecular insights into the mechanism of HBV-mediated IFN inhibition and may inform the development of new IFN-α based therapies.
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Affiliation(s)
- Shuang Ding
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Haibin Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
- Hubei JiangXia Laboratory, Wuhan, Hubei, 430200, China
| | - Lijuan Liu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Li Ma
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Zhen Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Miao Zhu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Lishi Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Xueyan Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Haojie Hao
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Li Zuo
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Jingwen Yang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China
| | - Xiulin Wu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Ping Zhou
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Fang Huang
- Hubei JiangXia Laboratory, Wuhan, Hubei, 430200, China
| | - Fan Zhu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan, Hubei, 430071, China.
| | - Wuxiang Guan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430207, China.
- Hubei JiangXia Laboratory, Wuhan, Hubei, 430200, China.
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20
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Sun YH, Zhao TJ, Li LH, Wang Z, Li HB. Emerging role of N6-methyladenosine in the homeostasis of glucose metabolism. Am J Physiol Endocrinol Metab 2024; 326:E1-E13. [PMID: 37938178 DOI: 10.1152/ajpendo.00225.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/21/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent post-transcriptional internal RNA modification, which is involved in the regulation of diverse physiological processes. Dynamic and reversible m6A modification has been shown to regulate glucose metabolism, and dysregulation of m6A modification contributes to glucose metabolic disorders in multiple organs and tissues including the pancreas, liver, adipose tissue, skeletal muscle, kidney, blood vessels, and so forth. In this review, the role and molecular mechanism of m6A modification in the regulation of glucose metabolism were summarized, the potential therapeutic strategies that improve glucose metabolism by targeting m6A modifiers were outlined, and feasible directions of future research in this field were discussed as well, providing clues for translational research on combating metabolic diseases based on m6A modification in the future.
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Affiliation(s)
- Yuan-Hai Sun
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Teng-Jiao Zhao
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Ling-Huan Li
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, People's Republic of China
- College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, People's Republic of China
| | - Zhen Wang
- Center for Laboratory Medicine, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Han-Bing Li
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Section of Endocrinology, School of Medicine, Yale University, New Haven, Connecticut, United States
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21
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Gionco JT, Bernstein AI. Emerging Role of Environmental Epitranscriptomics and RNA Modifications in Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2024; 14:643-656. [PMID: 38578904 PMCID: PMC11191529 DOI: 10.3233/jpd-230457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/10/2024] [Indexed: 04/07/2024]
Abstract
Environmental risk factors and gene-environment interactions play a critical role in Parkinson's disease (PD). However, the relatively large contribution of environmental risk factors in the overwhelming majority of PD cases has been widely neglected in the field. A "PD prevention agenda" proposed in this journal laid out a set of research priorities focused on preventing PD through modification of environmental risk factors. This agenda includes a call for preclinical studies to employ new high-throughput methods for analyzing transcriptomics and epigenomics to provide a deeper understanding of the effects of exposures linked to PD. Here, we focus on epitranscriptomics as a novel area of research with the potential to add to our understanding of the interplay between genes and environmental exposures in PD. Both epigenetics and epitranscriptomics have been recognized as potential mediators of the complex relationship between genes, environment, and disease. Multiple studies have identified epigenetic alterations, such as DNA methylation, associated with PD and PD-related exposures in human studies and preclinical models. In addition, recent technological advancements have made it possible to study epitranscriptomic RNA modifications, such as RNA N6-methyladenosine (m6A), and a handful of recent studies have begun to explore epitranscriptomics in PD-relevant exposure models. Continued exploration of epitranscriptomic mechanisms in environmentally relevant PD models offers the opportunity to identify biomarkers, pre-degenerative changes that precede symptom onset, and potential mitigation strategies for disease prevention and treatment.
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Affiliation(s)
- John T. Gionco
- Graduate Program in Cell and Developmental Biology, Rutgers University, Piscataway, NJ, USA
| | - Alison I. Bernstein
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NJ, USA
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ, USA
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22
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Hu YX, Diao LT, Hou YR, Lv G, Tao S, Xu WY, Xie SJ, Ren YH, Xiao ZD. Pseudouridine synthase 1 promotes hepatocellular carcinoma through mRNA pseudouridylation to enhance the translation of oncogenic mRNAs. Hepatology 2023:01515467-990000000-00664. [PMID: 38015993 DOI: 10.1097/hep.0000000000000702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND AND AIMS Pseudouridine is a prevalent RNA modification and is highly present in the serum and urine of patients with HCC. However, the role of pseudouridylation and its modifiers in HCC remains unknown. We investigated the function and underlying mechanism of pseudouridine synthase 1 (PUS1) in HCC. APPROACH AND RESULTS By analyzing the TCGA data set, PUS1 was found to be significantly upregulated in human HCC specimens and positively correlated with tumor grade and poor prognosis of HCC. Knockdown of PUS1 inhibited cell proliferation and the growth of tumors in a subcutaneous xenograft mouse model. Accordingly, increased cell proliferation and tumor growth were observed in PUS1-overexpressing cells. Furthermore, overexpression of PUS1 significantly accelerates tumor formation in a mouse HCC model established by hydrodynamic tail vein injection, while knockout of PUS1 decreases it. Additionally, PUS1 catalytic activity is required for HCC tumorigenesis. Mechanistically, we profiled the mRNA targets of PUS1 by utilizing surveying targets by apolipoprotein B mRNA-editing enzyme 1 (APOBEC1)-mediated profiling and found that PUS1 incorporated pseudouridine into mRNAs of a set of oncogenes, thereby endowing them with greater translation capacity. CONCLUSIONS Our study highlights the critical role of PUS1 and pseudouridylation in HCC development, and provides new insight that PUS1 enhances the protein levels of a set of oncogenes, including insulin receptor substrate 1 (IRS1) and c-MYC, by means of pseudouridylation-mediated mRNA translation.
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Affiliation(s)
- Yan-Xia Hu
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Li-Ting Diao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Ya-Rui Hou
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Guo Lv
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Shuang Tao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Wan-Yi Xu
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Shu-Juan Xie
- Institute of Vaccine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Ya-Han Ren
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Zhen-Dong Xiao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
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23
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Liu T, Gu J, Li C, Guo M, Yuan L, Lv Q, Qin C, Du M, Chu H, Liu H, Zhang Z. Alternative polyadenylation-related genetic variants contribute to bladder cancer risk. J Biomed Res 2023; 37:405-417. [PMID: 37936490 PMCID: PMC10687529 DOI: 10.7555/jbr.37.20230063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 11/09/2023] Open
Abstract
Aberrant alternative polyadenylation (APA) events play an important role in cancers, but little is known about whether APA-related genetic variants contribute to the susceptibility to bladder cancer. Previous genome-wide association study performed APA quantitative trait loci (apaQTL) analyses in bladder cancer, and identified 17 955 single nucleotide polymorphisms (SNPs). We found that gene symbols of APA affected by apaQTL-associated SNPs were closely correlated with cancer signaling pathways, high mutational burden, and immune infiltration. Association analysis showed that apaQTL-associated SNPs rs34402449 C>A, rs2683524 C>T, and rs11540872 C>G were significantly associated with susceptibility to bladder cancer (rs34402449: OR = 1.355, 95% confidence interval [CI]: 1.159-1.583, P = 1.33 × 10 -4; rs2683524: OR = 1.378, 95% CI: 1.164-1.632, P = 2.03 × 10 -4; rs11540872: OR = 1.472, 95% CI: 1.193-1.815, P = 3.06 × 10 -4). Cumulative effect analysis showed that the number of risk genotypes and smoking status were significantly associated with an increased risk of bladder cancer ( P trend = 2.87 × 10 -12). We found that PRR13, being demonstrated the most significant effect on cell proliferation in bladder cancer cell lines, was more highly expressed in bladder cancer tissues than in adjacent normal tissues. Moreover, the rs2683524 T allele was correlated with shorter 3' untranslated regions of PRR13 and increased PRR13 expression levels. Collectively, our findings have provided informative apaQTL resources and insights into the regulatory mechanisms linking apaQTL-associated variants to bladder cancer risk.
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Affiliation(s)
- Ting Liu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jingjing Gu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Chuning Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Mengfan Guo
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Lin Yuan
- Department of Urology, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu 210029, China
| | - Qiang Lv
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Chao Qin
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Hanting Liu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
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24
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Tsao N, Ashour ME, Mosammaparast N. How RNA impacts DNA repair. DNA Repair (Amst) 2023; 131:103564. [PMID: 37776841 PMCID: PMC11232704 DOI: 10.1016/j.dnarep.2023.103564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 10/02/2023]
Abstract
The central dogma of molecular biology posits that genetic information flows unidirectionally, from DNA, to RNA, and finally to protein. However, this directionality is broken in some cases, such as reverse transcription where RNA is converted to DNA by retroviruses and certain transposable elements. Our genomes have evolved and adapted to the presence of reverse transcription. Similarly, our genome is continuously maintained by several repair pathways to reverse damage due to various endogenous and exogenous sources. More recently, evidence has revealed that RNA, while in certain contexts may be detrimental for genome stability, is involved in promoting certain types of DNA repair. Depending on the pathway in question, the size of these DNA repair-associated RNAs range from one or a few ribonucleotides to long fragments of RNA. Moreover, RNA is highly modified, and RNA modifications have been revealed to be functionally associated with specific DNA repair pathways. In this review, we highlight aspects of this unexpected layer of genomic maintenance, demonstrating how RNA may influence DNA integrity.
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Affiliation(s)
- Ning Tsao
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mohamed E Ashour
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Division of Laboratory and Genomic Medicine, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA.
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25
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Varenyk Y, Spicher T, Hofacker IL, Lorenz R. Modified RNAs and predictions with the ViennaRNA Package. Bioinformatics 2023; 39:btad696. [PMID: 37971965 PMCID: PMC10676514 DOI: 10.1093/bioinformatics/btad696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/24/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023] Open
Abstract
MOTIVATION In living organisms, many RNA molecules are modified post-transcriptionally. This turns the widely known four-letter RNA alphabet ACGU into a much larger one with currently more than 300 known distinct modified bases. The roles for the majority of modified bases remain uncertain, but many are already well-known for their ability to influence the preferred structures that an RNA may adopt. In fact, tRNAs sometimes require certain modifications to fold into their cloverleaf shaped structure. However, predicting the structure of RNAs with base modifications is still difficult due to the lack of efficient algorithms that can deal with the extended sequence alphabet, as well as missing parameter sets that account for the changes in stability induced by the modified bases. RESULTS We present an approach to include sparse energy parameter data for modified bases into the ViennaRNA Package. Our method does not require any changes to the underlying efficient algorithms but instead uses a set of plug-in constraints that adapt the predictions in terms of loop evaluation at runtime. These adaptations are efficient in the sense that they are only performed for loops where additional parameters are actually available for. In addition, our approach also facilitates the inclusion of more modified bases as soon as further parameters become available. AVAILABILITY AND IMPLEMENTATION Source code and documentation are available at https://www.tbi.univie.ac.at/RNA.
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Affiliation(s)
- Yuliia Varenyk
- Department of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Thomas Spicher
- Department of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
- UniVie Doctoral School Computer Science (DoCS), University of Vienna, Vienna 1090, Austria
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna 1090, Austria
| | - Ronny Lorenz
- Department of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
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26
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Yang X, Cao D. DXO gears mRNA with alternative NAD and m 7G caps. TRENDS IN PLANT SCIENCE 2023; 28:1083-1085. [PMID: 37357082 DOI: 10.1016/j.tplants.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/27/2023]
Abstract
NAD is a noncanonical mRNA cap that challenges our traditional dogma of N7-methylguanosine (m7G)-capped eukaryotic mRNAs. The relationship between NAD and m7G caps has been elusive. Xiao et al. find that the deNADding enzyme DXO promotes maturation of m7G caps, suggesting that DXO fine-tunes the dynamic balance between alternative RNA cap structures.
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Affiliation(s)
- Xiaofei Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Dechang Cao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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27
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Chen Y, Lai Y, Liu R, Yao L, Yu XQ, Wang X. Transcriptome-wide analysis of mRNA N 6 -methyladenosine modification in the embryonic development of Spodoptera frugiperda. INSECT SCIENCE 2023; 30:1229-1244. [PMID: 36606528 DOI: 10.1111/1744-7917.13172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/17/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
N6 -methyladenosine (m6 A) RNA is the most abundant modification of mRNA, and has been demonstrated in regulating various post-transcriptional processes. Many studies have shown that m6 A methylation plays key roles in sex determination, neuronal functions, and embryonic development in Drosophila and mammals. Here, we analyzed transcriptome-wide profile of m6 A modification in the embryonic development of the destructive agricultural pest Spodoptera frugiperda. We found that the 2 key mRNA m6 A methyltransferases SfrMETTL3 and SfrMETTL14 have high homologies with other insects and mammals, suggesting that SfrMETTL3 and SfrMETTL14 may have conserved function among different species. From methylated RNA immunoprecipitation sequencing analysis, we obtained 46 869 m6 A peaks representing 8 587 transcripts in the 2-h embryos after oviposition, and 41 389 m6 A peaks representing 9 230 transcripts in the 24-h embryos. In addition, 5 995 m6 A peaks were differentially expressed including 3 752 upregulated and 2243 downregulated peaks. Functional analysis with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes suggested that differentially expressed m6 A peak-modified genes were enriched in cell and organ development between the 2- and 24-h embryos. By conjoint analysis of methylated RNA immunoprecipitation-seq and RNA-seq data, we found that RNA m6 A methylation may regulate the transcriptional levels of genes related to tissue and organ development from 2- to 24-h embryos. Our study reveals the role of RNA m6 A epigenetic regulation in the embryonic development of S. frugiperda, and provides new insights for the embryonic development of insects.
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Affiliation(s)
- Yaqing Chen
- 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, China
| | - Yushan Lai
- 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, China
| | - Runzhou Liu
- 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, China
| | - Lin Yao
- 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, China
| | - Xiao-Qiang Yu
- 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, China
| | - Xiaoyun Wang
- 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, China
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28
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Ning N, Luo D, Xia W, Mou G, Zhao J, Zhang J, Li C, Wang H, Li J. Dysregulation of TMEM16A impairs oviductal transport of embryos. Am J Physiol Cell Physiol 2023; 325:C623-C632. [PMID: 37458439 DOI: 10.1152/ajpcell.00031.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 08/25/2023]
Abstract
Ectopic pregnancy is an acute abdominalgia in obstetrics and gynecology, especially in fallopian tubal pregnancy. The ion channel protein transmembrane protein 16A (TMEM16A) is widely distributed in various tissues, even in the oviduct. In this study, we showed that TMEM16A was expressed in the human fallopian tube and was upregulated in patients with tubal pregnancy. By measuring isolated fallopian tube tissues, we found that TMEM16A was involved in regulating not only the contraction of muscle strips but also the beat frequency of cilia. In addition, pharmacological activation or inhibition of TMEM16A could lead to retention of embryos in oviducts. Moreover, the embryos in oviducts were delayed in development and some of them had malformations and deletions. The total number of embryos in the oviducts and uterus was significantly less than that of the control group. Furthermore, we detected changes in the level of m6A methylation, where the relevant writers and readers were reduced in tubal tissues from tubal pregnancies. In m6A mRNA methylation, writers catalyze the addition of methyl groups to cytosine residues and readers bind to the methyl groups and affect gene translation. In human fallopian tube epithelial cell line FTE187, we found that interference with methyltransferase 3 (METTL3) expression increased TMEM16A, suggesting that TMEM16A might be regulated by m6A methylation. In general, our study revealed a novel regulatory point for embryo transport and development, introducing a new role for the diagnosis and treatment of tubal pregnancy.NEW & NOTEWORTHY The ion channel protein TMEM16A is expressed in the epithelium and smooth muscle of the human fallopian tube and is upregulated in patients with tubal pregnancy. TMEM16A is involved in regulating the smooth muscle contraction and the cilia beating. Dysregulated TMEM16A may result in embryo retention in the oviduct and delayed early embryo development. Our study reveals a new regulatory point for embryo transport and development.
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Affiliation(s)
- Nannan Ning
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, People's Republic of China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, People's Republic of China
| | - Dan Luo
- Department of Breast Surgery, Qilu Hospital of Shandong University, Jinan, People's Republic of China
| | - Wei Xia
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, People's Republic of China
- Shanghai Key Laboratory Embryo Original Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Guangjing Mou
- Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Jiangli Zhao
- Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Jian Zhang
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - Cheng Li
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, People's Republic of China
| | - Hongchun Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, People's Republic of China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, People's Republic of China
| | - Jingxin Li
- Department of Physiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
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Ahmadi Ghezeldasht S, Bidkhori HR, Miri R, Baghban A, Mosavat A, Rezaee SA. Momordica charantia phytoconstituents can inhibit human T-lymphotropic virus type-1 (HTLV-1) infectivity in vitro and in vivo. J Neurovirol 2023:10.1007/s13365-023-01160-0. [PMID: 37531001 DOI: 10.1007/s13365-023-01160-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/04/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
There is an urgent need to find an effective therapy for life-threatening HTLV-1-associated diseases. Bitter melon (Momordica charantia) is considered a traditional herb with antiviral and anticancer properties and was tested in this study on HTLV-1 infectivity. GC-MS analyzed the alcoholic extract. In vitro assay was carried out using transfection of HUVEC cells by HTLV-1-MT2 cell line. The cells were exposed to alcoholic and aqueous extracts at 5,10, and 20 µg/mL concentrations. In vivo, mice were divided into four groups. Three groups were treated with HTLV-1-MT-2 cells as test groups and positive control, and PBS as the negative control group in the presence and absence of M. charantia extracts. Peripheral blood mononuclear cells (PBMCs), mesenteric lymph nodes (MLNs), and splenocytes were collected for HTLV-1-proviral load (PVL) assessment, TaqMan-qPCR. The GC-MS analysis revealed 36 components in M. charantia. The studies showed significant reductions in HTLV-1-PVL in the presence of extract in the HUVEC-treated groups (P = 0.001). Furthermore, the inhibitory effects of extracts on HTLV-1 infected mice showed significant differences in HTLV-1-PVL among M. charantia treated groups with untreated (P = 0.001). The T-cells in MLNs were significantly more susceptible to HTLV-1 than others (P = 0.001). There were significant differences among HTLV-1-infected cells in MLNs and splenocytes (P = 0.001 and 0.046, respectively). Also, aqueous and alcoholic extract-treated groups significantly affected HTLV-1-infected PBMCs (P = 0.002 and 0.009, respectively). M. charantia may have effective antiviral properties. The substantial compound of M. charantia could have inhibitory effects on the proliferation and transmission of HTLV-1 oncovirus.
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Affiliation(s)
- Sanaz Ahmadi Ghezeldasht
- Blood Borne Infections Research Center, Academic Center for Education, Culture and Research (ACECR), Azadi-Square, Ferdowsi University Campus, Razavi Khorasan, Mashhad, 9177949367, Iran
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Reza Bidkhori
- Stem Cells and Regenerative Medicine Department, Academic Center for Education, Culture and Research (ACECR), Razavi Khorasan, Mashhad, Iran
| | - Raheleh Miri
- Blood Borne Infections Research Center, Academic Center for Education, Culture and Research (ACECR), Azadi-Square, Ferdowsi University Campus, Razavi Khorasan, Mashhad, 9177949367, Iran
| | - Arezoo Baghban
- Department of Chemistry, Faculty of Science, Azad University of Mashhad, Mashhad, Iran
| | - Arman Mosavat
- Blood Borne Infections Research Center, Academic Center for Education, Culture and Research (ACECR), Azadi-Square, Ferdowsi University Campus, Razavi Khorasan, Mashhad, 9177949367, Iran.
| | - Seyed Abdolrahim Rezaee
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran.
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Faculty of Medicine, Mashhad University of Medical Sciences, Azadi-Square, Medical Campus, 9177948564, Mashhad, Iran.
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Luo Z, Ma Q, Sun S, Li N, Wang H, Ying Z, Ke S. Exon-intron boundary inhibits m 6A deposition, enabling m 6A distribution hallmark, longer mRNA half-life and flexible protein coding. Nat Commun 2023; 14:4172. [PMID: 37443320 PMCID: PMC10345190 DOI: 10.1038/s41467-023-39897-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Regional bias of N6-methyladenosine (m6A) mRNA modification avoiding splice site region, calls for an open hypothesis whether exon-intron boundary could affect m6A deposition. By deep learning modeling, we find that exon-intron boundary represses a proportion (12% to 34%) of m6A deposition at adjacent exons (~100 nt to splice site). Experiments validate that m6A signal increases once the host gene does not undergo pre-mRNA splicing to produce the same mRNA. Inhibited m6A sites have higher m6A enhancers and lower m6A silencers locally and show high heterogeneity at different exons genome-widely, with only a small proportion (12% to 15%) of exons showing strong inhibition, enabling more stable mRNAs and flexible protein coding. m6A is majorly responsible for why mRNAs with more exons be more stable. Exon junction complex (EJC) only partially contributes to this exon-intron boundary m6A inhibition in some short internal exons, highlighting additional factors yet to be identified.
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Affiliation(s)
- Zhiyuan Luo
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Qilian Ma
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Shan Sun
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Ningning Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Hongfeng Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zheng Ying
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Shengdong Ke
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
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Li Y, Yi Y, Lv J, Gao X, Yu Y, Babu S, Bruno I, Zhao D, Xia B, Peng W, Zhu J, Chen H, Zhang L, Cao Q, Chen K. Low RNA stability signifies increased post-transcriptional regulation of cell identity genes. Nucleic Acids Res 2023; 51:6020-6038. [PMID: 37125636 PMCID: PMC10325912 DOI: 10.1093/nar/gkad300] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023] Open
Abstract
Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g. by super-enhancers and broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m6A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains and their associated genes. METTL3 binding intensity is positively correlated with RNA m6A methylation and negatively correlated with RNA stability of cell identity genes, probably due to co-transcriptional m6A modifications promoting RNA decay. Nanopore direct RNA-sequencing showed that METTL3 knockdown has a stronger effect on RNA m6A and mRNA stability for cell identity genes. Our data suggest a run-and-brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression.
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Affiliation(s)
- Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yi
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jie Lv
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yu
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sahana Suresh Babu
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Ivone Bruno
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Dongyu Zhao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Bo Xia
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC 20052, USA
| | - Jun Zhu
- Systems Biology Center, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Hong Chen
- Vascular Biology Program, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
- Broad Institute of MIT and Harvard, Boston, MA 02115, USA
- Dana-Farber/Harvard Cancer Center, Boston, MA 02115, USA
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32
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Xiao YL, Liu S, Ge R, Wu Y, He C, Chen M, Tang W. Transcriptome-wide profiling and quantification of N 6-methyladenosine by enzyme-assisted adenosine deamination. Nat Biotechnol 2023; 41:993-1003. [PMID: 36593412 PMCID: PMC10625715 DOI: 10.1038/s41587-022-01587-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/24/2022] [Indexed: 01/03/2023]
Abstract
N6-methyladenosine (m6A), the most abundant internal messenger RNA modification in higher eukaryotes, serves myriad roles in regulating cellular processes. Functional dissection of m6A is, however, hampered in part by the lack of high-resolution and quantitative detection methods. Here we present evolved TadA-assisted N6-methyladenosine sequencing (eTAM-seq), an enzyme-assisted sequencing technology that detects and quantifies m6A by global adenosine deamination. With eTAM-seq, we analyze the transcriptome-wide distribution of m6A in HeLa and mouse embryonic stem cells. The enzymatic deamination route employed by eTAM-seq preserves RNA integrity, facilitating m6A detection from limited input samples. In addition to transcriptome-wide m6A profiling, we demonstrate site-specific, deep-sequencing-free m6A quantification with as few as ten cells, an input demand orders of magnitude lower than existing quantitative profiling methods. We envision that eTAM-seq will enable researchers to not only survey the m6A landscape at unprecedented resolution, but also detect m6A at user-specified loci with a simple workflow.
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Affiliation(s)
- Yu-Lan Xiao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Ruiqi Ge
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Yuan Wu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
| | - Mengjie Chen
- Department of Medicine, The University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
| | - Weixin Tang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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33
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Abstract
Chemical modifications on mRNA represent a critical layer of gene expression regulation. Research in this area has continued to accelerate over the last decade, as more modifications are being characterized with increasing depth and breadth. mRNA modifications have been demonstrated to influence nearly every step from the early phases of transcript synthesis in the nucleus through to their decay in the cytoplasm, but in many cases, the molecular mechanisms involved in these processes remain mysterious. Here, we highlight recent work that has elucidated the roles of mRNA modifications throughout the mRNA life cycle, describe gaps in our understanding and remaining open questions, and offer some forward-looking perspective on future directions in the field.
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Affiliation(s)
- Wendy V Gilbert
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA;
| | - Sigrid Nachtergaele
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA;
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34
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Li L, Zhu C, Xu S, Xu Q, Xu D, Gan S, Cui X, Tang C. PUS1 is a novel biomarker for evaluating malignancy of human renal cell carcinoma. Aging (Albany NY) 2023; 15:204799. [PMID: 37315299 PMCID: PMC10292901 DOI: 10.18632/aging.204799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023]
Abstract
Renal cell carcinoma (RCC) is one of the most common malignancies. Despite the rapid development of the oncology research and surgical treatment, the prognosis of RCC has not significantly improved. Thus, exploration of the pathological molecular mechanism and development of new therapeutic targets of RCC are of great importance. Herein, by bioinformatic analysis and in vitro cell experiments, we report that, the expression of pseudouridine synthase 1 (PUS1), belonging to the family of PUS enzymes that participate in RNA modifications, is closely associated with RCC progression. In addition, the upregulated PUS1 expression results in the elevated RCC cancer cell viability, migration, invasion and colony formation ability, whereas the decreased PUS1 expression exerts the opposite effects on RCC cells. Thus, our findings show the potential role of PUS1 in RCC cells, providing with evidence that PUS1 is involved in RCC progression, which may help contribute to RCC diagnosis and intervention in clinic.
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Affiliation(s)
- Lin Li
- National Clinical Research Center for Child Health of the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai 201805, China
| | - Chongying Zhu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Shouying Xu
- National Clinical Research Center for Child Health of the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Qiang Xu
- National Clinical Research Center for Child Health of the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Da Xu
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai 201805, China
| | - Sishun Gan
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai 201805, China
| | - Xingang Cui
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, China
| | - Chao Tang
- National Clinical Research Center for Child Health of the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
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35
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Yu L, Zhang Y, Xue L, Liu F, Jing R, Luo J. Evaluation and development of deep neural networks for RNA 5-Methyluridine classifications using autoBioSeqpy. Front Microbiol 2023; 14:1175925. [PMID: 37275146 PMCID: PMC10232852 DOI: 10.3389/fmicb.2023.1175925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023] Open
Abstract
Post-transcriptionally RNA modifications, also known as the epitranscriptome, play crucial roles in the regulation of gene expression during development. Recently, deep learning (DL) has been employed for RNA modification site prediction and has shown promising results. However, due to the lack of relevant studies, it is unclear which DL architecture is best suited for some pyrimidine modifications, such as 5-methyluridine (m5U). To fill this knowledge gap, we first performed a comparative evaluation of various commonly used DL models for epigenetic studies with the help of autoBioSeqpy. We identified optimal architectural variations for m5U site classification, optimizing the layer depth and neuron width. Second, we used this knowledge to develop Deepm5U, an improved convolutional-recurrent neural network that accurately predicts m5U sites from RNA sequences. We successfully applied Deepm5U to transcriptomewide m5U profiling data across different sequencing technologies and cell types. Third, we showed that the techniques for interpreting deep neural networks, including LayerUMAP and DeepSHAP, can provide important insights into the internal operation and behavior of models. Overall, we offered practical guidance for the development, benchmark, and analysis of deep learning models when designing new algorithms for RNA modifications.
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Affiliation(s)
- Lezheng Yu
- School of Chemistry and Materials Science, Guizhou Education University, Guiyang, China
| | - Yonglin Zhang
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Li Xue
- School of Public Health, Southwest Medical University, Luzhou, China
| | - Fengjuan Liu
- School of Geography and Resources, Guizhou Education University, Guiyang, China
| | - Runyu Jing
- School of Cyber Science and Engineering, Sichuan University, Chengdu, China
| | - Jiesi Luo
- Basic Medical College, Southwest Medical University, Luzhou, China
- Sichuan Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Southwest Medical University, Luzhou, China
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36
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Liu Y, Yang D, Liu T, Chen J, Yu J, Yi P. N6-methyladenosine-mediated gene regulation and therapeutic implications. Trends Mol Med 2023; 29:454-467. [PMID: 37068987 DOI: 10.1016/j.molmed.2023.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/11/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023]
Abstract
N6-methyladenosine (m6A) RNA methylation is the most abundant form of mRNA modification in eukaryotes and is at the front line of biological and biomedical research. This dynamic and reversible m6A RNA modification determines the fates of modified RNA molecules at the post-transcriptional level, affecting almost all important biological processes. Notably, m6A is also involved in chromatin and transcriptional regulation, while m6A dysregulation is implicated in various diseases. Here, we review current knowledge of post-transcriptional and transcriptional regulatory mechanisms involving m6A modification. We also discuss their involvement in the occurrence and development of diseases, including cancer, as well as potential theranostic targets, in hope of facilitating the translation of preclinical findings to the clinic.
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Affiliation(s)
- Yujiao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Dan Yang
- 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
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Los Angeles, CA 91010, USA
| | - Jianhua Yu
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA.
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China.
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Hesser CR, Walsh D. YTHDF2 Is Downregulated in Response to Host Shutoff Induced by DNA Virus Infection and Regulates Interferon-Stimulated Gene Expression. J Virol 2023; 97:e0175822. [PMID: 36916936 PMCID: PMC10062140 DOI: 10.1128/jvi.01758-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 03/15/2023] Open
Abstract
Recent studies have begun to reveal the complex and multifunctional roles of N6-methyladenosine (m6A) modifications and their associated writer, reader, and eraser proteins in infection by diverse RNA and DNA viruses. However, little is known about their regulation and functions during infection by several viruses, including poxviruses. Here, we show that members of the YTH Domain Family (YTHDF), in particular YTHDF2, are downregulated as the prototypical poxvirus, vaccinia virus (VacV) enters later stages of replication in a variety of natural target cell types, but not in commonly used transformed cell lines wherein the control of YTHDF2 expression appears to be dysregulated. YTHDF proteins also decreased at late stages of infection by herpes simplex virus 1 (HSV-1) but not human cytomegalovirus, suggesting that YTHDF2 is downregulated in response to infections that induce host shutoff. In line with this idea, YTHDF2 was potently downregulated upon infection with a VacV mutant expressing catalytically inactive forms of the decapping enzymes, D9 and D10, which fails to degrade dsRNA and induces a protein kinase R response that itself inhibits protein synthesis. Overexpression and RNAi-mediated depletion approaches further demonstrate that YTHDF2 does not directly affect VacV replication. Instead, experimental downregulation of YTHDF2 or the related family member, YTHDF1, induces a potent increase in interferon-stimulated gene expression and establishes an antiviral state that suppresses infection by either VacV or HSV-1. Combined, our data suggest that YTHDF2 is destabilized in response to infection-induced host shutoff and serves to augment host antiviral responses. IMPORTANCE There is increasing recognition of the importance of N6-methyladenosine (m6A) modifications to both viral and host mRNAs and the complex roles this modification plays in determining the fate of infection by diverse RNA and DNA viruses. However, in many instances, the functional contributions and importance of specific m6A writer, reader, and eraser proteins remains unknown. Here, we show that natural target cells but not transformed cell lines downregulate the YTH Domain Family (YTHDF) of m6A reader proteins, in particular YTHDF2, in response to shutoff of protein synthesis upon infection with the large DNA viruses, vaccinia virus (VacV), or herpes simplex virus type 1. We further reveal that YTHDF2 downregulation also occurs as part of the host protein kinase R response to a VacV shutoff mutant and that this downregulation of YTHDF family members functions to enhance interferon-stimulated gene expression to create an antiviral state.
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Affiliation(s)
- Charles R. Hesser
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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38
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Ren W, Yuan Y, Li Y, Mutti L, Peng J, Jiang X. The function and clinical implication of YTHDF1 in the human system development and cancer. Biomark Res 2023; 11:5. [PMID: 36650570 PMCID: PMC9847098 DOI: 10.1186/s40364-023-00452-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/26/2022] [Indexed: 01/19/2023] Open
Abstract
YTHDF1 is a well-characterized m6A reader protein that is essential for protein translation, stem cell self-renewal, and embryonic development. YTHDF1 regulates target gene expression by diverse molecular mechanisms, such as promoting protein translation or modulating the stability of mRNA. The cellular levels of YTHDF1 are precisely regulated by a complicated transcriptional, post-transcriptional, and post-translational network. Very solid evidence supports the pivotal role of YTHDF1 in embryonic development and human cancer progression. In this review, we discuss how YTHDF1 influences both the physiological and pathological biology of the central nervous, reproductive and immune systems. Therefore we focus on some relevant aspects of the regulatory role played by YTHDF1 as gene expression, complex cell networking: stem cell self-renewal, embryonic development, and human cancers progression. We propose that YTHDF1 is a promising future cancer biomarker for detection, progression, and prognosis. Targeting YTHDF1 holds therapeutic potential, as the overexpression of YTHDF1 is associated with tumor resistance to chemotherapy and immunotherapy.
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Affiliation(s)
- Wenjun Ren
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Yixiao Yuan
- grid.452206.70000 0004 1758 417XKey Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yongwu Li
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Luciano Mutti
- grid.264727.20000 0001 2248 3398Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122 USA ,grid.158820.60000 0004 1757 2611Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2 67100 L’Aquila, Italy
| | - Jun Peng
- grid.414918.1Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan China
| | - Xiulin Jiang
- grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049 China
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Genetically encoded chemical crosslinking of RNA in vivo. Nat Chem 2023; 15:21-32. [PMID: 36202986 PMCID: PMC9840682 DOI: 10.1038/s41557-022-01038-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/08/2022] [Indexed: 01/17/2023]
Abstract
Protein-RNA interactions regulate RNA fate and function, and defects can lead to various disorders. Such interactions have mainly been studied by nucleoside-based UV crosslinking methods, which lack broad in vivo compatibility and the ability to resolve specific amino acids. In this study we genetically encoded latent bioreactive unnatural amino acids into proteins to react with bound RNA by proximity-enabled reactivity and demonstrated genetically encoded chemical crosslinking of proteins with target RNA (GECX-RNA) in vivo. Applying GECX-RNA to the RNA chaperone Hfq in Escherichia coli identified target RNAs with amino acid specificity. Combining GECX-RNA with immunoprecipitation and high-throughput sequencing of an N6-methyladenosine reader protein in mammalian cells allowed the in vivo identification of unknown N6-methyladenosine on RNA with single-nucleotide resolution throughout the transcriptome. GECX-RNA thus affords resolution at the nucleotide and amino acid level for interrogating protein-RNA interactions in vivo. It also enables the precise engineering of covalent linkages between a protein and RNA, which will inspire innovative solutions for RNA-related research and therapeutics.
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40
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Abstract
Methyltransferase-like protein 16 (METTL16) is one of four catalytically active, S-adenosylmethionine (SAM)-dependent m6A RNA methyltransferases in humans. Well-known methylation targets of METTL16 are U6 small nuclear RNA (U6 snRNA) and the MAT2A mRNA hairpins; however, METTL16 binds to other RNAs, including the 3' triple helix of the metastasis-associated lung adenocarcinoma transcript 1 (MALAT1). Herein, we investigated the kinetic mechanism and biochemical properties of METTL16. METTL16 is a monomer in complex with either the MALAT1 triple helix or U6 snRNA and binds to these RNAs with respective dissociation constants of 31 nM and 18 nM, whereas binding to the methylated U6 snRNA product is 1.1 μM. The MALAT1 triple helix, on the other hand, is not methylated by METTL16 under in vitro conditions. Using the U6 snRNA to study methylation steps, preincubation and isotope partitioning assays indicated an ordered-sequential mechanism, whereby METTL16 binds U6 snRNA before SAM. The apparent dissociation constant for the METTL16·U6 snRNA·SAM ternary complex is 126 μM. Steady-state kinetic assays established a kcat of 0.07 min-1, and single-turnover assays established a kchem of 0.56 min-1. Furthermore, the methyltransferase domain of METTL16 methylated U6 snRNA with an apparent dissociation constant of 736 μM and a kchem of 0.42 min-1, suggesting that the missing vertebrate conserved regions weaken the ternary complex but do not induce any rate-limiting conformational rearrangements of the U6 snRNA. This study helps us to better understand the catalytic activity of METTL16 in the context of its biological functions.
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41
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Du Y, Xia M, Hu Z. Analysis of N 6 -methyladenosine RNA Modification Levels by Dot Blotting. Bio Protoc 2022; 12:e4565. [PMID: 36561121 PMCID: PMC9729852 DOI: 10.21769/bioprotoc.4565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/13/2022] [Accepted: 10/17/2022] [Indexed: 12/08/2022] Open
Abstract
N 6 -methyladenosine (m 6 A) is the most prevalent internal modification of eukaryotic messenger RNAs (mRNAs), affecting their fold, stability, degradation, and cellular interaction(s) and implicating them in processes such as splicing, translation, export, and decay. The m 6 A modification is also extensively present in non-coding RNAs, including microRNAs (miRNAs), ribosomal RNAs (rRNAs), and transfer RNAs (tRNAs). Common m 6 A methylation detection techniques play an important role in understanding the biological function and potential mechanism of m 6 A, mainly including the quantification and specific localization of m 6 A modification sites. Here, we describe in detail the dot blotting method for detecting m 6 A levels in RNA (mRNA as an example), including total RNA extraction, mRNA purification, dot blotting, and data analysis. This protocol can also be used to enrich specific RNAs (such as tRNA, rRNA, or miRNA) by isolation technology to detect the m 6 A level of single RNA species, so as to facilitate further studies of the role of m 6 A in biological processes. This protocol was validated in: eLife (2022), DOI: 10.7554/eLife.75231.
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Affiliation(s)
- Yu Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Mingyue Xia
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
,
*For correspondence:
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Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Deciphering cancer etiopathogenesis has proven to be an especially challenging task since the mechanisms that drive tumor development and progression are far from simple. An astonishing amount of research has revealed a wide spectrum of defects, including genomic abnormalities, epigenomic alterations, disturbance of gene transcription, as well as post-translational protein modifications, which cooperatively promote carcinogenesis. These findings suggest that the adoption of a multidimensional approach can provide a much more precise and comprehensive picture of the tumor landscape, hence serving as a powerful tool in cancer research and precision oncology. The introduction of next- and third-generation sequencing technologies paved the way for the decoding of genetic information and the elucidation of cancer-related cellular compounds and mechanisms. In the present review, we discuss the current and emerging applications of both generations of sequencing technologies, also referred to as massive parallel sequencing (MPS), in the fields of cancer genomics, transcriptomics and proteomics, as well as in the progressing realms of epi-omics. Finally, we provide a brief insight into the expanding scope of sequencing applications in personalized cancer medicine and pharmacogenomics.
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43
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Hong J, Xu K, Lee JH. Biological roles of the RNA m 6A modification and its implications in cancer. Exp Mol Med 2022; 54:1822-1832. [PMID: 36446846 PMCID: PMC9722703 DOI: 10.1038/s12276-022-00897-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/30/2022] Open
Abstract
The N6-Methyladenosine (m6A) modification of RNA transcripts is the most prevalent and abundant internal modification in eukaryotic messenger RNAs (mRNAs) and plays diverse and important roles in normal biological processes. Extensive studies have indicated that dysregulated m6A modification and m6A-associated proteins play critical roles in tumorigenesis and cancer progression. However, m6A-mediated physiological consequences often lead to opposite outcomes in a biological context-dependent manner. Therefore, context-related complexity must be meaningfully considered to obtain a comprehensive understanding of RNA methylation. Recently, it has been reported that m6A-modified RNAs are closely related to the regulation of the DNA damage response and genomic integrity maintenance. Here, we present an overview of the current knowledge on the m6A modification and its function in human cancer, particularly in relation to the DNA damage response and genomic instability.
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Affiliation(s)
- Juyeong Hong
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Kexin Xu
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Ji Hoon Lee
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
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Li W, Deng X, Chen J. RNA-binding proteins in regulating mRNA stability and translation: roles and mechanisms in cancer. Semin Cancer Biol 2022; 86:664-677. [PMID: 35381329 PMCID: PMC9526761 DOI: 10.1016/j.semcancer.2022.03.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/10/2023]
Abstract
RNA-binding proteins (RBPs) are key players in cellular physiology through posttranscriptional regulation of the expression of target RNA transcripts. By modulating the processing, stability and translation of cancer-related messenger RNA (mRNA) transcripts, a large set of RBPs play essential roles in various types of cancers. Perturbations in RBP activity have been causally associated with cancer development, tumor metabolism, drug resistance, cancer stem cell self-renewal, and tumor immune evasion. Here, we summarize the recent advances in cancer pathological roles and mechanisms of RBPs in regulating mRNA stability and translation with an emphasis on the emerging category of RNA modification-associated RBPs. The functional diversity of RBPs in different types of cancers and the therapeutic potential of targeting dysregulated RBPs for cancer treatment are also discussed.
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Affiliation(s)
- Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA.
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45
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New insights into the epitranscriptomic control of pluripotent stem cell fate. Exp Mol Med 2022; 54:1643-1651. [PMID: 36266446 PMCID: PMC9636187 DOI: 10.1038/s12276-022-00824-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 12/29/2022] Open
Abstract
Each cell in the human body has a distinguishable fate. Pluripotent stem cells are challenged with a myriad of lineage differentiation options. Defects are more likely to be fatal to stem cells than to somatic cells due to the broad impact of the former on early development. Hence, a detailed understanding of the mechanisms that determine the fate of stem cells is needed. The mechanisms by which human pluripotent stem cells, although not fully equipped with complex chromatin structures or epigenetic regulatory mechanisms, accurately control gene expression and are important to the stem cell field. In this review, we examine the events driving pluripotent stem cell fate and the underlying changes in gene expression during early development. In addition, we highlight the role played by the epitranscriptome in the regulation of gene expression that is necessary for each fate-related event.
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46
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Wang S, Zhang L, Xuan R, Li Q, Ji Z, Chao T, Wang J, Zhang C. Identification and functional analysis of m6A in the mammary gland tissues of dairy goats at the early and peak lactation stages. Front Cell Dev Biol 2022; 10:945202. [PMID: 36330333 PMCID: PMC9623301 DOI: 10.3389/fcell.2022.945202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/04/2022] [Indexed: 12/01/2022] Open
Abstract
N6-methyladenosine (m6A) is the most common reversible epigenetic RNA modification in the mRNA of all higher eukaryotic organisms and plays an important role in the regulation of gene expression and cell function. In this study, m6A-modified methylated RNA immunoprecipitation sequencing (MeRIP-seq) and transcriptome sequencing (RNA-seq) were used to identify the key genes with m6A modification during mammary gland development and lactation in dairy goats. The results showed that m6A methylation occurred at 3,927 loci, which were significantly enriched in the 3′ untranslated region (3′UTR) and the termination codon region. In the early stage and peak stage of lactation, m6A methylation occurred extensively in mammary tissues, and a total of 725 differentially expressed m6A-modified genes were obtained, all negatively correlated with mRNA expression. In addition, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that different methylated genes were mainly involved in the growth and apoptosis of mammary epithelial cells through signaling pathways, such as the mitogen-activated protein kinase (MAPK) and phospholipase D pathways, and then affected the development and lactation of mammary gland. All in all, we identified and analyzed the methylation events related to the development and lactation regulation of mammary gland at the early and peak lactation stages, and provided a theoretical basis to reveal the physiological regulatory system of mammary gland development and lactation in dairy goats.
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Affiliation(s)
- Shujun Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Lu Zhang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Rong Xuan
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Qing Li
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Zhibin Ji
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
- *Correspondence: Zhibin Ji,
| | - Tianle Chao
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Jianmin Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Chunlan Zhang
- College of Biological and Agricultural Engineering, Weifang University, Weifang, China
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47
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Zha L, Wang J, Cheng X. The effects of
RNA
methylation on immune cells development and function. FASEB J 2022; 36:e22552. [DOI: 10.1096/fj.202200716r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/23/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Ling‐Feng Zha
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Jing‐Lin Wang
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Xiang Cheng
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
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Hao H, Liu W, Miao Y, Ma L, Yu B, Liu L, Yang C, Zhang K, Chen Z, Yang J, Zheng Z, Zhang B, Deng F, Gong P, Yuan J, Hu Z, Guan W. N4-acetylcytidine regulates the replication and pathogenicity of enterovirus 71. Nucleic Acids Res 2022; 50:9339-9354. [PMID: 35971620 PMCID: PMC9458434 DOI: 10.1093/nar/gkac675] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/06/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
Chemical modifications are important for RNA function and metabolism. N4-acetylcytidine (ac4C) is critical for the translation and stability of mRNA. Although ac4C is found in RNA viruses, the detailed mechanisms through which ac4C affects viral replication are unclear. Here, we reported that the 5' untranslated region of the enterovirus 71 (EV71) genome was ac4C modified by the host acetyltransferase NAT10. Inhibition of NAT10 and mutation of the ac4C sites within the internal ribosomal entry site (IRES) suppressed EV71 replication. ac4C enhanced viral RNA translation via selective recruitment of PCBP2 to the IRES and boosted RNA stability. Additionally, ac4C increased the binding of RNA-dependent RNA polymerase (3D) to viral RNA. Notably, ac4C-deficient mutant EV71 showed reduced pathogenicity in vivo. Our findings highlighted the essential role of ac4C in EV71 infection and provided insights into potential antiviral treatments.
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Affiliation(s)
- Haojie Hao
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China,College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China,Hanshan Normal University, Chaozhou 521041, China,Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Weichi Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Yuanjiu Miao
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Ma
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baocheng Yu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lishi Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunjie Yang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Kui Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Jingwen Yang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Zhenhua Zheng
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Bo Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Fei Deng
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Peng Gong
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Jianhui Yuan
- Correspondence may also be addressed to Jianhui Yuan.
| | - Zhangli Hu
- Correspondence may also be addressed to Zhangli Hu.
| | - Wuxiang Guan
- To whom correspondence should be addressed. Tel: +86 27 87197258; Fax: +86 27 87197258;
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49
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RNA Modifications in Gastrointestinal Cancer: Current Status and Future Perspectives. Biomedicines 2022; 10:biomedicines10081918. [PMID: 36009465 PMCID: PMC9405978 DOI: 10.3390/biomedicines10081918] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 01/05/2023] Open
Abstract
Gastrointestinal (GI) cancer, referring to cancers of the digestive system such as colorectal cancer (CRC), gastric cancer (GC), and liver cancer, is a major cause of cancer-related deaths in the world. A series of genetic, epigenetic, and epitranscriptomic changes occur during the development of GI cancer. The identification of these molecular events provides potential diagnostic, prognostic, and therapeutic targets for cancer patients. RNA modification is required in the posttranscriptional regulation of RNA metabolism, including splicing, intracellular transport, degradation, and translation. RNA modifications such as N6-methyladenosine (m6A) and N1-methyladenosine (m1A) are dynamically regulated by three different types of regulators named methyltransferases (writers), RNA binding proteins (readers), and demethylases (erasers). Recent studies have pointed out that abnormal RNA modification contributes to GI tumorigenesis and progression. In this review, we summarize the latest findings on the functional significance of RNA modification in GI cancer and discuss the therapeutic potential of epitranscriptomic inhibitors for cancer treatment.
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50
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Yang Q, Ciebiera M, Bariani MV, Ali M, Elkafas H, Boyer TG, Al-Hendy A. Comprehensive Review of Uterine Fibroids: Developmental Origin, Pathogenesis, and Treatment. Endocr Rev 2022; 43:678-719. [PMID: 34741454 PMCID: PMC9277653 DOI: 10.1210/endrev/bnab039] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Indexed: 11/24/2022]
Abstract
Uterine fibroids are benign monoclonal neoplasms of the myometrium, representing the most common tumors in women worldwide. To date, no long-term or noninvasive treatment option exists for hormone-dependent uterine fibroids, due to the limited knowledge about the molecular mechanisms underlying the initiation and development of uterine fibroids. This paper comprehensively summarizes the recent research advances on uterine fibroids, focusing on risk factors, development origin, pathogenetic mechanisms, and treatment options. Additionally, we describe the current treatment interventions for uterine fibroids. Finally, future perspectives on uterine fibroids studies are summarized. Deeper mechanistic insights into tumor etiology and the complexity of uterine fibroids can contribute to the progress of newer targeted therapies.
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Affiliation(s)
- Qiwei Yang
- Qiwei Yang, Ph.D. Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave, M167, Billings, Chicago, IL 60637, USA.
| | - Michal Ciebiera
- Second Department of Obstetrics and Gynecology, Center of Postgraduate Medical Education, ul. Cegłowska 80, 01-809, Warsaw, Poland
| | | | - Mohamed Ali
- Clinical Pharmacy Department, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Hoda Elkafas
- Department of Anesthesiology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Pharmacology and Toxicology, Egyptian Drug Authority, formerly National Organization for Drug Control and Research, Cairo 35521, Egypt
| | - Thomas G Boyer
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900, USA
| | - Ayman Al-Hendy
- Correspondence: Ayman Al-Hendy, MD, Ph.D. Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave, N112, Peck Pavilion, Chicago, IL 60637. USA.
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