1
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Bhattarai PY, Kim G, Lim SC, Choi HS. METTL3-STAT5B interaction facilitates the co-transcriptional m 6A modification of mRNA to promote breast tumorigenesis. Cancer Lett 2024; 603:217215. [PMID: 39218290 DOI: 10.1016/j.canlet.2024.217215] [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: 05/20/2024] [Revised: 08/07/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
Enhanced expression of methyltransferase-like 3 (METTL3) promotes the m6A modification of specific mRNAs, contributing to breast tumorigenesis. While the mRNA substrates targeted by METTL3 are well characterized, the factors dictating the selection of these specific mRNA remain elusive. This study aimed to examine the regulatory role of the transcription factor STAT5B in METTL3-induced m6A modification. METTL3 specifically interacts with STAT5B in response to mitogenic stimulation by epidermal growth factor (EGF). Chromatin immunoprecipitation and CRISPR/Cas9 mutagenesis showed that STAT5B recruits METTL3 to gene promoters like CCND1, where METTL3 interacts with RPB1, dependent on CDK9-mediated RPB1 (Ser2) phosphorylation during transcription elongation. Inhibition and depletion of either STAT5B or CDK9 prevented the EGF-induced m6A modification of CCND1. The translation efficiency of CCND1 was increased following m6A modification, thereby increasing cell proliferation. STAT5B facilitated METTL3-induced tumor formation by increasing CCND1 expression in an orthotopic mouse model. In clinical context, a positive correlation was observed between p-STAT5B and METTL3 expression in high-grade breast tumors. This study elucidates a novel mechanism that underlies the specificity of m6A modification in breast cancer cells, thereby underscoring its potential therapeutic value.
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Affiliation(s)
- Poshan Yugal Bhattarai
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chosun University, Gwangju, 61452, Republic of Korea
| | - Garam Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chosun University, Gwangju, 61452, Republic of Korea
| | - Sung-Chul Lim
- Department of Pathology, School of Medicine, Chosun University, Gwangju, 61452, Republic of Korea
| | - Hong Seok Choi
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chosun University, Gwangju, 61452, Republic of Korea.
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2
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Dierks D, Schwartz S. Timing is everything: When is m6A deposited? Mol Cell 2024; 84:3572-3573. [PMID: 39366343 DOI: 10.1016/j.molcel.2024.09.012] [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: 09/11/2024] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 10/06/2024]
Abstract
In this issue of Molecular Cell, Tang et al. suggest that m6A deposition is predominantly post-transcriptional.1 They further propose that nuclear dwell time dictates the post-transcriptional accumulation of m6A. These findings have important implications for m6A biogenesis and function.
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Affiliation(s)
- David Dierks
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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3
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Tang P, Yang J, Chen Z, Du C, Yang Y, Zhao H, Huang L, Li G, Liu F, Dong B, Shan T, Bao X, Zhou Y. Nuclear retention coupled with sequential polyadenylation dictates post-transcriptional m 6A modification in the nucleus. Mol Cell 2024; 84:3758-3774.e10. [PMID: 39127036 DOI: 10.1016/j.molcel.2024.07.017] [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: 01/09/2023] [Revised: 06/28/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024]
Abstract
N6-methyladenosine (m6A) modification is deemed to be co-transcriptionally installed on pre-mRNAs, thereby influencing various downstream RNA metabolism events. However, the causal relationship between m6A modification and RNA processing is often unclear, resulting in premature or even misleading generalizations on the function of m6A modification. Here, we develop 4sU-coupled m6A-level and isoform-characterization sequencing (4sU-m6A-LAIC-seq) and 4sU-GLORI to quantify the m6A levels for both newly synthesized and steady-state RNAs at transcript and single-base-resolution levels, respectively, which enable dissecting the relationship between m6A modification and alternative RNA polyadenylation. Unexpectedly, our results show that many m6A addition events occur post-transcriptionally, especially on transcripts with high m6A levels. Importantly, we find higher m6A levels on shorter 3' UTR isoforms, which likely result from sequential polyadenylation of longer 3' UTR isoforms with prolonged nuclear dwelling time. Therefore, m6A modification can also take place post-transcriptionally to intimately couple with other key RNA metabolism processes to establish and dynamically regulate epi-transcriptomics in mammalian cells.
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Affiliation(s)
- Peng Tang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jiayi Yang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Zonggui Chen
- Institute of Advanced Studies, Wuhan University, Wuhan, China
| | - Chen Du
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Yang Yang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China; Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Haiping Zhao
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Li Huang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Guangnan Li
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Feiyan Liu
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Bei Dong
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ting Shan
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Xichen Bao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China; Institute of Advanced Studies, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China.
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4
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Han J, Song Y, Xie J, Tano V, Shen H, Gan WL, Ng L, Ng BYL, Ng VHE, Sui X, Tang SJ, Chen L. Modulation of m 6A RNA modification by DAP3 in cancer cells. Proc Natl Acad Sci U S A 2024; 121:e2404509121. [PMID: 39316047 PMCID: PMC11459197 DOI: 10.1073/pnas.2404509121] [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: 03/04/2024] [Accepted: 08/23/2024] [Indexed: 09/25/2024] Open
Abstract
N6-methyladenosine (m6A) RNA methylation is a prevalent RNA modification that significantly impacts RNA metabolism and cancer development. Maintaining the global m6A levels in cancer cells relies on RNA accessibility to methyltransferases and the availability of the methyl donor S-adenosylmethionine (SAM). Here, we reveal that death associated protein 3 (DAP3) plays a crucial role in preserving m6A levels through two distinct mechanisms. First, although DAP3 is not a component of the m6A writer complex, it directly binds to m6A target regions, thereby facilitating METTL3 binding. Second, DAP3 promotes MAT2A's last intron splicing, increasing MAT2A protein, cellular SAM, and m6A levels. Silencing DAP3 hinders tumorigenesis, which can be rescued by MAT2A overexpression. This evidence suggests DAP3's role in tumorigenesis, partly through m6A regulation. Our findings unveil DAP3's complex role as an RNA-binding protein and tumor promoter, impacting RNA processing, splicing, and m6A modification in cancer transcriptomes.
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Affiliation(s)
- Jian Han
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Jinghe Xie
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Vincent Tano
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Wei Liang Gan
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Larry Ng
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | | | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Xiaohui Sui
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, 8, Singapore117599, Singapore
- National University of Singapore (NUS) Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117594, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117594, Singapore
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5
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Tegowski M, Prater AK, Holley CL, Meyer KD. Single-cell m 6A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation. Nat Neurosci 2024:10.1038/s41593-024-01768-3. [PMID: 39317796 DOI: 10.1038/s41593-024-01768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/19/2024] [Indexed: 09/26/2024]
Abstract
N6-methyladenosine (m6A) is an abundant mRNA modification in the brain that has important roles in neurodevelopment and brain function. However, because of technical limitations, global profiling of m6A sites within the individual cell types that make up the brain has not been possible. Here, we develop a mouse model that enables transcriptome-wide m6A detection in any tissue of interest at single-cell resolution. We use these mice to map m6A across different brain regions and within single cells of the mouse cortex and discover a high degree of shared methylation across brain regions and cell types. However, we also identify a small number of differentially methylated mRNAs in neurons that encode important regulators of neuronal signaling, and we discover that microglia have lower levels of m6A than other cell types. Finally, we perform single-cell m6A mapping in aged mice and identify many transcripts with age-dependent changes in m6A.
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Affiliation(s)
- Matthew Tegowski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Anna K Prater
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Christopher L Holley
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA.
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6
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Park D, Cenik C. Long-read RNA sequencing reveals allele-specific N 6-methyladenosine modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602538. [PMID: 39026828 PMCID: PMC11257478 DOI: 10.1101/2024.07.08.602538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Long-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights into the effects of genetic variation on splicing and RNA abundance. Furthermore, the ability to directly sequence RNA promises the detection of RNA modifications in tandem with ascertaining the allelic origin of each molecule. Here, we leverage these advantages to determine allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNA. We utilized human and mouse cells with known genetic variants to assign allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses revealed the importance of sequences adjacent to the DRACH-motif in determining m6A deposition, in addition to allelic differences that directly alter the motif. Moreover, we discovered allele-specific m6A modification (ASM) events with no genetic variants in close proximity to the differentially modified nucleotide, demonstrating the unique advantage of using long reads and surpassing the capabilities of antibody-based short-read approaches. This technological advancement promises to advance our understanding of the role of genetics in determining mRNA modifications.
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Affiliation(s)
- Dayea Park
- 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
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7
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Cui H, Shi Q, Macarios CM, Schimmel P. Metabolic regulation of mRNA splicing. Trends Cell Biol 2024; 34:756-770. [PMID: 38431493 DOI: 10.1016/j.tcb.2024.02.002] [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: 11/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Alternative mRNA splicing enables the diversification of the proteome from a static genome and confers plasticity and adaptiveness on cells. Although this is often explored in development, where hard-wired programs drive the differentiation and specialization, alternative mRNA splicing also offers a way for cells to react to sudden changes in outside stimuli such as small-molecule metabolites. Fluctuations in metabolite levels and availability in particular convey crucial information to which cells react and adapt. We summarize and highlight findings surrounding the metabolic regulation of mRNA splicing. We discuss the principles underlying the biochemistry and biophysical properties of mRNA splicing, and propose how these could intersect with metabolite levels. Further, we present examples in which metabolites directly influence RNA-binding proteins and splicing factors. We also discuss the interplay between alternative mRNA splicing and metabolite-responsive signaling pathways. We hope to inspire future research to obtain a holistic picture of alternative mRNA splicing in response to metabolic cues.
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Affiliation(s)
- Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Qingyu Shi
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | | - Paul Schimmel
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
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8
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Palos K, Nelson Dittrich AC, Lyons EH, Gregory BD, Nelson ADL. Comparative analyses suggest a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants. BMC PLANT BIOLOGY 2024; 24:768. [PMID: 39134938 PMCID: PMC11318313 DOI: 10.1186/s12870-024-05486-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
BACKGROUND In recent years, covalent modifications on RNA nucleotides have emerged as pivotal moieties influencing the structure, function, and regulatory processes of RNA Polymerase II transcripts such as mRNAs and lncRNAs. However, our understanding of their biological roles and whether these roles are conserved across eukaryotes remains limited. RESULTS In this study, we leveraged standard polyadenylation-enriched RNA-sequencing data to identify and characterize RNA modifications that introduce base-pairing errors into cDNA reads. Our investigation incorporated data from three Poaceae (Zea mays, Sorghum bicolor, and Setaria italica), as well as publicly available data from a range of stress and genetic contexts in Sorghum and Arabidopsis thaliana. We uncovered a strong enrichment of RNA covalent modifications (RCMs) deposited on a conserved core set of nuclear mRNAs involved in photosynthesis and translation across these species. However, the cohort of modified transcripts changed based on environmental context and developmental program, a pattern that was also conserved across flowering plants. We determined that RCMs can partly explain accession-level differences in drought tolerance in Sorghum, with stress-associated genes receiving a higher level of RCMs in a drought tolerant accession. To address function, we determined that RCMs are significantly enriched near exon junctions within coding regions, suggesting an association with splicing. Intriguingly, we found that these base-pair disrupting RCMs are associated with stable mRNAs, are highly correlated with protein abundance, and thus likely associated with facilitating translation. CONCLUSIONS Our data point to a conserved role for RCMs in mRNA stability and translation across the flowering plant lineage.
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Affiliation(s)
- Kyle Palos
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY, 14853, USA
| | | | - Eric H Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D L Nelson
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY, 14853, USA.
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9
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Lu L, Zhang X, Zhou Y, Shi Z, Xie X, Zhang X, Gao L, Fu A, Liu C, He B, Xiong X, Yin Y, Wang Q, Yi C, Li X. Base-resolution m 5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach. Mol Cell 2024; 84:2984-3000.e8. [PMID: 39002544 DOI: 10.1016/j.molcel.2024.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 06/03/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024]
Abstract
5-methylcytosine (m5C) is a prevalent RNA modification crucial for gene expression regulation. However, accurate and sensitive m5C sites identification remains challenging due to severe RNA degradation and reduced sequence complexity during bisulfite sequencing (BS-seq). Here, we report m5C-TAC-seq, a bisulfite-free approach combining TET-assisted m5C-to-f5C oxidation with selective chemical labeling, therefore enabling direct base-resolution m5C detection through pre-enrichment and C-to-T transitions at m5C sites. With m5C-TAC-seq, we comprehensively profiled the m5C methylomes in human and mouse cells, identifying a substantially larger number of confident m5C sites. Through perturbing potential m5C methyltransferases, we deciphered the responsible enzymes for most m5C sites, including the characterization of NSUN5's involvement in mRNA m5C deposition. Additionally, we characterized m5C dynamics during mESC differentiation. Notably, the mild reaction conditions and preservation of nucleotide composition in m5C-TAC-seq allow m5C detection in chromatin-associated RNAs. The accurate and robust m5C-TAC-seq will advance research into m5C methylation functional investigation.
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Affiliation(s)
- Liang Lu
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaoting Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuenan Zhou
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zuokun Shi
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiwen Xie
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xinyue Zhang
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Liaoliao Gao
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Anbo Fu
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Cong Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Bo He
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xushen Xiong
- The Second Affiliated Hospital and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou 311121, China
| | - Yafei Yin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qingqing Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Xiaoyu Li
- Department of Biochemistry and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
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10
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Cun Y, Guo W, Ma B, Okuno Y, Wang J. Decoding the specificity of m 6A RNA methylation and its implication in cancer therapy. Mol Ther 2024; 32:2461-2469. [PMID: 38796701 PMCID: PMC11405154 DOI: 10.1016/j.ymthe.2024.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 05/28/2024] Open
Abstract
N6-methyladenosine (m6A) is the most abundant endogenous modification in eukaryotic RNAs. It plays important roles in various biological processes and diseases, including cancers. More and more studies have revealed that the deposition of m6A is specifically regulated in a context-dependent manner. Here, we review the diverse mechanisms that determine the topology of m6A along RNAs and the cell-type-specific m6A methylomes. The exon junction complex (EJC) as well as histone modifications play important roles in determining the topological distribution of m6A along nascent RNAs, while the transcription factors and RNA-binding proteins, which usually bind specific DNAs and RNAs in a cell-type-specific manner, largely account for the cell-type-specific m6A methylomes. Due to the lack of specificity of m6A writers and readers, there are still challenges to target the core m6A machinery for cancer therapies. Therefore, understanding the mechanisms underlying the specificity of m6A modifications in cancers would be important for future cancer therapies through m6A intervention.
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Affiliation(s)
- Yixian Cun
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangdong 510080, China
| | - Wenbing Guo
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangdong 510080, China
| | - Biao Ma
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasushi Okuno
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Jinkai Wang
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangdong 510080, China.
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11
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Wells GR, Pillai RS. Roles of N 6-methyladenosine writers, readers and erasers in the mammalian germline. Curr Opin Genet Dev 2024; 87:102224. [PMID: 38981182 DOI: 10.1016/j.gde.2024.102224] [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: 03/28/2024] [Revised: 06/06/2024] [Accepted: 06/23/2024] [Indexed: 07/11/2024]
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification of mRNAs in eukaryotes. Numerous studies have shown that m6A plays key roles in many biological and pathophysiological processes, including fertility. The factors involved in m6A-dependent mRNA regulation include writers, which deposit the m6A mark, erasers, which remove it, and readers, which bind to m6A-modified transcripts and mediate the regulation of mRNA fate. Many of these proteins are highly expressed in the germ cells of mammals, and some have been linked to fertility disorders in human patients. In this review, we summarise recent findings on the important roles played by proteins involved in m6A biology in mammalian gametogenesis and fertility. Continued study of the m6A pathway in the mammalian germline will shed further light on the importance of epitranscriptomics in reproduction and may lead to effective treatment of human fertility disorders.
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Affiliation(s)
- Graeme R Wells
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
| | - Ramesh S Pillai
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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12
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Chen K, Nan J, Xiong X. Genetic regulation of m 6A RNA methylation and its contribution in human complex diseases. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1591-1600. [PMID: 38764000 DOI: 10.1007/s11427-024-2609-8] [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: 01/08/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
N6-methyladenosine (m6A) has been established as the most prevalent chemical modification in message RNA (mRNA), playing an essential role in determining the fate of RNA molecules. Dysregulation of m6A has been revealed to lead to abnormal physiological conditions and cause various types of human diseases. Recent studies have delineated the genetic regulatory maps for m6A methylation by mapping the quantitative trait loci of m6A (m6A-QTLs), thereby building up the regulatory circuits linking genetic variants, m6A, and human complex traits. Here, we review the recent discoveries concerning the genetic regulatory maps of m6A, describing the methodological and technical details of m6A-QTL identification, and introducing the key findings of the cis- and trans-acting drivers of m6A. We further delve into the tissue- and ethnicity-specificity of m6A-QTL, the association with other molecular phenotypes in light of genetic regulation, the regulators underlying m6A genetics, and importantly, the functional roles of m6A in mediating human complex diseases. Lastly, we discuss potential research avenues that can accelerate the translation of m6A genetics studies toward the development of therapies for human genetic diseases.
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Affiliation(s)
- Kexuan Chen
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Jiuhong Nan
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Xushen Xiong
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China.
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 311121, China.
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13
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Zha X, Gao Z, Li M, Xia X, Mao Z, Wang S. Insight into the regulatory mechanism of m 6A modification: From MAFLD to hepatocellular carcinoma. Biomed Pharmacother 2024; 177:116966. [PMID: 38906018 DOI: 10.1016/j.biopha.2024.116966] [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: 04/10/2024] [Revised: 06/05/2024] [Accepted: 06/15/2024] [Indexed: 06/23/2024] Open
Abstract
In recent years, there has been a significant increase in the incidence of metabolic-associated fatty liver disease (MAFLD), which has been attributed to the increasing prevalence of type 2 diabetes mellitus (T2DM) and obesity. MAFLD affects more than one-third of adults worldwide, making it the most prevalent liver disease globally. Moreover, MAFLD is considered a significant risk factor for hepatocellular carcinoma (HCC), with MAFLD-related HCC cases increasing. Approximately 1 in 6 HCC patients are believed to have MAFLD, and nearly 40 % of these HCC patients do not progress to cirrhosis, indicating direct transformation from MAFLD to HCC. N6-methyladenosine (m6A) is commonly distributed in eukaryotic mRNA and plays a crucial role in normal development and disease progression, particularly in tumors. Numerous studies have highlighted the close association between abnormal m6A modification and cellular metabolic alterations, underscoring its importance in the onset and progression of MAFLD. However, the specific impact of m6A modification on the progression of MAFLD to HCC remains unclear. Can targeting m6A effectively halt the progression of MAFLD-related HCC? In this review, we investigated the pivotal role of abnormal m6A modification in the transition from MAFLD to HCC, explored the potential of m6A modification as a therapeutic target for MAFLD-related HCC, and proposed possible directions for future investigations.
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Affiliation(s)
- Xuan Zha
- Department of Laboratory Medicine, the Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zewei Gao
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Min Li
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xueli Xia
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zhenwei Mao
- Department of Laboratory Medicine, Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.
| | - Shengjun Wang
- Department of Laboratory Medicine, the Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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14
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Mehravar M, Wong JJL. Interplay between N 6-adenosine RNA methylation and mRNA splicing. Curr Opin Genet Dev 2024; 87:102211. [PMID: 38838495 DOI: 10.1016/j.gde.2024.102211] [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: 02/24/2024] [Revised: 05/11/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024]
Abstract
N6-methyladenosine (m6A) is the most abundant modification to mRNAs. Loss-of-function studies of main m6A regulators have indicated the role of m6A in pre-mRNA splicing. Recent studies have reported the role of splicing in preventing m6A deposition. Understanding the interplay between m6A and mRNA splicing holds the potential to clarify the significance of these fundamental molecular mechanisms in cell development and function, thereby shedding light on their involvement in the pathogenesis of myriad diseases.
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Affiliation(s)
- Majid Mehravar
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Justin J-L Wong
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia.
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15
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Fernandez Rodriguez G, Tarullo M, Fatica A. N 6-methyladenosine (m 6A) RNA modification in chronic myeloid leukemia: unveiling a novel therapeutic target. Cell Mol Life Sci 2024; 81:326. [PMID: 39085650 PMCID: PMC11335252 DOI: 10.1007/s00018-024-05379-w] [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: 05/28/2024] [Revised: 07/02/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
N6-methyladenosine (m6A), the most prevalent internal mRNA modification, plays a critical role in physiological processes by regulating gene expression through modulation of mRNA metabolism at multiple stages. In recent years, m6A has garnered significant attention for a deeper understanding of the initiation, progression, and drug resistance of various cancers, including hematological malignancies. Dysregulation of m6A has been implicated in both cancer promotion and suppression. m6A methylation is a complex regulatory process involving methyltransferases (writers), demethylases (erasers), and proteins that recognize specific m6A modifications (readers). This intricate interplay presents challenges for precisely modulating m6A levels, either globally or at specific sites. This review specifically focuses on the role of m6A in chronic myeloid leukemia (CML), a blood cancer characterized by the BCR-ABL1 fusion. We emphasize its impact on leukemia cell survival and drug resistance mechanisms. Notably, inhibitors targeting m6A regulators show promise in preclinical models, suggesting a potential therapeutic avenue for CML. Integrating our understanding of m6A biology with current treatment strategies may lead to more effective therapies, especially for patients with advanced-stage or resistant CML.
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MESH Headings
- Humans
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Drug Resistance, Neoplasm/genetics
- Animals
- Methyltransferases/metabolism
- Methyltransferases/antagonists & inhibitors
- Methyltransferases/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Methylation
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Affiliation(s)
| | - Marco Tarullo
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185, Rome, Italy.
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16
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Wang G, Li H, Ye C, He K, Liu S, Jiang B, Ge R, Gao B, Wei J, Zhao Y, Li A, Zhang D, Zhang J, He C. Quantitative profiling of m 6A at single base resolution across the life cycle of rice and Arabidopsis. Nat Commun 2024; 15:4881. [PMID: 38849358 PMCID: PMC11161662 DOI: 10.1038/s41467-024-48941-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
N6-methyladenosine (m6A) plays critical roles in regulating mRNA metabolism. However, comprehensive m6A methylomes in different plant tissues with single-base precision have yet to be reported. Here, we present transcriptome-wide m6A maps at single-base resolution in different tissues of rice and Arabidopsis using m6A-SAC-seq. Our analysis uncovers a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis. The evolutionarily conserved m6A sites in rice and Arabidopsis ortholog gene pairs are involved in controlling tissue development, photosynthesis and stress response. We observe an overall mRNA stabilization effect by 3' UTR m6A sites in certain plant tissues. Like in mammals, a positive correlation between the m6A level and the length of internal exons is also observed in plant mRNA, except for the last exon. Our data suggest an active m6A deposition process occurring near the stop codon in plant mRNA. In addition, the MTA-installed plant mRNA m6A sites correlate with both translation promotion and translation suppression, depicting a more complicated regulatory picture. Our results therefore provide in-depth resources for relating single-base resolution m6A sites with functions in plants and uncover a suppression-activation model controlling m6A biogenesis across species.
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Affiliation(s)
- Guanqun Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Haoxuan Li
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Chang Ye
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Kayla He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Bochen Jiang
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Ruiqi Ge
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Boyang Gao
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Chemistry and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yutao Zhao
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Aixuan Li
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Di Zhang
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA.
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17
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Xu W, Shen H. m 6A regulates heterochromatin in mammalian embryonic stem cells. Curr Opin Genet Dev 2024; 86:102196. [PMID: 38669774 DOI: 10.1016/j.gde.2024.102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
As the most well-studied modification in mRNA, m6A has been shown to regulate multiple biological processes, including RNA degradation, processing, and translation. Recent studies showed that m6A modification is enriched in chromatin-associated RNAs and nascent RNAs, suggesting m6A might play regulatory roles in chromatin contexts. Indeed, in the past several years, a number of studies have clarified how m6A and its modulators regulate different types of chromatin states. Specifically, in the past 2-3 years, several studies discovered the roles of m6A and/or its modulators in regulating constitutive and facultative heterochromatin, shedding interesting lights on RNA-dependent heterochromatin formation in mammalian cells. This review will summarize and discuss the mechanisms underlying m6A's regulation in different types of heterochromatin, with a specific emphasis on the regulation in mammalian embryonic stem cells, which exhibit distinct features of multiple heterochromatin marks.
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Affiliation(s)
- Wenqi Xu
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Hongjie Shen
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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18
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Hou R, Wang Y, Cao S, Sun X, Jiang L. N 6-Methyladenosine-Modified KREMEN2 Promotes Tumorigenesis and Malignant Progression of High-Grade Serous Ovarian Cancer. J Transl Med 2024; 104:102059. [PMID: 38615731 DOI: 10.1016/j.labinv.2024.102059] [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: 11/23/2023] [Revised: 03/20/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024] Open
Abstract
High-grade serous ovarian cancer (HGSOC) remains the most lethal female cancer by far. Herein, clinical HGSOC samples had higher N6-methyladenosine (m6A) modification than normal ovarian tissue, and its dysregulation had been reported to drive aberrant transcription and translation programs. However, Kringle-containing transmembrane protein 2 (KREMEN2) and its m6A modification have not been fully elucidated in HGSOC. In this study, the data from the high-throughput messenger RNA (mRNA) sequencing of clinical samples were processed using the weighted correlation network analysis and functional enrichment analysis. Results revealed that KREMEN2 was a driver gene in the tumorigenesis of HGSOC and a potential target of m6A demethylase fat-mass and obesity-associated protein (FTO). KREMEN2 and FTO levels were upregulated and downregulated, respectively, and correlation analysis showed a significant negative correlation in HGSOC samples. Importantly, upregulated KREMEN2 was remarkably associated with lymph node metastasis, distant metastasis, peritoneal metastasis, and high International Federation of Gynecology and Obstetrics stage (Ⅲ/Ⅳ), independent of the age of patients. KREMEN2 promoted the growth of HGSOC in vitro and in vivo, which was dependent on FTO. The methylated RNA immunoprecipitation qPCR and RNA immunoprecipitation assays were performed to verify the m6A level and sites of KREMEN2. FTO overexpression significantly decreased m6A modification in the 3' and 5' untranslated regions of KREMEN2 mRNA and downregulated its expression. In addition, we found that FTO-mediated m6A modification of KREMEN2 mRNA was recognized and stabilized by the m6A reader IGF2BP1 rather than by IGF2BP2 or IGF2BP3. This study highlights the m6A modification of KREMEN2 and extends the importance of RNA epigenetics in HGSOC.
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Affiliation(s)
- Rui Hou
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yadong Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shiyao Cao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xinrui Sun
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Luo Jiang
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, China.
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19
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Acera Mateos P, J Sethi A, Ravindran A, Srivastava A, Woodward K, Mahmud S, Kanchi M, Guarnacci M, Xu J, W S Yuen Z, Zhou Y, Sneddon A, Hamilton W, Gao J, M Starrs L, Hayashi R, Wickramasinghe V, Zarnack K, Preiss T, Burgio G, Dehorter N, E Shirokikh N, Eyras E. Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications. Nat Commun 2024; 15:3899. [PMID: 38724548 PMCID: PMC11082244 DOI: 10.1038/s41467-024-47953-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.
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Affiliation(s)
- P Acera Mateos
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - A J Sethi
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - A Ravindran
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - A Srivastava
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - K Woodward
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - S Mahmud
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - M Kanchi
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - M Guarnacci
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - J Xu
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
| | - Z W S Yuen
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - Y Zhou
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - A Sneddon
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - W Hamilton
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3052, Australia
| | - J Gao
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - L M Starrs
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - R Hayashi
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | | | - K Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - T Preiss
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - G Burgio
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - N Dehorter
- The Eccles Institute of Neuroscience, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - N E Shirokikh
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
| | - E Eyras
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
- Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain.
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20
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Hao JD, Liu QL, Liu MX, Yang X, Wang LM, Su SY, Xiao W, Zhang MQ, Zhang YC, Zhang L, Chen YS, Yang YG, Ren J. DDX21 mediates co-transcriptional RNA m 6A modification to promote transcription termination and genome stability. Mol Cell 2024; 84:1711-1726.e11. [PMID: 38569554 DOI: 10.1016/j.molcel.2024.03.006] [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: 06/14/2023] [Revised: 02/09/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
N6-methyladenosine (m6A) is a crucial RNA modification that regulates diverse biological processes in human cells, but its co-transcriptional deposition and functions remain poorly understood. Here, we identified the RNA helicase DDX21 with a previously unrecognized role in directing m6A modification on nascent RNA for co-transcriptional regulation. DDX21 interacts with METTL3 for co-recruitment to chromatin through its recognition of R-loops, which can be formed co-transcriptionally as nascent transcripts hybridize onto the template DNA strand. Moreover, DDX21's helicase activity is needed for METTL3-mediated m6A deposition onto nascent RNA following recruitment. At transcription termination regions, this nexus of actions promotes XRN2-mediated termination of RNAPII transcription. Disruption of any of these steps, including the loss of DDX21, METTL3, or their enzymatic activities, leads to defective termination that can induce DNA damage. Therefore, we propose that the R-loop-DDX21-METTL3 nexus forges the missing link for co-transcriptional modification of m6A, coordinating transcription termination and genome stability.
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Affiliation(s)
- Jin-Dong Hao
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian-Lan Liu
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Meng-Xia Liu
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xing Yang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liu-Ming Wang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si-Yi Su
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Xiao
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng-Qi Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Chang Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lan Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yu-Sheng Chen
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun-Gui Yang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jie Ren
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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21
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Baek A, Lee GE, Golconda S, Rayhan A, Manganaris AA, Chen S, Tirumuru N, Yu H, Kim S, Kimmel C, Zablocki O, Sullivan MB, Addepalli B, Wu L, Kim S. Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m 6As. Nat Microbiol 2024; 9:1340-1355. [PMID: 38605174 PMCID: PMC11087264 DOI: 10.1038/s41564-024-01638-5] [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: 03/10/2023] [Accepted: 02/15/2024] [Indexed: 04/13/2024]
Abstract
Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods. Our data reveal an unexpectedly simple HIV-1 modification landscape, highlighting three predominant N6-methyladenosine (m6A) modifications near the 3' end. More densely installed in spliced viral messenger RNAs than in genomic RNAs, these m6As play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. HIV-1 generates diverse RNA subspecies with distinct m6A ensembles, and maintaining multiple of these m6As on its RNAs provides additional stability and resilience to HIV-1 replication, suggesting an unexplored viral RNA-level evolutionary strategy.
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Affiliation(s)
- Alice Baek
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Ga-Eun Lee
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
| | - Sarah Golconda
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Asif Rayhan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Anastasios A Manganaris
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
- Department of Computer Science and Engineering, Ohio State University, Columbus, OH, USA
| | - Shuliang Chen
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Nagaraja Tirumuru
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Hannah Yu
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Shihyoung Kim
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Christopher Kimmel
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Matthew B Sullivan
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sanggu Kim
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA.
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA.
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA.
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, Ohio State University, Columbus, OH, USA.
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22
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Zhao S, Xiao M, Li L, Zhang H, Shan M, Cui S, Zhang L, Zhang G, Wu S, Jin C, Yang J, Lu X. A unique circ_0067716/EIF4A3 double-negative feedback loop impacts malignant transformation of human bronchial epithelial cells induced by benzo(a)pyrene. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171349. [PMID: 38438030 DOI: 10.1016/j.scitotenv.2024.171349] [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: 01/03/2024] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024]
Abstract
Benzo(a)pyrene as a pervasive environmental contaminant is characterized by its substantial genotoxicity, and epidemiological investigations have established a correlation between benzo(a)pyrene exposure and the susceptibility to human lung cancer. Notably, much research has focused on the link between epigenetic alterations and lung cancer induced by chemicals, although circRNAs are also emerging as relevant contributors to the carcinogenic process of benzo(a)pyrene. In this study, we identified circ_0067716 as being significantly upregulated in response to stress injury and downregulated during malignant transformation induced by benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE) in human bronchial epithelial cells. The observed differential expression of circ_0067716 in cells treated with BPDE for varying durations suggests a strong correlation between this circRNA and BPDE exposure. The tissue samples of lung cancer patients also suggest that a lower circ_0067716 expression is associated with BPDE-DNA adduct levels. Remarkably, we demonstrate that EIF4A3, located in the nucleus, interacts with the flanking sequences of circ_0067716 and inhibits its biogenesis. Conversely, circ_0067716 is capable of sequestering EIF4A3 in the cytoplasm, thereby preventing its translocation into the nucleus. EIF4A3 and circ_0067716 can form a double-negative feedback loop that could be affected by BPDE. During the initial phase of BPDE exposure, the expression of circ_0067716 was increased in response to stress injury, resulting in cell apoptosis through the involvement of miR-324-5p/DRAM1/BAX axis. Subsequently, as cellular adaptation progressed, long-term induction due to BPDE exposure led to an elevated EIF4A3 and a reduced circ_0067716 expression, which facilitated the proliferation of cells by stabilizing the PI3K/AKT pathway. Thus, our current study describes the effects of circ_0067716 on the genotoxicity and carcinogenesis induced by benzo(a)pyrene and puts forwards to the possible regulatory mechanism on the occurrence of smoking-related lung cancer, providing a unique insight based on epigenetics.
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Affiliation(s)
- Shuang Zhao
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education (China Medical University), Shenyang 110122, People's Republic of China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, People's Republic of China
| | - Mingyang Xiao
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education (China Medical University), Shenyang 110122, People's Republic of China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, People's Republic of China
| | - Liuli Li
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education (China Medical University), Shenyang 110122, People's Republic of China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, People's Republic of China
| | - Hongchao Zhang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education (China Medical University), Shenyang 110122, People's Republic of China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, People's Republic of China
| | - Mingming Shan
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education (China Medical University), Shenyang 110122, People's Republic of China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, People's Republic of China
| | - Su Cui
- Department of Thoracic Surgery Ward 2, The First Hospital of China Medical University, Shenyang 110005, People's Republic of China
| | - Liang Zhang
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Guopei Zhang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education (China Medical University), Shenyang 110122, People's Republic of China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, People's Republic of China
| | - Shengwen Wu
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education (China Medical University), Shenyang 110122, People's Republic of China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, People's Republic of China
| | - Cuihong Jin
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education (China Medical University), Shenyang 110122, People's Republic of China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, People's Republic of China
| | - Jinghua Yang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education (China Medical University), Shenyang 110122, People's Republic of China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, People's Republic of China
| | - Xiaobo Lu
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education (China Medical University), Shenyang 110122, People's Republic of China; Department of Toxicology, School of Public Health, China Medical University, Shenyang 110122, People's Republic of China.
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23
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Wang Y, Wang S, Meng Z, Liu XM, Mao Y. Determinant of m6A regional preference by transcriptional dynamics. Nucleic Acids Res 2024; 52:3510-3521. [PMID: 38452220 DOI: 10.1093/nar/gkae169] [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: 01/28/2023] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant chemical modification occurring on eukaryotic mRNAs, and has been reported to be involved in almost all stages of mRNA metabolism. The distribution of m6A sites is notably asymmetric along mRNAs, with a strong preference toward the 3' terminus of the transcript. How m6A regional preference is shaped remains incompletely understood. In this study, by performing m6A-seq on chromatin-associated RNAs, we found that m6A regional preference arises during transcription. Nucleosome occupancy is remarkedly increased in the region downstream of m6A sites, suggesting an intricate interplay between m6A methylation and nucleosome-mediated transcriptional dynamics. Notably, we found a remarkable slowdown of Pol-II movement around m6A sites. In addition, inhibiting Pol-II movement increases nearby m6A methylation levels. By analyzing massively parallel assays for m6A, we found that RNA secondary structures inhibit m6A methylation. Remarkably, the m6A sites associated with Pol-II pausing tend to be embedded within RNA secondary structures. These results suggest that Pol-II pausing could affect the accessibility of m6A motifs to the methyltransferase complex and subsequent m6A methylation by mediating RNA secondary structure. Overall, our study reveals a crucial role of transcriptional dynamics in the formation of m6A regional preference.
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Affiliation(s)
- Yalan Wang
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Shen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Zhen Meng
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yuanhui Mao
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
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24
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Tegowski M, Meyer KD. Studying m 6A in the brain: a perspective on current methods, challenges, and future directions. Front Mol Neurosci 2024; 17:1393973. [PMID: 38711483 PMCID: PMC11070500 DOI: 10.3389/fnmol.2024.1393973] [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: 02/29/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024] Open
Abstract
A major mechanism of post-transcriptional RNA regulation in cells is the addition of chemical modifications to RNA nucleosides, which contributes to nearly every aspect of the RNA life cycle. N6-methyladenosine (m6A) is a highly prevalent modification in cellular mRNAs and non-coding RNAs, and it plays important roles in the control of gene expression and cellular function. Within the brain, proper regulation of m6A is critical for neurodevelopment, learning and memory, and the response to injury, and m6A dysregulation has been implicated in a variety of neurological disorders. Thus, understanding m6A and how it is regulated in the brain is important for uncovering its roles in brain function and potentially identifying novel therapeutic pathways for human disease. Much of our knowledge of m6A has been driven by technical advances in the ability to map and quantify m6A sites. Here, we review current technologies for characterizing m6A and highlight emerging methods. We discuss the advantages and limitations of current tools as well as major challenges going forward, and we provide our perspective on how continued developments in this area can propel our understanding of m6A in the brain and its role in brain disease.
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Affiliation(s)
- Matthew Tegowski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Kate D. Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, United States
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25
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Horner SM, Thompson MG. Challenges to mapping and defining m 6A function in viral RNA. RNA (NEW YORK, N.Y.) 2024; 30:482-490. [PMID: 38531643 PMCID: PMC11019751 DOI: 10.1261/rna.079959.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Viral RNA molecules contain multiple layers of regulatory information. This includes features beyond the primary sequence, such as RNA structures and RNA modifications, including N6-methyladenosine (m6A). Many recent studies have identified the presence and location of m6A in viral RNA and have found diverse regulatory roles for this modification during viral infection. However, to date, viral m6A mapping strategies have limitations that prevent a complete understanding of the function of m6A on individual viral RNA molecules. While m6A sites have been profiled on bulk RNA from many viruses, the resulting m6A maps of viral RNAs described to date present a composite picture of m6A across viral RNA molecules in the infected cell. Thus, for most viruses, it is unknown if unique viral m6A profiles exist throughout infection, nor if they regulate specific viral life cycle stages. Here, we describe several challenges to defining the function of m6A in viral RNA molecules and provide a framework for future studies to help in the understanding of how m6A regulates viral infection.
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Affiliation(s)
- Stacy M Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Matthew G Thompson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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26
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Da Cunha D, Miro J, Van Goethem C, Notarnicola C, Hugon G, Carnac G, Cossée M, Koenig M, Tuffery-Giraud S. The exon junction complex is required for DMD gene splicing fidelity and myogenic differentiation. Cell Mol Life Sci 2024; 81:150. [PMID: 38512499 PMCID: PMC10957711 DOI: 10.1007/s00018-024-05188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 02/14/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
Deposition of the exon junction complex (EJC) upstream of exon-exon junctions helps maintain transcriptome integrity by preventing spurious re-splicing events in already spliced mRNAs. Here we investigate the importance of EJC for the correct splicing of the 2.2-megabase-long human DMD pre-mRNA, which encodes dystrophin, an essential protein involved in cytoskeletal organization and cell signaling. Using targeted RNA-seq, we show that knock-down of the eIF4A3 and Y14 core components of EJC in a human muscle cell line causes an accumulation of mis-splicing events clustered towards the 3' end of the DMD transcript (Dp427m). This deregulation is conserved in the short Dp71 isoform expressed ubiquitously except in adult skeletal muscle and is rescued with wild-type eIF4A3 and Y14 proteins but not with an EJC assembly-defective mutant eIF4A3. MLN51 protein and EJC-associated ASAP/PSAP complexes independently modulate the inclusion of the regulated exons 71 and 78. Our data confirm the protective role of EJC in maintaining splicing fidelity, which in the DMD gene is necessary to preserve the function of the critical C-terminal protein-protein interaction domain of dystrophin present in all tissue-specific isoforms. Given the role of the EJC in maintaining the integrity of dystrophin, we asked whether the EJC could also be involved in the regulation of a mechanism as complex as skeletal muscle differentiation. We found that eIF4A3 knockdown impairs myogenic differentiation by blocking myotube formation. Collectively, our data provide new insights into the functional roles of EJC in human skeletal muscle.
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Affiliation(s)
- Dylan Da Cunha
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Julie Miro
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Charles Van Goethem
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
- Montpellier BioInformatique Pour Le Diagnostic Clinique (MOBIDIC), Plateau de Médecine Moléculaire Et Génomique (PMMG), CHU Montpellier, 34295, Montpellier, France
| | | | - Gérald Hugon
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Gilles Carnac
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Mireille Cossée
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
| | - Michel Koenig
- PhyMedExp, Univ Montpellier, CNRS, INSERM, Montpellier, France
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Montpellier, France
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27
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Tsao N, Olabode J, Rodell R, Sun H, Brickner JR, Tsai MS, Pollina EA, Chen CK, Mosammaparast N. YTHDC1 cooperates with the THO complex to prevent RNA damage-induced DNA breaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585107. [PMID: 38559256 PMCID: PMC10979943 DOI: 10.1101/2024.03.14.585107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Certain environmental toxins are nucleic acid damaging agents, as are many chemotherapeutics used for cancer therapy. These agents induce various adducts in DNA as well as RNA. Indeed, most of the nucleic acid adducts (>90%) formed due to these chemicals, such as alkylating agents, occur in RNA 1 . However, compared to the well-studied mechanisms for DNA alkylation repair, the biological consequences of RNA damage are largely unexplored. Here, we demonstrate that RNA damage can directly result in loss of genome integrity. Specifically, we show that a human YTH domain-containing protein, YTHDC1, regulates alkylation damage responses in association with the THO complex (THOC) 2 . In addition to its established binding to N 6-methyladenosine (m6A)-containing RNAs, YTHDC1 binds to N 1-methyladenosine (m1A)-containing RNAs upon alkylation. In the absence of YTHDC1, alkylation damage results in increased alkylation damage sensitivity and DNA breaks. Such phenotypes are fully attributable to RNA damage, since an RNA-specific dealkylase can rescue these phenotypes. These R NA d amage-induced DNA b reaks (RDIBs) depend on R-loop formation, which in turn are processed by factors involved in transcription-coupled nucleotide excision repair. Strikingly, in the absence of YTHDC1 or THOC, an RNA m1A methyltransferase targeted to the nucleus is sufficient to induce DNA breaks. Our results uncover a unique role for YTHDC1-THOC in base damage responses by preventing RDIBs, providing definitive evidence for how damaged RNAs can impact genomic integrity.
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28
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He PC, He C. mRNA accessibility within mRNPs as a determinant of gene expression. Trends Biochem Sci 2024; 49:199-207. [PMID: 38071089 PMCID: PMC10939938 DOI: 10.1016/j.tibs.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/05/2023] [Accepted: 11/10/2023] [Indexed: 01/31/2024]
Abstract
Gene expression is a complex process requiring many control mechanisms to achieve a desired phenotype. DNA accessibility within chromatin is well established as an important determinant of gene expression. By contrast, while mRNA also associates with a complement of proteins, the exact nature of messenger ribonucleoprotein (mRNP) packaging and its functional relevance is not as clear. Recent reports indicate that exon junction complex (EJC)-mediated mRNP packaging renders exon junction-proximal regions inaccessible for m6A methylation, and that EJCs reside within the inaccessible interior of globular transcription and export (TREX) complex-associated nuclear mRNPs. We propose that 'mRNA accessibility' within mRNPs is an important determinant of gene expression that may modulate the specificity of a broad array of regulatory processes including but not limited to m6A methylation.
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Affiliation(s)
- P Cody He
- Pritzker School of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA.
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29
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Shachar R, Dierks D, Garcia-Campos MA, Uzonyi A, Toth U, Rossmanith W, Schwartz S. Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids. Genome Biol 2024; 25:48. [PMID: 38360609 PMCID: PMC10870504 DOI: 10.1186/s13059-024-03182-1] [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: 07/20/2023] [Accepted: 02/04/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between and within species. Yet, it is unclear to what extent this variability is driven by changes in genetic sequences ('cis') or cellular environments ('trans') and via which mechanisms. RESULTS Here we dissect the determinants governing RNA methylation via interspecies and intraspecies hybrids in yeast and mammalian systems, coupled with massively parallel reporter assays and m6A-QTL reanalysis. We find that m6A evolution and variability is driven primarily in 'cis', via two mechanisms: (1) variations altering m6A consensus motifs, and (2) variation impacting mRNA secondary structure. We establish that mutations impacting RNA structure - even when distant from an m6A consensus motif - causally dictate methylation propensity. Finally, we demonstrate that allele-specific differences in m6A levels lead to allele-specific changes in gene expression. CONCLUSIONS Our findings define the determinants governing m6A evolution and diversity and characterize the consequences thereof on gene expression regulation.
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Affiliation(s)
- Ran Shachar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - David Dierks
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | | | - Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Ursula Toth
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, 1090, Austria
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, 1090, Austria
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel.
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30
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Goh WSS, Kuang Y. Heterogeneity of chemical modifications on RNA. Biophys Rev 2024; 16:79-87. [PMID: 38495447 PMCID: PMC10937866 DOI: 10.1007/s12551-023-01128-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/27/2023] [Indexed: 03/19/2024] Open
Abstract
The chemical modifications of RNAs broadly impact almost all cellular events and influence various diseases. The rapid advance of sequencing and other technologies opened the door to global methods for profiling all RNA modifications, namely the "epitranscriptome." The mapping of epitranscriptomes in different cells and tissues unveiled that RNA modifications exhibit extensive heterogeneity, in type, amount, and in location. In this mini review, we first introduce the current understanding of modifications on major types of RNAs and the methods that enabled their discovery. We next discuss the tissue and cell heterogeneity of RNA modifications and briefly address the limitations of current technologies. With much still remaining unknown, the development of the epitranscriptomic field lies in the further developments of novel technologies.
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Affiliation(s)
- W. S. Sho Goh
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yi Kuang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
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31
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Delaunay S, Helm M, Frye M. RNA modifications in physiology and disease: towards clinical applications. Nat Rev Genet 2024; 25:104-122. [PMID: 37714958 DOI: 10.1038/s41576-023-00645-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules - to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.
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Affiliation(s)
- Sylvain Delaunay
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Michaela Frye
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany.
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32
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Guo H, Han Q, Guan X, Li Z, Wang Y, He L, Guo Y, Zhao L, Xue X, Liu H, Zhang C. M6A reader YTHDF1 promotes malignant progression of laryngeal squamous carcinoma through activating the EMT pathway by EIF4A3. Cell Signal 2024; 114:111002. [PMID: 38048860 DOI: 10.1016/j.cellsig.2023.111002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/09/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Laryngeal squamous cell carcinoma (LSCC) is one of the common malignant tumors in the head and neck region, and its high migration and invasion seriously threaten the survival and health of patients. In cancer development, m6A RNA modification plays a crucial role in regulating gene expression and signaling. This study delved into the function and mechanism of the m6A reading protein YTHDF1 in LSCC. It was found that YTHDF1 was highly expressed in the GEO database and LSCC tissues. Cell function experiments confirmed that the downregulation of YTHDF1 significantly inhibited the proliferation, migration, and invasion ability of LSCC cells. Further studies revealed that EIF4A3 was a downstream target gene of YTHDF1, and knockdown of EIF4A3 similarly significantly inhibited the malignant progression of LSCC in both in vivo and in vitro experiments. The molecular mechanism studies suggested that YTHDF1-EIF4A3 may promote the malignant development of LSCC by activating the EMT signaling pathway. This study provides important clues for an in-depth understanding of the pathogenesis of LSCC and is a solid foundation for the discovery of new therapeutic targets and approaches.
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Affiliation(s)
- Huina Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Qi Han
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Xiaoya Guan
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Zhongxun Li
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Ying Wang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Long He
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Yujia Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Liting Zhao
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Xuting Xue
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Hongliang Liu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Department of Cell Biology and Genetics, the Basic Medical School of Shanxi Medical University, Taiyuan 030001, Shanxi, China.
| | - Chunming Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, China.
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33
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Xia W, Guo L, Su H, Li J, Lu J, Li H, Huang B. A low-cost, low-input method establishment for m6A MeRIP-seq. Biosci Rep 2024; 44:BSR20231430. [PMID: 38113135 PMCID: PMC10776898 DOI: 10.1042/bsr20231430] [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: 08/19/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023] Open
Abstract
N6-methyladenosine (m6A) is a highly prevalent modification found in mammal mRNA molecules that plays a crucial role in the regulation of cellular function. m6A RNA immunoprecipitation sequencing (MeRIP-seq) has been frequently used in transcriptomics research to identify the location of m6A. MABE572 (Millipore) is the most widely utilized and efficient anti-m6A antibody for MeRIP-seq. However, due to the high dose and price of this antibody, which has also been taken off the market, we discovered that CST's anti-m6A antibody can be used instead of MABE572 to map the m6A transcriptome. In the present study, we performed different concentrations of the CST anti-m6A antibodies with the corresponding initiation RNA of HEK293T cells, 2.5 μg antibody with 1 μg total RNA, 1.25 μg antibody with 0.5 μg total RNA, and 1.25 μg antibody with 0.1 μg total RNA. By comparing the m6A peak calling, enriched motifs, alternative splicing events, and nuclear transcripts modified by m6A between the CST and Millipore libraries, it was found that the CST library presented similar data to Millipore, even at incredibly low doses. The volume and cost of antibodies are significantly reduced by this refined MeRIP-seq using CST antibody, making it convenient to map future large-scale sample m6A methylation.
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Affiliation(s)
- Wenjuan Xia
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Ling Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Huapeng Su
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Jincheng Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Jiafeng Lu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Hong Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Boxian Huang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
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34
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Aufgebauer CJ, Bland KM, Horner SM. Modifying the antiviral innate immune response by selective writing, erasing, and reading of m 6A on viral and cellular RNA. Cell Chem Biol 2024; 31:100-109. [PMID: 38176419 PMCID: PMC10872403 DOI: 10.1016/j.chembiol.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
Viral infection and the antiviral innate immune response are regulated by the RNA modification m6A. m6A directs nearly all aspects of RNA metabolism by recruiting RNA-binding proteins that mediate the fate of m6A-containing RNA. m6A controls the antiviral innate immune response in diverse ways, including shielding viral RNA from detection by antiviral sensors and influencing the expression of cellular mRNAs encoding antiviral signaling proteins, cytokines, and effector proteins. While m6A and the m6A machinery are important for the antiviral response, the precise mechanisms that determine how the m6A machinery selects specific viral or cellular RNA molecules for modification during infection are not fully understood. In this review, we highlight recent findings that shed light on how viral infection redirects the m6A machinery during the antiviral response. A better understanding of m6A targeting during viral infection could lead to new immunomodulatory and therapeutic strategies against viral infection.
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Affiliation(s)
- Caroline J Aufgebauer
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katherine M Bland
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
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35
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Palazzo AF, Qiu Y, Kang YM. mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts. RNA Biol 2024; 21:1-12. [PMID: 38091265 PMCID: PMC10732640 DOI: 10.1080/15476286.2023.2293339] [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] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machinery. Here, we explore how properly processed mRNAs are distinguished from both misprocessed mRNAs and junk RNAs by the presence or absence of various 'identity features'.
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Affiliation(s)
| | - Yi Qiu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yoon Mo Kang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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36
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Yoshinaga M, Takeuchi O. RNA Metabolism Governs Immune Function and Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:145-161. [PMID: 38467978 DOI: 10.1007/978-981-99-9781-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Inflammation is a complex process that protects our body from various insults such as infection, injury, and stress. Proper inflammation is beneficial to eliminate the insults and maintain organ homeostasis, however, it can become detrimental if uncontrolled. To tightly regulate inflammation, post-transcriptional mechanisms governing RNA metabolism play a crucial role in monitoring the expression of immune-related genes, such as tumor necrosis factor (TNF) and interleukin-6 (IL-6). These mechanisms involve the coordinated action of various RNA-binding proteins (RBPs), including the Regnase family, Roquin, and RNA methyltransferases, which are responsible for mRNA decay and/or translation regulation. The collaborative efforts of these RBPs are essential in preventing aberrant immune response activation and consequently safeguarding against inflammatory and autoimmune diseases. This review provides an overview of recent advancements in our understanding of post-transcriptional regulation within the immune system and explores the specific roles of individual RBPs in RNA metabolism and regulation.
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Affiliation(s)
- Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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37
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Bhattarai PY, Kim G, Bhandari D, Shrestha P, Choi HS. Regulation of m 6A Methylome in Cancer: Mechanisms, Implications, and Therapeutic Strategies. Cells 2023; 13:66. [PMID: 38201270 PMCID: PMC10778393 DOI: 10.3390/cells13010066] [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: 11/26/2023] [Revised: 12/16/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Reversible N6-adenosine methylation of mRNA, referred to as m6A modification, has emerged as an important regulator of post-transcriptional RNA processing. Numerous studies have highlighted its crucial role in the pathogenesis of diverse diseases, particularly cancer. Post-translational modifications of m6A-related proteins play a fundamental role in regulating the m6A methylome, thereby influencing the fate of m6A-methylated RNA. A comprehensive understanding of the mechanisms that regulate m6A-related proteins and the factors contributing to the specificity of m6A deposition has the potential to unveil novel therapeutic strategies for cancer treatment. This review provides an in-depth overview of our current knowledge of post-translational modifications of m6A-related proteins, associated signaling pathways, and the mechanisms that drive the specificity of m6A modifications. Additionally, we explored the role of m6A-dependent mechanisms in the progression of various human cancers. Together, this review summarizes the mechanisms underlying the regulation of the m6A methylome to provide insight into its potential as a novel therapeutic strategy for the treatment of cancer.
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Affiliation(s)
| | | | | | | | - Hong Seok Choi
- College of Pharmacy, Chosun University, Gwangju 61452, Republic of Korea; (P.Y.B.); (G.K.); (D.B.); (P.S.)
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38
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Morillo L, Paternina T, Alasseur Q, Genovesio A, Schwartz S, Le Hir H. Comprehensive mapping of exon junction complex binding sites reveals universal EJC deposition in Drosophila. BMC Biol 2023; 21:246. [PMID: 37936138 PMCID: PMC10630996 DOI: 10.1186/s12915-023-01749-1] [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: 08/04/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND The exon junction complex (EJC) is involved in most steps of the mRNA life cycle, ranging from splicing to nonsense-mediated mRNA decay (NMD). It is assembled by the splicing machinery onto mRNA in a sequence-independent manner. A fundamental open question is whether the EJC is deposited onto all exon‒exon junctions or only on a subset of them. Several previous studies have made observations supportive of the latter, yet these have been limited by methodological constraints. RESULTS In this study, we sought to overcome these limitations via the integration of two different approaches for transcriptome-wide mapping of EJCs. Our results revealed that nearly all, if not all, internal exons consistently harbor an EJC in Drosophila, demonstrating that EJC presence is an inherent consequence of the splicing reaction. Furthermore, our study underscores the limitations of eCLIP methods in fully elucidating the landscape of RBP binding sites. Our findings highlight how highly specific (low false positive) methodologies can lead to erroneous interpretations due to partial sensitivity (high false negatives). CONCLUSIONS This study contributes to our understanding of EJC deposition and its association with pre-mRNA splicing. The universal presence of EJC on internal exons underscores its significance in ensuring proper mRNA processing. Additionally, our observations highlight the need to consider both specificity and sensitivity in RBP mapping methodologies.
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Affiliation(s)
- Lucía Morillo
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Toni Paternina
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Quentin Alasseur
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Auguste Genovesio
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Hervé Le Hir
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France.
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Jung I, Kim YK. Exon Junction Complex Is a Molecular Compass of N 6-Methyladenosine Modification. Mol Cells 2023; 46:589-591. [PMID: 37853685 PMCID: PMC10590705 DOI: 10.14348/molcells.2023.0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/09/2023] [Accepted: 07/09/2023] [Indexed: 10/20/2023] Open
Affiliation(s)
- Inhong Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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40
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [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: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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41
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Yan H, Zhang L, Li R. Identification of m6A suppressor EIF4A3 as a novel cancer prognostic and immunotherapy biomarker through bladder cancer clinical data validation and pan-cancer analysis. Sci Rep 2023; 13:16457. [PMID: 37777564 PMCID: PMC10542776 DOI: 10.1038/s41598-023-43500-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023] Open
Abstract
EIF4A3 represents a novel m6A suppressor that exerts control over the global m6A mRNA modification level, therefore influencing gene destiny. Despite increasing evidence that highlights a pivotal role of EIF4A3 in tumor progression and immunity, a comprehensive pan-cancer analysis of EIF4A3 has yet to be conducted, in order to ascertain whether EIF4A3 could be a viable biomarker for cancer screening, prediction of prognosis, and to facilitate accurate therapy design in various human malignancies. We analyzed the expression levels of EIF4A3 in bladder cancer compared to para-cancer tissue. Subsequently survival analysis was conducted to ascertain the potential association between EIF4A3 expression and patient prognosis. To further corroborate this evidence, we conducted an extensive data mining process of several publicly available databases, including UCSC Xena database, TCGA, and GTEx. Raw data from the UCSC Xena database was processed using online tools to obtain results that could be subjected to further analysis. Our study unveiled a considerable increase in the expression levels of EIF4A3 in bladder cancer compared to para-cancer tissue. Subsequent validation experiments confirmed that bladder cancer patients exhibiting higher levels of EIF4A3 expression have significantly worse prognostic outcomes. Next, our pan-cancer analysis found that the expression level of EIF4A3 is significantly higher in most cancers. Notably, high expression levels of EIF4A3 were negatively associated with patient prognosis across various cancer types. Furthermore, as a novel m6A suppressor, EIF4A3 was found to be correlated with numerous RNA modification genes in multiple cancer types. Meanwhile, analysis of publicly available databases revealed that EIF4A3 expression was significantly related to immune score and immune cell levels in most cancer types. Interestingly, EIF4A3 was also identified as a superior immunotherapy biomarker when compared to several traditional immunotherapy biomarkers. Lastly, genetic alterations analysis revealed that amplification was the most frequently occurring abnormality in the EIF4A3 gene. EIF4A3 emerges as a promising biomarker with the potential to significantly enhance tumor screening, prognostic evaluation, and the design of individualized treatment strategies across a diverse array of malignancies.
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Affiliation(s)
- Huaqing Yan
- Department of Urology, Ningbo Medical Center Lihuili Hospital, Ningbo, 315000, Zhejiang, People's Republic of China
| | - Liqi Zhang
- Department of Reproductive Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, 315000, Zhejiang, People's Republic of China
| | - Rubing Li
- Department of Urology, Ningbo Medical Center Lihuili Hospital, Ningbo, 315000, Zhejiang, People's Republic of China.
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42
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Breger K, Kunkler CN, O'Leary NJ, Hulewicz JP, Brown JA. Ghost authors revealed: The structure and function of human N 6 -methyladenosine RNA methyltransferases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1810. [PMID: 37674370 PMCID: PMC10915109 DOI: 10.1002/wrna.1810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 09/08/2023]
Abstract
Despite the discovery of modified nucleic acids nearly 75 years ago, their biological functions are still being elucidated. N6 -methyladenosine (m6 A) is the most abundant modification in eukaryotic messenger RNA (mRNA) and has also been detected in non-coding RNAs, including long non-coding RNA, ribosomal RNA, and small nuclear RNA. In general, m6 A marks can alter RNA secondary structure and initiate unique RNA-protein interactions that can alter splicing, mRNA turnover, and translation, just to name a few. Although m6 A marks in human RNAs have been known to exist since 1974, the structures and functions of methyltransferases responsible for writing m6 A marks have been established only recently. Thus far, there are four confirmed human methyltransferases that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to the N6 position of adenosine, producing m6 A: methyltransferase-like protein (METTL) 3/METTL14 complex, METTL16, METTL5, and zinc-finger CCHC-domain-containing protein 4. Though the methyltransferases have unique RNA targets, all human m6 A RNA methyltransferases contain a Rossmann fold with a conserved SAM-binding pocket, suggesting that they utilize a similar catalytic mechanism for methyl transfer. For each of the human m6 A RNA methyltransferases, we present the biological functions and links to human disease, RNA targets, catalytic and kinetic mechanisms, and macromolecular structures. We also discuss m6 A marks in human viruses and parasites, assigning m6 A marks in the transcriptome to specific methyltransferases, small molecules targeting m6 A methyltransferases, and the enzymes responsible for hypermodified m6 A marks and their biological functions in humans. Understanding m6 A methyltransferases is a critical steppingstone toward establishing the m6 A epitranscriptome and more broadly the RNome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nathan J O'Leary
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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43
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Jalloh B, Lancaster CL, Rounds JC, Brown BE, Leung SW, Banerjee A, Morton DJ, Bienkowski RS, Fasken MB, Kremsky IJ, Tegowski M, Meyer K, Corbett A, Moberg K. The Drosophila Nab2 RNA binding protein inhibits m 6A methylation and male-specific splicing of Sex lethal transcript in female neuronal tissue. eLife 2023; 12:e64904. [PMID: 37458420 PMCID: PMC10351920 DOI: 10.7554/elife.64904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
The Drosophila polyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls adult locomotion, axon projection, dendritic arborization, and memory through a largely undefined set of target RNAs. Here, we show a specific role for Nab2 in regulating splicing of ~150 exons/introns in the head transcriptome and focus on retention of a male-specific exon in the sex determination factor Sex-lethal (Sxl) that is enriched in female neurons. Previous studies have revealed that this splicing event is regulated in females by N6-methyladenosine (m6A) modification by the Mettl3 complex. At a molecular level, Nab2 associates with Sxl pre-mRNA in neurons and limits Sxl m6A methylation at specific sites. In parallel, reducing expression of the Mettl3, Mettl3 complex components, or the m6A reader Ythdc1 rescues mutant phenotypes in Nab2 flies. Overall, these data identify Nab2 as an inhibitor of m6A methylation and imply significant overlap between Nab2 and Mettl3 regulated RNAs in neuronal tissue.
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Affiliation(s)
- Binta Jalloh
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Carly L Lancaster
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory UniversityAtlantaUnited States
| | - J Christopher Rounds
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Brianna E Brown
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
| | - Sara W Leung
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ayan Banerjee
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Derrick J Morton
- Department of Biology, Emory UniversityAtlantaUnited States
- Emory Institutional Research and Academic Career Development Award (IRACDA), Fellowships in Research and Science Teaching (FIRST) Postdoctoral FellowshipAtlantaUnited States
| | - Rick S Bienkowski
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Milo B Fasken
- Department of Biology, Emory UniversityAtlantaUnited States
| | | | - Matthew Tegowski
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
| | - Kate Meyer
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
| | - Anita Corbett
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ken Moberg
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
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44
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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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45
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Lei Y, Yuan Z, Zeng Q, Wan B, Liu J, Wang W. Dynamic N6-methyladenosine RNA methylation landscapes reveal epi-transcriptomic modulation induced by ammonia nitrogen exposure in the Pacific whiteleg shrimp Litopenaeus vannamei. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131996. [PMID: 37423135 DOI: 10.1016/j.jhazmat.2023.131996] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Despite the versatility of RNA m6A methylation in regulating various biological processes, its involvement in the physiological response to ammonia nitrogen toxicity in decapod crustaceans like shrimp remains enigmatic. Here, we provided the first characterization of dynamic RNA m6A methylation landscapes induced by toxic ammonia exposure in the Pacific whiteleg shrimp Litopenaeus vannamei. The global m6A methylation level showed significant decrease following ammonia exposure, and most of the m6A methyltransferases and m6A binding proteins were significantly repressed. Distinct from many well-studied model organisms, m6A methylated peaks in the transcriptome of L. vannamei were enriched not only near the termination codon and in the 3' untranslated region (UTR), but also around the start codon and in the 5' UTR. Upon ammonia exposure, 11,430 m6A peaks corresponding to 6113 genes were hypo-methylated, and 5660 m6A peaks from 3912 genes were hyper-methylated. The differentially methylated genes showing significant changes in expression were over-represented by genes associated with metabolism, cellular immune defense and apoptotic signaling pathways. Notably, the m6A-modified ammonia-responsive genes encompassed a subset of genes related to glutamine synthesis, purine conversion and urea production, implying that m6A methylation may modulate shrimp ammonia stress responses partly through these ammonia metabolic processes.
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Affiliation(s)
- Yiguo Lei
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Zhixiang Yuan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Qingtian Zeng
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Boquan Wan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jianyong Liu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Modern Seed Industry Park of the Pacific Whiteleg Shrimp, Zhanjiang 524088, China
| | - Wei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China; Guangdong Provincial Modern Seed Industry Park of the Pacific Whiteleg Shrimp, Zhanjiang 524088, China.
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46
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Pomaville MM, He C. Advances in targeting RNA modifications for anticancer therapy. Trends Cancer 2023; 9:528-542. [PMID: 37147166 PMCID: PMC10330282 DOI: 10.1016/j.trecan.2023.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
Numerous strategies are employed by cancer cells to control gene expression and facilitate tumorigenesis. In the study of epitranscriptomics, a diverse set of modifications to RNA represent a new player of gene regulation in disease and in development. N6-methyladenosine (m6A) is the most common modification on mammalian messenger RNA and tends to be aberrantly placed in cancer. Recognized by a series of reader proteins that dictate the fate of the RNA, m6A-modified RNA could promote tumorigenesis by driving protumor gene expression signatures and altering the immunologic response to tumors. Preclinical evidence suggests m6A writer, reader, and eraser proteins are attractive therapeutic targets. First-in-human studies are currently testing small molecule inhibition against the methyltransferase-like 3 (METTL3)/methyltransferase-like 14 (METTL14) methyltransferase complex. Additional modifications to RNA are adopted by cancers to drive tumor development and are under investigation.
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Affiliation(s)
- Monica M Pomaville
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA; Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| | - Chuan He
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA; Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
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47
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Leseva MN, Buttari B, Saso L, Dimitrova PA. Infection Meets Inflammation: N6-Methyladenosine, an Internal Messenger RNA Modification as a Tool for Pharmacological Regulation of Host-Pathogen Interactions. Biomolecules 2023; 13:1060. [PMID: 37509095 PMCID: PMC10377384 DOI: 10.3390/biom13071060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
The significance of internal mRNA modifications for the modulation of transcript stability, for regulation of nuclear export and translation efficiency, and their role in suppressing innate immunity is well documented. Over the years, the molecular complexes involved in the dynamic regulation of the most prevalent modifications have been characterized-we have a growing understanding of how each modification is set and erased, where it is placed, and in response to what cues. Remarkably, internal mRNA modifications, such as methylation, are emerging as an additional layer of regulation of immune cell homeostasis, differentiation, and function. A fascinating recent development is the investigation into the internal modifications of host/pathogen RNA, specifically N6-methyladenosine (m6A), its abundance and distribution during infection, and its role in disease pathogenesis and in shaping host immune responses. Low molecular weight compounds that target RNA-modifying enzymes have shown promising results in vitro and in animal models of different cancers and are expanding the tool-box in immuno-oncology. Excitingly, such modulators of host mRNA methyltransferase or demethylase activity hold profound implications for the development of new broad-spectrum therapeutic agents for infectious diseases as well. This review describes the newly uncovered role of internal mRNA modification in infection and in shaping the function of the immune system in response to invading pathogens. We will also discuss its potential as a therapeutic target and identify pitfalls that need to be overcome if it is to be effectively leveraged against infectious agents.
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Affiliation(s)
- Milena N Leseva
- Laboratory of Experimental Immunotherapy, Department of Immunology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Brigitta Buttari
- Department of Cardiovascular and Endocrine-Metabolic Diseases and Aging, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", La Sapienza University of Rome, 00185 Rome, Italy
| | - Petya A Dimitrova
- Laboratory of Experimental Immunotherapy, Department of Immunology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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48
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Abstract
Over the past decade, mRNA modifications have emerged as important regulators of gene expression control in cells. Fueled in large part by the development of tools for detecting RNA modifications transcriptome wide, researchers have uncovered a diverse epitranscriptome that serves as an additional layer of gene regulation beyond simple RNA sequence. Here, we review the proteins that write, read, and erase these marks, with a particular focus on the most abundant internal modification, N6-methyladenosine (m6A). We first describe the discovery of the key enzymes that deposit and remove m6A and other modifications and discuss how our understanding of these proteins has shaped our views of modification dynamics. We then review current models for the function of m6A reader proteins and how our knowledge of these proteins has evolved. Finally, we highlight important future directions for the field and discuss key questions that remain unanswered.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Matthew Tegowski
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
- Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, USA
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49
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Jin Z, MacPherson K, Liu Z, Vu LP. RNA modifications in hematological malignancies. Int J Hematol 2023; 117:807-820. [PMID: 36929506 DOI: 10.1007/s12185-023-03576-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023]
Abstract
RNA modifications play an important role in various cancers including blood cancers by controlling gene expression programs critical for survival, proliferation and differentiation of cancer cells. While hundreds of RNA modifications have been identified, many have not been functionally characterized. With development of enabling technologies to identify and map RNA modifications, tremendous advancement has been made in our understanding of the biological functions of these molecular markers in diverse cellular contexts. In the last 5 years, N6-methyladenosine (m6A), the most prevalent internal mRNA modification, has been extensively implicated in many facets of leukemogenesis. Other types of RNA modifications are also involved in the regulation of cell fate decisions and tumorigenesis. Here, we summarize existing knowledge and recent discoveries regarding the role of RNA modifications in leukemia. We choose to highlight cutting-edge techniques to characterize and profile RNA modifications while discussing critical functions of key modifiers and regulatory mechanisms in the pathogenesis of hematological malignancies and touch on therapeutic strategies targeting RNA modifications. These important advancements in the field will continue to foster a strong foundation for the development of innovative treatments for hematological malignancies.
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Affiliation(s)
- Zhen Jin
- Terry Fox Laboratory, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Kyle MacPherson
- Terry Fox Laboratory, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, Canada
| | - Zongmin Liu
- Terry Fox Laboratory, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Ly P Vu
- Terry Fox Laboratory, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, Canada. .,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
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50
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Xu X, Chang CW, Li M, Omabe K, Le N, Chen YH, Liang F, Liu Y. DNA replication initiation factor RECQ4 possesses a role in antagonizing DNA replication initiation. Nat Commun 2023; 14:1233. [PMID: 36871012 PMCID: PMC9985596 DOI: 10.1038/s41467-023-36968-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Deletion of the conserved C-terminus of the Rothmund-Thomson syndrome helicase RECQ4 is highly tumorigenic. However, while the RECQ4 N-terminus is known to facilitate DNA replication initiation, the function of its C-terminus remains unclear. Using an unbiased proteomic approach, we identify an interaction between the RECQ4 N-terminus and the anaphase-promoting complex/cyclosome (APC/C) on human chromatin. We further show that this interaction stabilizes APC/C co-activator CDH1 and enhances APC/C-dependent degradation of the replication inhibitor Geminin, allowing replication factors to accumulate on chromatin. In contrast, the function is blocked by the RECQ4 C-terminus, which binds to protein inhibitors of APC/C. A cancer-prone, C-terminal-deleted RECQ4 mutation increases origin firing frequency, accelerates G1/S transition, and supports abnormally high DNA content. Our study reveals a role of the human RECQ4 C-terminus in antagonizing its N-terminus, thereby suppressing replication initiation, and this suppression is impaired by oncogenic mutations.
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Affiliation(s)
- Xiaohua Xu
- Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, CA, 92008, USA
| | - Chou-Wei Chang
- Vesigen Therapeutics, 790 Memorial Drive, Suite 103, Cambridge, MA, 02139, USA
| | - Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Kenneth Omabe
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Nhung Le
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA
| | - Yi-Hsuan Chen
- Department of Computer Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Feng Liang
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, 90089, USA
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, 91010-3000, USA.
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