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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Liu ZY, You QY, Liu ZY, Lin LC, Yang JJ, Tao H. m6A control programmed cell death in cardiac fibrosis. Life Sci 2024; 353:122922. [PMID: 39032691 DOI: 10.1016/j.lfs.2024.122922] [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: 05/09/2024] [Revised: 06/29/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
N6-methyladenosine (m6A) modification is closely related to cardiac fibrosis. As the most common and abundant form of mRNA modification in eukaryotes, m6A is deposited by methylases ("writers"), recognized and effected by RNA-binding proteins ("readers"), and removed by demethylases ("erasers"), achieving highly dynamic reversibility. m6A modification is involved in regulating the entire biological process of target RNA, including transcription, processing and splicing, export from the nucleus to the cytoplasm, and enhancement or reduction of stability and translation. Programmed cell death (PCD) comprises many forms and pathways, with apoptosis and autophagy being the most common. Other forms include pyroptosis, ferroptosis, necroptosis, mitochondrial permeability transition (MPT)-dependent necrosis, and parthanatos. In recent years, increasing evidence suggests that m6A modification can mediate PCD, affecting cardiac fibrosis. Since the correlation between some PCD types and m6A modification is not yet clear, this article mainly introduces the relationship between four common PCD types (apoptosis, autophagy, pyroptosis, and ferroptosis) and m6A modification, as well as their role and influence in cardiac fibrosis.
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Affiliation(s)
- Zhen-Yu Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Qing-Ye You
- Anhui Women and Children's Medical Center, Hefei 230001, PR China
| | - Zhi-Yan Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Li-Chan Lin
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Jing-Jing Yang
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China.
| | - Hui Tao
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China; Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China.
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3
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Stasevich EM, Simonova AV, Bogomolova EA, Murashko MM, Uvarova AN, Zheremyan EA, Korneev KV, Schwartz AM, Kuprash DV, Demin DE. Cut from the same cloth: RNAs transcribed from regulatory elements. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195049. [PMID: 38964653 DOI: 10.1016/j.bbagrm.2024.195049] [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: 04/22/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
A certain degree of chromatin openness is necessary for the activity of transcription-regulating regions within the genome, facilitating accessibility to RNA polymerases and subsequent synthesis of regulatory element RNAs (regRNAs) from these regions. The rapidly increasing number of studies underscores the significance of regRNAs across diverse cellular processes and diseases, challenging the paradigm that these transcripts are non-functional transcriptional noise. This review explores the multifaceted roles of regRNAs in human cells, encompassing rather well-studied entities such as promoter RNAs and enhancer RNAs (eRNAs), while also providing insights into overshadowed silencer RNAs and insulator RNAs. Furthermore, we assess notable examples of shorter regRNAs, like miRNAs, snRNAs, and snoRNAs, playing important roles. Expanding our discourse, we deliberate on the potential usage of regRNAs as biomarkers and novel targets for cancer and other human diseases.
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Affiliation(s)
- E M Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A V Simonova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Bogomolova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - M M Murashko
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - A N Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - K V Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A M Schwartz
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - D V Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D E Demin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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4
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Fosseprez O, Cuvier O. Uncovering the functions and mechanisms of regulatory elements-associated non-coding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195059. [PMID: 39226990 DOI: 10.1016/j.bbagrm.2024.195059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/12/2024] [Accepted: 08/23/2024] [Indexed: 09/05/2024]
Abstract
Over the past decade, regulatory non-coding RNAs (ncRNAs) produced by RNA Pol II have been revealed as meaningful players in various essential cellular functions. In particular, thousands of ncRNAs are produced at transcriptional regulatory elements such as enhancers and promoters, where they may exert multiple functions to regulate proper development, cellular programming, transcription or genomic stability. Here, we review the mechanisms involving these regulatory element-associated ncRNAs, and particularly enhancer RNAs (eRNAs) and PROMoter uPstream Transcripts (PROMPTs). We contextualize the mechanisms described to the processing and degradation of these short lived RNAs. We summarize recent findings explaining how ncRNAs operate locally at promoters and enhancers, or further away, either shortly after their production by RNA Pol II, or through post-transcriptional stabilization. Such discoveries lead to a converging model accounting for how ncRNAs influence cellular fate, by acting on transcription and chromatin structure, which may further involve factors participating to 3D nuclear organization.
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Affiliation(s)
- Olivier Fosseprez
- Chromatin Dynamics and Cell Proliferation team; Center of Integrative Biology (CBI), Molecular Cellular and Developmental Biology Unit (MCD/UMR5077) Center of Integrative Biology (CBI-CNRS), Université de Toulouse (UPS), F-31000, France.
| | - Olivier Cuvier
- Chromatin Dynamics and Cell Proliferation team; Center of Integrative Biology (CBI), Molecular Cellular and Developmental Biology Unit (MCD/UMR5077) Center of Integrative Biology (CBI-CNRS), Université de Toulouse (UPS), F-31000, France.
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5
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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 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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6
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Jia K, Duan J, Cheng G, Li H, Li S, Hu M. DNA Methylation is Involved in Sex Determination in Spinach. Biochem Genet 2024; 62:2455-2468. [PMID: 37950843 DOI: 10.1007/s10528-023-10524-4] [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: 10/09/2022] [Accepted: 09/07/2023] [Indexed: 11/13/2023]
Abstract
DNA methylation plays a critical role in the modulation of gene expression. The role of DNA methylation in sex determination was investigated in spinach. The differentiated cytosine CpG methylation profiles of CCGG motifs were assessed with methylation sensitivity amplification polymorphism (MSAP) in spinach. Among 442 DNA fragments from four plants, 134 methylated fragments were found. Relative proportions of methylation sites were 28.8% in male plants and 31.8% in female plants. At the same time, cytosine methylation levels were higher in females than in males in CCGG motifs of genomes in the spinach. These findings suggest that methylation of CG islands is involved in sex determination and differentiation in spinach.
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Affiliation(s)
- Keli Jia
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | - Jiaming Duan
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | | | - Heng Li
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
| | - Miao Hu
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China.
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7
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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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8
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Elvira-Blázquez D, Fernández-Justel JM, Arcas A, Statello L, Goñi E, González J, Ricci B, Zaccara S, Raimondi I, Huarte M. YTHDC1 m 6A-dependent and m 6A-independent functions converge to preserve the DNA damage response. EMBO J 2024; 43:3494-3522. [PMID: 38951610 PMCID: PMC11329685 DOI: 10.1038/s44318-024-00153-x] [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: 08/09/2023] [Revised: 05/07/2024] [Accepted: 06/05/2024] [Indexed: 07/03/2024] Open
Abstract
Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding of its impact on a fully efficient DNA damage response remains limited. Here, through a targeted CRISPR-knockout screen, we identify RNA-binding proteins and modifiers that participate in the p53 response. Among the top hits, we find the m6A reader YTHDC1 as a master regulator of p53 expression. YTHDC1 binds to the transcription start sites of TP53 and other genes involved in the DNA damage response, promoting their transcriptional elongation. YTHDC1 deficiency also causes the retention of introns and therefore aberrant protein production of key DNA damage factors. While YTHDC1-mediated intron retention requires m6A, TP53 transcriptional pause-release is promoted by YTHDC1 independently of m6A. Depletion of YTHDC1 causes genomic instability and aberrant cancer cell proliferation mediated by genes regulated by YTHDC1. Our results uncover YTHDC1 as an orchestrator of the DNA damage response through distinct mechanisms of co-transcriptional mRNA regulation.
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Affiliation(s)
- Daniel Elvira-Blázquez
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - José Miguel Fernández-Justel
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Aida Arcas
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
- Clarivate, Barcelona, Spain
| | - Luisa Statello
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Enrique Goñi
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Jovanna González
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Benedetta Ricci
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sara Zaccara
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ivan Raimondi
- New York Genome Center, New York, NY, USA.
- Weill Cornell Medicine, New York, NY, USA.
| | - Maite Huarte
- Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain.
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9
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Cai Z, Tang Q, Song P, Tian E, Yang J, Jia G. The m6A reader ECT8 is an abiotic stress sensor that accelerates mRNA decay in Arabidopsis. THE PLANT CELL 2024; 36:2908-2926. [PMID: 38835286 PMCID: PMC11289641 DOI: 10.1093/plcell/koae149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/11/2024] [Indexed: 06/06/2024]
Abstract
N 6-methyladenosine (m6A) is the most abundant mRNA modification and plays diverse roles in eukaryotes, including plants. It regulates various processes, including plant growth, development, and responses to external or internal stress responses. However, the mechanisms underlying how m6A is related to environmental stresses in both mammals and plants remain elusive. Here, we identified EVOLUTIONARILY CONSERVED C-TERMINAL REGION 8 (ECT8) as an m6A reader protein and showed that its m6A-binding capability is required for salt stress responses in Arabidopsis (Arabidopsis thaliana). ECT8 accelerates the degradation of its target transcripts through direct interaction with the decapping protein DECAPPING 5 within processing bodies. We observed a significant increase in the ECT8 expression level under various environmental stresses. Using salt stress as a representative stressor, we found that the transcript and protein levels of ECT8 rise in response to salt stress. The increased abundance of ECT8 protein results in the enhanced binding capability to m6A-modified mRNAs, thereby accelerating their degradation, especially those of negative regulators of salt stress responses. Our results demonstrated that ECT8 acts as an abiotic stress sensor, facilitating mRNA decay, which is vital for maintaining transcriptome homeostasis and enhancing stress tolerance in plants. Our findings not only advance the understanding of epitranscriptomic gene regulation but also offer potential applications for breeding more resilient crops in the face of rapidly changing environmental conditions.
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Affiliation(s)
- Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qian Tang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Enlin Tian
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China
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10
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Haghani V, Goyal A, Zhang A, Sharifi O, Mariano N, Yasui D, Korf I, LaSalle J. Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602975. [PMID: 39071274 PMCID: PMC11275724 DOI: 10.1101/2024.07.10.602975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
As genome sequencing technologies advance, the accumulation of sequencing data in public databases necessitates more robust and adaptable data analysis workflows. Here, we present Rocketchip, which aims to offer a solution to this problem by allowing researchers to easily compare and swap out different components of ChIP-seq, CUT&RUN, and CUT&Tag data analysis, thereby facilitating the identification of reliable analysis methodologies. Rocketchip enables researchers to efficiently process large datasets while ensuring reproducibility and allowing for the reanalysis of existing data. By supporting comparative analyses across different datasets and methodologies, Rocketchip contributes to the rigor and reproducibility of scientific findings. Furthermore, Rocketchip serves as a platform for benchmarking algorithms, allowing researchers to identify the most accurate and efficient analytical approaches to be applied to their data. In emphasizing reproducibility and adaptability, Rocketchip represents a significant step towards fostering robust scientific research practices.
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Affiliation(s)
- Viktoria Haghani
- Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis. Davis, CA, USA
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Aditi Goyal
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Alan Zhang
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Osman Sharifi
- Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis. Davis, CA, USA
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Natasha Mariano
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Dag Yasui
- Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Ian Korf
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis. Davis, CA, USA
| | - Janine LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis. Davis, CA, USA
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11
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Du B, Wang P, Wei L, Qin K, Pei Z, Zheng J, Wang J. Unraveling the independent role of METTL3 in m6A modification and tumor progression in esophageal squamous cell carcinoma. Sci Rep 2024; 14:15398. [PMID: 38965238 PMCID: PMC11224396 DOI: 10.1038/s41598-024-64517-3] [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: 01/17/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
METTL3 and METTL14 are traditionally posited to assemble the m6A methyltransferase complex in a stoichiometric 1:1 ratio, modulating mRNA fate via m6A modifications. Nevertheless, recent investigations reveal inconsistent expression levels and prognostic significance of METTL3 and METTL14 across various tumor types, challenging their consistent functional engagement in neoplastic contexts. A pan-cancer analysis leveraging The Cancer Genome Atlas (TCGA) data has identified pronounced disparities in the expression patterns, functional roles, and correlations with tumor burden between METTL3 and METTL14, particularly in esophageal squamous cell carcinoma (ESCC). Knockdown experiments of METTL3 in EC109 cells markedly suppress cell proliferation both in vitro and in vivo, whereas METTL14 knockdown shows a comparatively muted effect on proliferation and does not significantly alter METTL3 protein levels. mRNA sequencing indicates that METTL3 singularly governs the expression of 1615 genes, with only 776 genes co-regulated with METTL14. Additionally, immunofluorescence co-localization studies suggest discrepancies in cellular localization between METTL3 and METTL14. High-performance liquid chromatography-mass spectrometry (HPLC-MS) analyses demonstrate that METTL3 uniquely associates with the Nop56p-linked pre-rRNA complex and mRNA splicing machinery, independent of METTL14. Preliminary bioinformatics and multi-omics investigations reveal that METTL3's autonomous role in modulating tumor cell proliferation and its involvement in mRNA splicing are potentially pivotal molecular mechanisms. Our study lays both experimental and theoretical groundwork for a deeper understanding of the m6A methyltransferase complex and the development of targeted tumor therapies focusing on METTL3.
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Affiliation(s)
- Bin Du
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Pu Wang
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Lingyu Wei
- Central Laboratory of Clinical Research, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, 047500, China
| | - Kai Qin
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Zhen Pei
- Department of Physiology, Changzhi Medical College, Changzhi, 047500, China
| | - Jinping Zheng
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Jia Wang
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China.
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12
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Chen Q, Ao L, Zhao Q, Tang L, Xiong Y, Yuan Y, Wu X, Xing W, Li Z, Guo W, Liang H, Zheng SG, Lian Q, Lu D, Wan W, Xu X. WTAP/YTHDF1-mediated m 6A modification amplifies IFN-γ-induced immunosuppressive properties of human MSCs. J Adv Res 2024:S2090-1232(24)00256-X. [PMID: 38944238 DOI: 10.1016/j.jare.2024.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
INTRODUCTION The immunosuppressive capacity of mesenchymal stem cells (MSCs) is dependent on the "license" of several pro-inflammatory factors to express immunosuppressive molecular profiles, which determines the therapeutic efficacy of MSCs in immune-mediated inflammatory diseases. Of those, interferon-γ (IFN-γ) is a key inducer for the expression of immunosuppressive molecular profiles; however, the mechanism underlying this effect is unknown. OBJECTIVES To elucidate the regulation mechanism and biological functions of N6-methyladenosine (m6A) modification in the immunosuppressive functions by the IFN-γ-licensing MSCs. METHODS Epitranscriptomic microarray analysis and MeRIP-qPCR assay were performed to identify the regulatory effect of WTAP in the IFN-γ-licensing MSCs. RIP-qPCR, western blot, qRT-PCR and RNA stability assays were used to determine the regulation of WTAP/m6A/YTHDF1 signaling axis in the expression of immunosuppressive molecules. Further, functional capacity of T cells was tested using flow cytometry, and both DSS-induced colitis mice and CIA mice were constructed to clarify the effect of WTAP and YTHDF1 in MSC-mediated immunosuppression. RESULTS We identified that IFN-γ increased the m6A methylation levels of immunosuppressive molecules, while WTAP deficiency abolished the IFN-γ-induced promotion of m6A modification. IFN-γ activated ERK signaling, which induced WTAP phosphorylation. Additionally, the stabilization of WTAP post-transcriptionally increased the mRNA expression of immunosuppressive molecules (IDO1, PD-L1, ICAM1, and VCAM1) in an m6A-YTHDF1-dependent manner; this effect further impacted the immunosuppressive capacity of IFN-γ licensing MSCs on activated T cells. Notably, WTAP/YTHDF1 overexpression enhanced the therapeutic efficacy of IFN-γ licensing MSCs and restructures the ecology of inflammation in both colitis and arthritis models. CONCLUSION Our results showed that m6A modification of IDO1, PD-L1, ICAM1, and VCAM1 mRNA mediated by WTAP-YTHDF1 is involved in the regulation of IFN-γ licensing MSCs immunosuppressive abilities, and shed a light to enhance the clinical therapeutic potential of IFN-γ-licensing MSCs.
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Affiliation(s)
- Quan Chen
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China; Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, China
| | - Luoquan Ao
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Qing Zhao
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Lu Tang
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Yanli Xiong
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China; Cancer Center, Daping Hospital, Army Medical University, Chongqing, China, No.10 Changjiang Zhi Rd, Yuzhong District, Chongqing 400042, China
| | - Yuchuan Yuan
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Xiaofeng Wu
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Wei Xing
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Zhan Li
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Wei Guo
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Huaping Liang
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Song Guo Zheng
- Department of Immunology, School of Cell and Gene Therapy, Songjiang Research Institute, Shanghai Songjiang District Central Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 201600, China
| | - Qizhou Lian
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China; Cord Blood Bank, Guangzhou Institute of Eugenics and Perinatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510000, China; State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Di Lu
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, China
| | - Weijun Wan
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China.
| | - Xiang Xu
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China; Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, China; Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China.
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13
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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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14
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Kahl M, Xu Z, Arumugam S, Edens BM, Fischietti M, Zhu AC, Platanias LC, He C, Zhuang X, Ma YC. m6A RNA methylation regulates mitochondrial function. Hum Mol Genet 2024; 33:969-980. [PMID: 38483349 PMCID: PMC11102592 DOI: 10.1093/hmg/ddae029] [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: 09/14/2023] [Revised: 02/17/2024] [Indexed: 05/20/2024] Open
Abstract
RNA methylation of N6-methyladenosine (m6A) is emerging as a fundamental regulator of every aspect of RNA biology. RNA methylation directly impacts protein production to achieve quick modulation of dynamic biological processes. However, whether RNA methylation regulates mitochondrial function is not known, especially in neuronal cells which require a high energy supply and quick reactive responses. Here we show that m6A RNA methylation regulates mitochondrial function through promoting nuclear-encoded mitochondrial complex subunit RNA translation. Conditional genetic knockout of m6A RNA methyltransferase Mettl14 (Methyltransferase like 14) by Nestin-Cre together with metabolomic analysis reveals that Mettl14 knockout-induced m6A depletion significantly downregulates metabolites related to energy metabolism. Furthermore, transcriptome-wide RNA methylation profiling of wild type and Mettl14 knockout mouse brains by m6A-Seq shows enrichment of methylation on mitochondria-related RNA. Importantly, loss of m6A leads to a significant reduction in mitochondrial respiratory capacity and membrane potential. These functional defects are paralleled by the reduced expression of mitochondrial electron transport chain complexes, as well as decreased mitochondrial super-complex assembly and activity. Mechanistically, m6A depletion decreases the translational efficiency of methylated RNA encoding mitochondrial complex subunits through reducing their association with polysomes, while not affecting RNA stability. Together, these findings reveal a novel role for RNA methylation in regulating mitochondrial function. Given that mitochondrial dysfunction and RNA methylation have been increasingly implicate in neurodegenerative disorders, our findings not only provide insights into fundamental mechanisms regulating mitochondrial function, but also open up new avenues for understanding the pathogenesis of neurological diseases.
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Affiliation(s)
- Michael Kahl
- Departments of Pediatrics, Neurology and Neuroscience, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL 60611, United States
- Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Chicago, IL 60611, United States
| | - Zhaofa Xu
- Departments of Pediatrics, Neurology and Neuroscience, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL 60611, United States
- Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Chicago, IL 60611, United States
| | - Saravanan Arumugam
- Departments of Pediatrics, Neurology and Neuroscience, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL 60611, United States
- Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Chicago, IL 60611, United States
| | - Brittany M Edens
- Departments of Pediatrics, Neurology and Neuroscience, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL 60611, United States
- Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Chicago, IL 60611, United States
| | - Mariafausta Fischietti
- Robert H. Lurie Comprehensive Cancer Center, Division of Hematology-Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL 60611, United States
| | - Allen C Zhu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, United States
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center, Division of Hematology-Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL 60611, United States
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, 924 East 57th Street, Chicago, IL 60612, United States
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, United States
| | - Xiaoxi Zhuang
- Department of Neurobiology, and Committee on Neurobiology, The University of Chicago, 924 East 57th Street, Chicago, IL 60637, United States
| | - Yongchao C Ma
- Departments of Pediatrics, Neurology and Neuroscience, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL 60611, United States
- Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Chicago, IL 60611, United States
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15
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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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16
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Rambout X, Maquat LE. Nuclear mRNA decay: regulatory networks that control gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00712-2. [PMID: 38637632 DOI: 10.1038/s41576-024-00712-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2024] [Indexed: 04/20/2024]
Abstract
Proper regulation of mRNA production in the nucleus is critical for the maintenance of cellular homoeostasis during adaptation to internal and environmental cues. Over the past 25 years, it has become clear that the nuclear machineries governing gene transcription, pre-mRNA processing, pre-mRNA and mRNA decay, and mRNA export to the cytoplasm are inextricably linked to control the quality and quantity of mRNAs available for translation. More recently, an ever-expanding diversity of new mechanisms by which nuclear RNA decay factors finely tune the expression of protein-encoding genes have been uncovered. Here, we review the current understanding of how mammalian cells shape their protein-encoding potential by regulating the decay of pre-mRNAs and mRNAs in the nucleus.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA.
- Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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17
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Wang Z, Zhong S, Zhang S, Zhang B, Zheng Y, Sun Y, Zhang Q, Liu X. A novel and ubiquitous miRNA-involved regulatory module ensures precise phosphorylation of RNA polymerase II and proper transcription. PLoS Pathog 2024; 20:e1012138. [PMID: 38640110 PMCID: PMC11062530 DOI: 10.1371/journal.ppat.1012138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 05/01/2024] [Accepted: 03/20/2024] [Indexed: 04/21/2024] Open
Abstract
Proper transcription orchestrated by RNA polymerase II (RNPII) is crucial for cellular development, which is rely on the phosphorylation state of RNPII's carboxyl-terminal domain (CTD). Sporangia, developed from mycelia, are essential for the destructive oomycetes Phytophthora, remarkable transcriptional changes are observed during the morphological transition. However, how these changes are rapidly triggered and their relationship with the versatile RNPII-CTD phosphorylation remain enigmatic. Herein, we found that Phytophthora capsici undergone an elevation of Ser5-phosphorylation in its uncanonical heptapeptide repeats of RNPII-CTD during sporangia development, which subsequently changed the chromosomal occupation of RNPII and primarily activated transcription of certain genes. A cyclin-dependent kinase, PcCDK7, was highly induced and phosphorylated RNPII-CTD during this morphological transition. Mechanistically, a novel DCL1-dependent microRNA, pcamiR1, was found to be a feedback modulator for the precise phosphorylation of RNPII-CTD by complexing with PcAGO1 and regulating the accumulation of PcCDK7. Moreover, this study revealed that the pcamiR1-CDK7-RNPII regulatory module is evolutionarily conserved and the impairment of the balance between pcamiR1 and PcCDK7 could efficiently reduce growth and virulence of P. capsici. Collectively, this study uncovers a novel and evolutionary conserved mechanism of transcription regulation which could facilitate correct development and identifies pcamiR1 as a promising target for disease control.
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Affiliation(s)
- Zhiwen Wang
- China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Shan Zhong
- China Agricultural University, Beijing, China
| | | | - Borui Zhang
- China Agricultural University, Beijing, China
| | - Yang Zheng
- China Agricultural University, Beijing, China
| | - Ye Sun
- China Agricultural University, Beijing, China
| | | | - Xili Liu
- China Agricultural University, Beijing, China
- State Key Laboratory or Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, China
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18
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Vaid R, Thombare K, Mendez A, Burgos-Panadero R, Djos A, Jachimowicz D, Lundberg K, Bartenhagen C, Kumar N, Tümmler C, Sihlbom C, Fransson S, Johnsen J, Kogner P, Martinsson T, Fischer M, Mondal T. METTL3 drives telomere targeting of TERRA lncRNA through m6A-dependent R-loop formation: a therapeutic target for ALT-positive neuroblastoma. Nucleic Acids Res 2024; 52:2648-2671. [PMID: 38180812 PMCID: PMC10954483 DOI: 10.1093/nar/gkad1242] [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: 12/06/2022] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
Telomerase-negative tumors maintain telomere length by alternative lengthening of telomeres (ALT), but the underlying mechanism behind ALT remains poorly understood. A proportion of aggressive neuroblastoma (NB), particularly relapsed tumors, are positive for ALT (ALT+), suggesting that a better dissection of the ALT mechanism could lead to novel therapeutic opportunities. TERRA, a long non-coding RNA (lncRNA) derived from telomere ends, localizes to telomeres in a R-loop-dependent manner and plays a crucial role in telomere maintenance. Here we present evidence that RNA modification at the N6 position of internal adenosine (m6A) in TERRA by the methyltransferase METTL3 is essential for telomere maintenance in ALT+ cells, and the loss of TERRA m6A/METTL3 results in telomere damage. We observed that m6A modification is abundant in R-loop enriched TERRA, and the m6A-mediated recruitment of hnRNPA2B1 to TERRA is critical for R-loop formation. Our findings suggest that m6A drives telomere targeting of TERRA via R-loops, and this m6A-mediated R-loop formation could be a widespread mechanism employed by other chromatin-interacting lncRNAs. Furthermore, treatment of ALT+ NB cells with a METTL3 inhibitor resulted in compromised telomere targeting of TERRA and accumulation of DNA damage at telomeres, indicating that METTL3 inhibition may represent a therapeutic approach for ALT+ NB.
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Affiliation(s)
- Roshan Vaid
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ketan Thombare
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Akram Mendez
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Rebeca Burgos-Panadero
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Anna Djos
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Jachimowicz
- Translational Genomics, Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Kristina Ihrmark Lundberg
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, and Pediatric Oncology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Navinder Kumar
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Conny Tümmler
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, and Pediatric Oncology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Susanne Fransson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, and Pediatric Oncology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, and Pediatric Oncology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Tanmoy Mondal
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg, 41345 Sweden
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19
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Yao L, Li T, Teng Y, Guo J, Zhang H, Xia L, Wu Q. ALKHB5-demethylated lncRNA SNHG15 promotes myeloma tumorigenicity by increasing chromatin accessibility and recruiting H3K36me3 modifier SETD2. Am J Physiol Cell Physiol 2024; 326:C684-C697. [PMID: 38145297 PMCID: PMC11193452 DOI: 10.1152/ajpcell.00348.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
Chromatin instability plays a crucial role in multiple myeloma (MM) relapse and progression, but its mechanism remains obscure. Here, we uncovered that m6A-demethylase ALKBH5 upregulated and stabilized long noncoding RNA (lncRNA) small nucleolar RNA host gene 15 (SNHG15), which was elevated in MM and positively correlated with unfavorable clinical prognosis factors. ALKBH5-SNHG15 axis participated in viability and migration/invasion of myeloma cell lines and MM-xenografted SCID/NOD mice. Mechanically, ALKBH5 promoted the expression of trimethylated histone H3 at lysine 36 (H3K36me3) methyltransferase SETD2 through lncRNA SNHG15-mediated protein stability. ALKBH5-SNHG15 axis increased chromatin accessibility and altered the H3K36me3 enrichment at the gene body, which is responsible for transcription elongation. Our study suggested a novel epigenetically interaction of N6-methyladenosine (m6A) methylation, lncRNA SNHG15, and histone SETD2/H3K36me3 modifications in myeloma progression, indicating that ALKBH5 and lncRNA SNHG15 could serve as potential novel therapeutic targets for MM treatment.NEW & NOTEWORTHY To our knowledge, this study first demonstrated the prognostic significance and biological function of long noncoding RNA (lncRNA) small nucleolar RNA host gene 15 (SNHG15) in multiple myeloma (MM), and indicated a novel revelation on the effect of N6-methyladenosine (m6A)-regulated lncRNA on MM tumorigenicity. Moreover, the novel chromatin-regulatory mechanism of lncRNA by interacting with epigenetic modifiers including m6A demethylase ALKBH5 and H3K36me3 methyltransferase SETD2 in myeloma progression elucidated intricate mechanism of tumor pathogenesis.
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Affiliation(s)
- Lan Yao
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Tingting Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Yao Teng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jingjing Guo
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Hongyong Zhang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Linghui Xia
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Qiuling Wu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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20
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Sato K, Takayama KI, Inoue S. Stress granule-mediated RNA regulatory mechanism in Alzheimer's disease. Geriatr Gerontol Int 2024; 24 Suppl 1:7-14. [PMID: 37726158 DOI: 10.1111/ggi.14663] [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: 08/01/2023] [Revised: 08/20/2023] [Accepted: 08/27/2023] [Indexed: 09/21/2023]
Abstract
Living organisms experience a range of stresses. To cope effectively with these stresses, eukaryotic cells have evolved a sophisticated mechanism involving the formation of stress granules (SGs), which play a crucial role in protecting various types of RNA species under stress, such as mRNAs and long non-coding RNAs (lncRNAs). SGs are non-membranous cytoplasmic ribonucleoprotein (RNP) granules, and the RNAs they contain are translationally stalled. Importantly, SGs have been thought to contribute to the pathophysiology of neurodegenerative diseases, including Alzheimer's disease (AD). SGs also contain multiple RNA-binding proteins (RBPs), several of which have been implicated in AD progression. SGs are transient structures that dissipate after stress relief. However, the chronic stresses associated with aging lead to the persistent formation of SGs and subsequently to solid-like pathological SGs, which could impair cellular RNA metabolism and also act as a nidus for the aberrant aggregation of AD-associated proteins. In this paper, we provide a comprehensive summary of the physical basis of SG-enriched RNAs and SG-resident RBPs. We then review the characteristics of AD-associated gene transcripts and their similarity to the SG-enriched RNAs. Furthermore, we summarize and discuss the functional implications of SGs in neuronal RNA metabolism and the aberrant aggregation of AD-associated proteins mediated by SG-resident RBPs in the context of AD pathogenesis. Geriatr Gerontol Int 2024; 24: 7-14.
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Affiliation(s)
- Kaoru Sato
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
- Integrated Research Initiative for Living Well with Dementia, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
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21
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Glancy E, Choy N, Eckersley-Maslin MA. Bivalent chromatin: a developmental balancing act tipped in cancer. Biochem Soc Trans 2024; 52:217-229. [PMID: 38385532 PMCID: PMC10903468 DOI: 10.1042/bst20230426] [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: 11/21/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Bivalent chromatin is defined by the co-occurrence of otherwise opposing H3K4me3 and H3K27me3 modifications and is typically located at unmethylated promoters of lowly transcribed genes. In embryonic stem cells, bivalent chromatin has been proposed to poise developmental genes for future activation, silencing or stable repression upon lineage commitment. Normally, bivalent chromatin is kept in tight balance in cells, in part through the activity of the MLL/COMPASS-like and Polycomb repressive complexes that deposit the H3K4me3 and H3K27me3 modifications, respectively, but also emerging novel regulators including DPPA2/4, QSER1, BEND3, TET1 and METTL14. In cancers, both the deregulation of existing domains and the creation of de novo bivalent states is associated with either the activation or silencing of transcriptional programmes. This may facilitate diverse aspects of cancer pathology including epithelial-to-mesenchymal plasticity, chemoresistance and immune evasion. Here, we review current methods for detecting bivalent chromatin and discuss the factors involved in the formation and fine-tuning of bivalent domains. Finally, we examine how the deregulation of chromatin bivalency in the context of cancer could facilitate and/or reflect cancer cell adaptation. We propose a model in which bivalent chromatin represents a dynamic balance between otherwise opposing states, where the underlying DNA sequence is primed for the future activation or repression. Shifting this balance in any direction disrupts the tight equilibrium and tips cells into an altered epigenetic and phenotypic space, facilitating both developmental and cancer processes.
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Affiliation(s)
- Eleanor Glancy
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Natalie Choy
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Melanie A. Eckersley-Maslin
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
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22
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Jia X, He X, Huang C, Li J, Dong Z, Liu K. Protein translation: biological processes and therapeutic strategies for human diseases. Signal Transduct Target Ther 2024; 9:44. [PMID: 38388452 PMCID: PMC10884018 DOI: 10.1038/s41392-024-01749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Protein translation is a tightly regulated cellular process that is essential for gene expression and protein synthesis. The deregulation of this process is increasingly recognized as a critical factor in the pathogenesis of various human diseases. In this review, we discuss how deregulated translation can lead to aberrant protein synthesis, altered cellular functions, and disease progression. We explore the key mechanisms contributing to the deregulation of protein translation, including functional alterations in translation factors, tRNA, mRNA, and ribosome function. Deregulated translation leads to abnormal protein expression, disrupted cellular signaling, and perturbed cellular functions- all of which contribute to disease pathogenesis. The development of ribosome profiling techniques along with mass spectrometry-based proteomics, mRNA sequencing and single-cell approaches have opened new avenues for detecting diseases related to translation errors. Importantly, we highlight recent advances in therapies targeting translation-related disorders and their potential applications in neurodegenerative diseases, cancer, infectious diseases, and cardiovascular diseases. Moreover, the growing interest lies in targeted therapies aimed at restoring precise control over translation in diseased cells is discussed. In conclusion, this comprehensive review underscores the critical role of protein translation in disease and its potential as a therapeutic target. Advancements in understanding the molecular mechanisms of protein translation deregulation, coupled with the development of targeted therapies, offer promising avenues for improving disease outcomes in various human diseases. Additionally, it will unlock doors to the possibility of precision medicine by offering personalized therapies and a deeper understanding of the molecular underpinnings of diseases in the future.
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Affiliation(s)
- Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Xinyu He
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Chuntian Huang
- Department of Pathology and Pathophysiology, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China
| | - Jian Li
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, 450000, China.
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23
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Kaye EG, Basavaraju K, Nelson GM, Zomer HD, Roy D, Joseph II, Rajabi-Toustani R, Qiao H, Adelman K, Reddi PP. RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis. Nat Commun 2024; 15:848. [PMID: 38287033 PMCID: PMC10824759 DOI: 10.1038/s41467-024-45177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Male germ cell development requires precise regulation of gene activity in a cell-type and stage-specific manner, with perturbations in gene expression during spermatogenesis associated with infertility. Here, we use steady-state, nascent and single-cell RNA sequencing strategies to comprehensively characterize gene expression across male germ cell populations, to dissect the mechanisms of gene control and provide new insights towards therapy. We discover a requirement for pausing of RNA Polymerase II (Pol II) at the earliest stages of sperm differentiation to establish the landscape of gene activity across development. Accordingly, genetic knockout of the Pol II pause-inducing factor NELF in immature germ cells blocks differentiation to spermatids. Further, we uncover unanticipated roles for Pol II pausing in the regulation of meiosis during spermatogenesis, with the presence of paused Pol II associated with double-strand break (DSB) formation, and disruption of meiotic gene expression and DSB repair in germ cells lacking NELF.
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Affiliation(s)
- Emily G Kaye
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Kavyashree Basavaraju
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Geoffrey M Nelson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Helena D Zomer
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Debarun Roy
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Irene Infancy Joseph
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Reza Rajabi-Toustani
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Huanyu Qiao
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Prabhakara P Reddi
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA.
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24
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Höfler S, Duss O. Interconnections between m 6A RNA modification, RNA structure, and protein-RNA complex assembly. Life Sci Alliance 2024; 7:e202302240. [PMID: 37935465 PMCID: PMC10629537 DOI: 10.26508/lsa.202302240] [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: 06/27/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Protein-RNA complexes exist in many forms within the cell, from stable machines such as the ribosome to transient assemblies like the spliceosome. All protein-RNA assemblies rely on spatially and temporally coordinated interactions between specific proteins and RNAs to achieve a functional form. RNA folding and structure are often critical for successful protein binding and protein-RNA complex formation. RNA modifications change the chemical nature of a given RNA and often alter its folding kinetics. Both these alterations can affect how and if proteins or other RNAs can interact with the modified RNA and assemble into complexes. N6-methyladenosine (m6A) is the most common base modification on mRNAs and regulatory noncoding RNAs and has been shown to impact RNA structure and directly modulate protein-RNA interactions. In this review, focusing on the mechanisms and available quantitative information, we discuss first how the METTL3/14 m6A writer complex is specifically targeted to RNA assisted by protein-RNA and other interactions to enable site-specific and co-transcriptional RNA modification and, once introduced, how the m6A modification affects RNA folding and protein-RNA interactions.
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Affiliation(s)
- Simone Höfler
- https://ror.org/03mstc592 Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Olivier Duss
- https://ror.org/03mstc592 Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
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25
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Liu L, Zhao Y, Siepel A. DNA-sequence and epigenomic determinants of local rates of transcription elongation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572932. [PMID: 38187771 PMCID: PMC10769381 DOI: 10.1101/2023.12.21.572932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Across all branches of life, transcription elongation is a crucial, regulated phase in gene expression. Many recent studies in eukaryotes have focused on the regulation of promoter-proximal pausing of RNA Polymerase II (Pol II), but rates of productive elongation also vary substantially throughout the gene body, both within and across genes. Here, we introduce a probabilistic model for systematically evaluating potential determinants of the local elongation rate based on nascent RNA sequencing (NRS) data. Our model is derived from a unified model for both the kinetics of Pol II movement along the DNA template and the generation of NRS read counts at steady state. It allows for a continuously variable elongation rate along the gene body, with the rate at each nucleotide defined by a generalized linear relationship with nearby genomic and epigenomic features. High-dimensional feature vectors are accommodated through a sparse-regression extension. We show with simulations that the model allows accurate detection of associated features and accurate prediction of local elongation rates. In an analysis of public PRO-seq and epigenomic data, we identify several features that are strongly associated with reductions in the local elongation rate, including DNA methylation, splice sites, RNA stem-loops, CTCF binding sites, and several histone marks, including H3K36me3 and H4K20me1. By contrast, low-complexity sequences and H3K79me2 marks are associated with increases in elongation rate. In an analysis of DNA k -mers, we find that cytosine nucleotides are strongly associated with reductions in local elongation rate, particularly when preceded by guanines and followed by adenines or thymines. Increases in elongation rate are associated with thymines and A+T-rich k -mers. These associations are generally shared across cell types, and by considering them our model is effective at predicting features of held-out PRO-seq data. Overall, our analysis is the first to permit genome-wide predictions of relative nucleotide-specific elongation rates based on complex sets of genomic and epigenomic covariates. We have made predictions available for the K562, CD14+, MCF-7, and HeLa-S3 cell types in a UCSC Genome Browser track.
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Affiliation(s)
- Lingjie Liu
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY
| | - Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY
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26
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Guo Q, Han S. The effect on m 6A methylation writer complex by the reduced MATR3 in pterygium. Acta Histochem 2023; 125:152101. [PMID: 37913560 DOI: 10.1016/j.acthis.2023.152101] [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: 07/13/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 11/03/2023]
Abstract
Pterygium is a common eye surface disease with high recurrence and unclear pathogenesis. In current study, RNA sequencing was conducted in 6 pairs of human pterygium and conjunctival tissues, and Matr3 as a novel candidate gene was significantly reduced in pterygium compared to control tissues. Moreover, immunoprecipitation was performed to pull down MATR3, and WTAP specially interacting with MATR3 in control but not pterygium was identified by mass spectrum. Immunoprecipitation was performed to validate the interaction between MATR3 and WTAP/METTL3/METTL14 complex. (Methylated) RNA immunoprecipitation was performed to further reveal that the binding affinity of WTAP and MATR3 was lost at 3' UTR of RNA molecules of down-regulated genes in pterygium. Overall, we figured out the loss of intercrossing between MATR3 and N6-methyladenosine methyltransferase complex, as well as indicated the potential impact on transcription of target genes in pterygium.
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Affiliation(s)
- Qianqian Guo
- Department of Ophthalmology Zibo Center Hospital, Zibo, Shandong Province 25500, China
| | - Shichao Han
- Department of Ophthalmology Zibo Center Hospital, Zibo, Shandong Province 25500, China.
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27
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Liu Y, Chen K, Shou Y, Li S, Wang J, Zhang Q, Huang Z, Xu J, Li M, Liu D, Liang H, Yang H, Zhang X. circRARS synergises with IGF2BP3 to regulate RNA methylation recognition to promote tumour progression in renal cell carcinoma. Clin Transl Med 2023; 13:e1512. [PMID: 38073586 PMCID: PMC10711645 DOI: 10.1002/ctm2.1512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
As the most prominent RNA modification, N6-methyladenosine (m6 A) participates in the regulation of tumour initiation and progression. Circular RNAs (circRNAs) also play crucial roles in ubiquitous life processes. Whether circRNAs are required for m6 A regulation in renal cell carcinoma (RCC) remains unclear. Meta-analysis and bioinformatics identified that IGF2BP3 was upregulated in RCC and indicated a worse prognosis. IGF2BP3 significantly promoted RCC progression in vitro and in vivo. Mechanistically, circRARS bound to KH1-KH2 domains of IGF2BP3 to enhance m6 A modification recognition. A 12-nt sequence (GUCUUCCAGCAA) was proven to be the IGF2BP3-binding site of circRARS. Additionally, CAPN15, CD44, HMGA2, TNRC6A and ZMIZ2 were screened to be the target genes regulated by the IGF2BP3/circRARS complex in an m6 A-dependent manner. Stabiliser proteins, including HuR, Matrin3 and pAbPC1, were recruited by circRARS, thereby increasing the mRNA stability of the forementioned five target genes. Consequently, the IGF2BP3/circRARS complex facilitated the lipid accumulation of RCC cells and promoted sunitinib resistance via target genes. circRARS synergised with IGF2BP3 to facilitate m6 A recognition, thereby promoting RCC progression. Thus, IGF2BP3 could be a potential biomarker for RCC diagnosis and prognosis and a therapeutic target.
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Affiliation(s)
- Yuenan Liu
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Kailei Chen
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Yi Shou
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Department of UrologySir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouP. R. China
| | - Sen Li
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Jun Wang
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Qingyang Zhang
- Department of Biomedical InformaticsHarvard Medical SchoolBostonMassachusettsUSA
| | - Ziwei Huang
- Department of Breast and Thyroid SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Jiaju Xu
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Mingfeng Li
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Di Liu
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Huageng Liang
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
| | - Hongmei Yang
- Department of Pathogenic BiologySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanP. R. China
| | - Xiaoping Zhang
- Department of UrologyUnion Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Institute of UrologyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanP. R. China
- Shenzhen Huazhong University of Science and Technology Research InstituteShenzhenP. R. China
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28
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Yang Y, Liu Z, Lu J, Sun Y, Fu Y, Pan M, Xie X, Ge Q. Analysis approaches for the identification and prediction of N6-methyladenosine sites. Epigenetics 2023; 18:2158284. [PMID: 36562485 PMCID: PMC9980620 DOI: 10.1080/15592294.2022.2158284] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The global dynamics in a variety of biological processes can be revealed by mapping transcriptional m6A sites, in particular full-transcriptome m6A. And individual m6A sites have contributed to biological function, which can be evaluated by stoichiometric information obtained from the single nucleotide resolution. Currently, the identification of m6A sites is mainly carried out by experiment and prediction methods, based on high-throughput sequencing and machine learning model respectively. This review summarizes the recent topics and progress made in bioinformatics methods of deciphering the m6A methylation, including the experimental detection of m6A methylation sites, techniques of data analysis, the way of predicting m6A methylation sites, m6A methylation databases, and detection of m6A modification in circRNA. At the end, the essay makes a brief discussion for the development perspective in this area.
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Affiliation(s)
- Yuwei Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Junru Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Yuqing Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Yue Fu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Min Pan
- Department of Pathology and Pathophysiology School of Medicine, Southeast University, Nanjing, China
| | - Xueying Xie
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
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29
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Gao X, Yi Y, Lv J, Li Y, Arulsamy K, Babu S, Bruno I, Zhang L, Cao Q, Chen K. Low RNA stability signifies strong expression regulatability of tumor suppressors. Nucleic Acids Res 2023; 51:11534-11548. [PMID: 37831104 PMCID: PMC10681714 DOI: 10.1093/nar/gkad838] [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: 04/25/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
RNA expression of a gene is determined by not only transcriptional regulation, but also post-transcriptional regulation of RNA decay. The precise regulation of RNA stability in the cell plays an important role in normal development. Dysregulation of RNA stability can lead to diseases such as cancer. Here we found tumor suppressor RNAs tended to decay fast in normal cell types when compared with other RNAs. Consistent with a negative effect of m6A modification on RNA stability, we observed preferential deposition of m6A on tumor suppressor RNAs. Moreover, abundant m6A and fast decay of tumor suppressor RNAs both tended to be further enhanced in prostate cancer cells relative to normal prostate epithelial cells. Further, knockdown of m6A methyltransferase METTL3 and reader YTHDF2 in prostate cancer cells both posed stronger effect on tumor suppressor RNAs than on other RNAs. These results indicated a strong post transcriptional expression regulatability mediated by abundant m6A modification on tumor suppressor RNAs.
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Affiliation(s)
- Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yi
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jie Lv
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Kulandaisamy Arulsamy
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sahana Suresh Babu
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Ivone Bruno
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
- Prostate Cancer Program, Dana-Farber Harvard cancer Center, Boston, MA 02115, USA
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Wang Y, Traugot CM, Bubenik JL, Li T, Sheng P, Hiers NM, Fernandez P, Li L, Bian J, Swanson MS, Xie M. N 6-methyladenosine in 7SK small nuclear RNA underlies RNA polymerase II transcription regulation. Mol Cell 2023; 83:3818-3834.e7. [PMID: 37820733 PMCID: PMC10873123 DOI: 10.1016/j.molcel.2023.09.020] [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: 02/27/2023] [Revised: 08/07/2023] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
N6-methyladenosine (m6A) modifications play crucial roles in RNA metabolism. How m6A regulates RNA polymerase II (RNA Pol II) transcription remains unclear. We find that 7SK small nuclear RNA (snRNA), a regulator of RNA Pol II promoter-proximal pausing, is highly m6A-modified in non-small cell lung cancer (NSCLC) cells. In A549 cells, we identified eight m6A sites on 7SK and discovered methyltransferase-like 3 (METTL3) and alkB homolog 5 (ALKBH5) as the responsible writer and eraser. When the m6A-7SK is specifically erased by a dCasRx-ALKBH5 fusion protein, A549 cell growth is attenuated due to reduction of RNA Pol II transcription. Mechanistically, removal of m6A leads to 7SK structural rearrangements that facilitate sequestration of the positive transcription elongation factor b (P-TEFb) complex, which results in reduction of serine 2 phosphorylation (Ser2P) in the RNA Pol II C-terminal domain and accumulation of RNA Pol II in the promoter-proximal region. Taken together, we uncover that m6A modifications of a non-coding RNA regulate RNA Pol II transcription and NSCLC tumorigenesis.
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Affiliation(s)
- Yuzhi Wang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Conner M Traugot
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Jodi L Bubenik
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL 32610, USA; UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Paul Fernandez
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Jiang Bian
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; Department of Health Outcomes & Biomedical Informatics, University of Florida, Gainesville, FL 32610, USA
| | - Maurice S Swanson
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL 32610, USA; UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
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31
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Yao S, Zhang J, Cheng X, Wang D, Yu W, Ji K, Yu Q. Genome-Wide Identification and Characterization of the YTH Domain-Containing RNA-Binding Protein Family in Liriodendron chinense. Int J Mol Sci 2023; 24:15189. [PMID: 37894868 PMCID: PMC10606907 DOI: 10.3390/ijms242015189] [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: 08/31/2023] [Revised: 10/03/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
N6-methyladenosine (m6A) is becoming one of the most important RNA modifications in plant growth and development, including defense, cell differentiation, and secondary metabolism. YT521-B homology (YTH) domain-containing RNA-binding proteins, identified as m6A readers in epitranscriptomics, could affect the fate of m6A-containing RNA by recognizing and binding the m6A site. Therefore, the identification and study of the YTH gene family in Liriodendron chinense (L. chinense) can provide a molecular basis for the study of the role of m6A in L. chinense, but studies on the YTH gene in L. chinense have not been reported. We identified nine putative YTH gene models in the L. chinense genome, which can be divided into DF subgroups and DC subgroups. Domain sequence analysis showed that the LcYTH protein had high sequence conservation. A LcYTH aromatic cage bag is composed of tryptophan and tryptophan (WWW). PrLDs were found in the protein results of YTH, suggesting that these genes may be involved in the process of liquid-liquid phase separation. LcYTH genes have different tissue expression patterns, but the expression of LcYTHDF2 is absolutely dominant in all tissues. In addition, the expression of the LcYTH genes is changed in response to ABA and MeJA. In this study, We identified and analyzed the expression pattern of LcYTH genes. Our results laid a foundation for further study of the function of the LcYTH gene and further genetic and functional analyses of m6A RNA modification in forest trees.
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Affiliation(s)
- Sheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jingjing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Dengbao Wang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wenya Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qiong Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China; (S.Y.); (J.Z.); (X.C.); (D.W.); (W.Y.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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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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Pu J, Xu Z, Huang Y, Nian J, Yang M, Fang Q, Wei Q, Huang Z, Liu G, Wang J, Wu X, Wei H. N 6 -methyladenosine-modified FAM111A-DT promotes hepatocellular carcinoma growth via epigenetically activating FAM111A. Cancer Sci 2023; 114:3649-3665. [PMID: 37400994 PMCID: PMC10475779 DOI: 10.1111/cas.15886] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 07/05/2023] Open
Abstract
As an epitranscriptomic modulation manner, N6 -methyladenosine (m6 A) modification plays important roles in various diseases, including hepatocellular carcinoma (HCC). m6 A modification affects the fate of RNAs. The potential contributions of m6 A to the functions of RNA still need further investigation. In this study, we identified long noncoding RNA FAM111A-DT as an m6 A-modified RNA and confirmed three m6 A sites on FAM111A-DT. The m6 A modification level of FAM111A-DT was increased in HCC tissues and cell lines, and increased m6 A level was correlated with poor survival of HCC patients. m6 A modification increased the stability of FAM111A-DT transcript, whose expression level showed similar clinical relevance to that of the m6 A level of FAM111A-DT. Functional assays found that only m6 A-modified FAM111A-DT promoted HCC cellular proliferation, DNA replication, and HCC tumor growth. Mutation of m6 A sites on FAM111A-DT abolished the roles of FAM111A-DT. Mechanistic investigations found that m6 A-modified FAM111A-DT bound to FAM111A promoter and also interacted with m6 A reader YTHDC1, which further bound and recruited histone demethylase KDM3B to FAM111A promoter, leading to the reduction of the repressive histone mark H3K9me2 and transcriptional activation of FAM111A. The expression of FAM111A was positively correlated with the m6 A level of FAM111A-DT, and the expression of methyltransferase complex, YTHDC1, and KDM3B in HCC tissues. Depletion of FAM111A largely attenuated the roles of m6 A-modified FAM111A-DT in HCC. In summary, the m6 A-modified FAM111A-DT/YTHDC1/KDM3B/FAM111A regulatory axis promoted HCC growth and represented a candidate therapeutic target for HCC.
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Affiliation(s)
- Jian Pu
- Department of Hepatobiliary SurgeryAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Zuoming Xu
- Department of Hepatobiliary SurgeryAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Youguan Huang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Jiahui Nian
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Meng Yang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Quan Fang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Qing Wei
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Zihua Huang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Guoman Liu
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Jianchu Wang
- Department of Hepatobiliary SurgeryAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Xianjian Wu
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Huamei Wei
- Department of PathologyAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
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Patrasso EA, Raikundalia S, Arango D. Regulation of the epigenome through RNA modifications. Chromosoma 2023; 132:231-246. [PMID: 37138119 PMCID: PMC10524150 DOI: 10.1007/s00412-023-00794-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023]
Abstract
Chemical modifications of nucleotides expand the complexity and functional properties of genomes and transcriptomes. A handful of modifications in DNA bases are part of the epigenome, wherein DNA methylation regulates chromatin structure, transcription, and co-transcriptional RNA processing. In contrast, more than 150 chemical modifications of RNA constitute the epitranscriptome. Ribonucleoside modifications comprise a diverse repertoire of chemical groups, including methylation, acetylation, deamination, isomerization, and oxidation. Such RNA modifications regulate all steps of RNA metabolism, including folding, processing, stability, transport, translation, and RNA's intermolecular interactions. Initially thought to influence all aspects of the post-transcriptional regulation of gene expression exclusively, recent findings uncovered a crosstalk between the epitranscriptome and the epigenome. In other words, RNA modifications feedback to the epigenome to transcriptionally regulate gene expression. The epitranscriptome achieves this feat by directly or indirectly affecting chromatin structure and nuclear organization. This review highlights how chemical modifications in chromatin-associated RNAs (caRNAs) and messenger RNAs (mRNAs) encoding factors involved in transcription, chromatin structure, histone modifications, and nuclear organization affect gene expression transcriptionally.
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Affiliation(s)
- Emmely A Patrasso
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Medical and Pharmaceutical Biotechnology Program, IMC University of Applied Sciences, Krems, Austria
| | - Sweta Raikundalia
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel Arango
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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Li Q, Liu X, Wen J, Chen X, Xie B, Zhao Y. Enhancer RNAs: mechanisms in transcriptional regulation and functions in diseases. Cell Commun Signal 2023; 21:191. [PMID: 37537618 PMCID: PMC10398997 DOI: 10.1186/s12964-023-01206-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/23/2023] [Indexed: 08/05/2023] Open
Abstract
In recent years, increasingly more non-coding RNAs have been detected with the development of high-throughput sequencing technology, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), small nucleolar RNAs (snoRNAs), and piwi-interacting RNA (piRNAs). The discovery of enhancer RNAs (eRNAs) in 2010 has further broadened the range of non-coding RNAs revealed. eRNAs are non-coding RNA molecules produced by the transcription of DNA cis-acting elements, enhancer fragments. Recent studies revealed that the transcription of eRNAs may be a biological marker responding to enhancer activity that can participate in the regulation of coding gene transcription. In this review, we discussed the biological characteristics of eRNAs, their functions in transcriptional regulation, the regulation factors of eRNAs production, and the research progress of eRNAs in different diseases. Video Abstract.
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Affiliation(s)
- Qianhui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Xin Liu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Jingtao Wen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Bumin Xie
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China.
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Qi YN, Liu Z, Hong LL, Li P, Ling ZQ. Methyltransferase-like proteins in cancer biology and potential therapeutic targeting. J Hematol Oncol 2023; 16:89. [PMID: 37533128 PMCID: PMC10394802 DOI: 10.1186/s13045-023-01477-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/10/2023] [Indexed: 08/04/2023] Open
Abstract
RNA modification has recently become a significant process of gene regulation, and the methyltransferase-like (METTL) family of proteins plays a critical role in RNA modification, methylating various types of RNAs, including mRNA, tRNA, microRNA, rRNA, and mitochondrial RNAs. METTL proteins consist of a unique seven-beta-strand domain, which binds to the methyl donor SAM to catalyze methyl transfer. The most typical family member METTL3/METTL14 forms a methyltransferase complex involved in N6-methyladenosine (m6A) modification of RNA, regulating tumor proliferation, metastasis and invasion, immunotherapy resistance, and metabolic reprogramming of tumor cells. METTL1, METTL4, METTL5, and METTL16 have also been recently identified to have some regulatory ability in tumorigenesis, and the rest of the METTL family members rely on their methyltransferase activity for methylation of different nucleotides, proteins, and small molecules, which regulate translation and affect processes such as cell differentiation and development. Herein, we summarize the literature on METTLs in the last three years to elucidate their roles in human cancers and provide a theoretical basis for their future use as potential therapeutic targets.
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Affiliation(s)
- Ya-Nan Qi
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, P.R. China
| | - Zhu Liu
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No.1 Banshan East Rd., Gongshu District, Hangzhou, 310022, Zhejiang, P.R. China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, P.R. China
| | - Lian-Lian Hong
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No.1 Banshan East Rd., Gongshu District, Hangzhou, 310022, Zhejiang, P.R. China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, P.R. China
| | - Pei Li
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450052, P.R. China.
| | - Zhi-Qiang Ling
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No.1 Banshan East Rd., Gongshu District, Hangzhou, 310022, Zhejiang, P.R. China.
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, P.R. China.
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Ni W, Zhou H, Lu H, Ma N, Hou B, Li W, Kong F, Yu J, Hou R, Jin J, Wen J, Zhang T, Meng X. Genetic and pharmacological inhibition of METTL3 alleviates renal fibrosis by reducing EVL m6A modification through an IGF2BP2-dependent mechanism. Clin Transl Med 2023; 13:e1359. [PMID: 37537731 PMCID: PMC10400756 DOI: 10.1002/ctm2.1359] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND N6 -methyladenosine (m6A) is of great importance in renal physiology and disease progression, but its function and mechanism in renal fibrosis remain to be comprehensively and extensively explored. Hence, this study will explore the function and potential mechanism of critical regulator-mediated m6A modification during renal fibrosis and thereby explore promising anti-renal fibrosis agents. METHODS Renal tissues from humans and mice as well as HK-2 cells were used as research subjects. The profiles of m6A modification and regulators in renal fibrosis were analysed at the protein and RNA levels using Western blotting, quantitative real-time polymerase chain reaction and other methods. Methylation RNA immunoprecipitation sequencing and RNA sequencing coupled with methyltransferase-like 3 (METTL3) conditional knockout were used to explore the function of METTL3 and potential targets. Gene silencing and overexpression combined with RNA immunoprecipitation were performed to investigate the underlying mechanism by which METTL3 regulates the Ena/VASP-like (EVL) m6A modification that promotes renal fibrosis. Molecular docking and virtual screening with in vitro and in vivo experiments were applied to screen promising traditional Chinese medicine (TCM) monomers and explore their mechanism of regulating the METTL3/EVL m6A axis and anti-renal fibrosis. RESULTS METTL3 and m6A modifications were hyperactivated in both the tubular region of fibrotic kidneys and HK-2 cells. Upregulated METTL3 enhanced the m6A modification of EVL mRNA to improve its stability and expression in an insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)-dependent manner. Highly expressed EVL binding to Smad7 abrogated the Smad7-induced suppression of transforming growth factor-β (TGF-β1)/Smad3 signal transduction, which conversely facilitated renal fibrosis progression. Molecular docking and virtual screening based on the structure of METTL3 identified a TCM monomer named isoforsythiaside, which inhibited METTL3 activity together with the METTL3/EVL m6A axis to exert anti-renal fibrosis effects. CONCLUSIONS Collectively, the overactivated METTL3/EVL m6A axis is a potential target for renal fibrosis therapy, and the pharmacological inhibition of METTL3 activity by isoforsythiaside suggests that it is a promising anti-renal fibrosis agent.
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Affiliation(s)
- Wei‐Jian Ni
- Department of PharmacyAnhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiPeople's Republic of China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceAnhui Institute of Innovative DrugsSchool of PharmacyAnhui Medical UniversityHefeiAnhuiPeople's Republic of China
| | - Hong Zhou
- Department of PharmacyAnhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiPeople's Republic of China
| | - Hao Lu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceAnhui Institute of Innovative DrugsSchool of PharmacyAnhui Medical UniversityHefeiAnhuiPeople's Republic of China
| | - Nan‐Nan Ma
- Department of UrologyThe Second Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiPeople's Republic of China
| | - Bing‐Bing Hou
- Department of UrologyThe First Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiPeople's Republic of China
| | - Wei Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceAnhui Institute of Innovative DrugsSchool of PharmacyAnhui Medical UniversityHefeiAnhuiPeople's Republic of China
| | - Fan‐Xu Kong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceAnhui Institute of Innovative DrugsSchool of PharmacyAnhui Medical UniversityHefeiAnhuiPeople's Republic of China
- Department of PharmacyThe Second People's Hospital of HefeiHefeiAnhuiPeople's Republic of China
| | - Ju‐Tao Yu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceAnhui Institute of Innovative DrugsSchool of PharmacyAnhui Medical UniversityHefeiAnhuiPeople's Republic of China
| | - Rui Hou
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceAnhui Institute of Innovative DrugsSchool of PharmacyAnhui Medical UniversityHefeiAnhuiPeople's Republic of China
| | - Juan Jin
- Research Center for Translational MedicineThe Second Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiPeople's Republic of China
- School of Basic MedicineAnhui Medical UniversityHefeiAnhuiPeople's Republic of China
| | - Jia‐Gen Wen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceAnhui Institute of Innovative DrugsSchool of PharmacyAnhui Medical UniversityHefeiAnhuiPeople's Republic of China
| | - Tao Zhang
- Department of UrologyThe Second Affiliated Hospital of Anhui Medical UniversityHefeiAnhuiPeople's Republic of China
| | - Xiao‐Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui ProvinceAnhui Institute of Innovative DrugsSchool of PharmacyAnhui Medical UniversityHefeiAnhuiPeople's Republic of China
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Sun Y, Ge J, Shao F, Ren Z, Huang Z, Ding Z, Dong L, Chen J, Zhang J, Zang Y. Long noncoding RNA AI662270 promotes kidney fibrosis through enhancing METTL3-mediated m 6 A modification of CTGF mRNA. FASEB J 2023; 37:e23071. [PMID: 37389924 DOI: 10.1096/fj.202202012rrr] [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: 12/01/2022] [Revised: 06/07/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
The sustained release of profibrotic cytokines, mainly transforming growth factor-β (TGF-β), leads to the occurrence of kidney fibrosis and chronic kidney disease (CKD). Connective tissue growth factor (CTGF) appears to be an alternative target to TGF-β for antifibrotic therapy in CKD. In this study, we found that long noncoding RNA AI662270 was significantly increased in various renal fibrosis models. In vivo, ectopic expression of AI662270 alone was sufficient to activate interstitial fibroblasts and drive kidney fibrosis, whereas inhibition of AI662270 blocked the activation of interstitial fibroblasts and ameliorated kidney fibrosis in various murine models. Mechanistic studies revealed that overexpression of AI662270 significantly increased CTGF product, which was required for the role of AI662270 in driving kidney fibrosis. Furthermore, AI662270 binds to the CTGF promoter and directly interacts with METTL3, the methyltransferase of RNA N6 -methyladenosine (m6 A) modification. Functionally, AI662270-mediated recruitment of METTL3 increased the m6 A methylation of CTGF mRNA and consequently enhanced CTGF mRNA stability. In conclusion, our results support that AI662270 promotes CTGF expression at the posttranscriptional stage by recruiting METTL3 to the CTGF promoter and depositing m6 A modifications on the nascent mRNA, thereby, uncovering a novel regulatory mechanism of CTGF in the pathogenesis of kidney fibrosis.
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Affiliation(s)
- Yanyan Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Jia Ge
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Fang Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Zhengrong Ren
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Zhen Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Zhi Ding
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Lei Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Jiangning Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P.R. China
- State Key Laboratory of Analytical Chemistry for Life Sciences and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Junfeng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P.R. China
| | - Yuhui Zang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P.R. China
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Kumari S, Singh M, Kumar S, Muthuswamy S. SETD2 controls m6A modification of transcriptome and regulates the molecular oncogenesis of glioma. Med Oncol 2023; 40:249. [PMID: 37490181 DOI: 10.1007/s12032-023-02121-7] [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: 05/25/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023]
Abstract
SETD2 is known for its epigenetic regulatory function and a frequently mutated gene in multiple cancers. Recently, it has been inferred that SETD2 regulates m6A mRNA methylation (epitranscriptome) via H3K36me3. The m6A RNA methylation is vital for tumor maintenance, self-renewal, and tumorigenesis. RNA modifications are executed by writers, readers, and erasers. m6A modifiers work along with the molecular cues, H3K36me3, laid down by SETD2. A positive correlation observed between SETD2 and RNA modifiers signifies their direct role in epitranscriptomics. Hence, understanding the epitranscriptomics will provide a new facet for molecular oncogenesis. Glioma is a common, malignant grade IV tumor with limited therapeutic alternatives and a poor prognosis. Yet, its function in glioma is not fully defined. In the present study, thorough investigations were done in the m6A RNA methylation regulators expression, the molecular pathways leading to tumor progression, and their respective outcomes in SETD2-mediated RNA methylation. In vitro analysis reveals that SETD2 knockdown positively affected the oncogenic properties of the glioma cell line and a global reduction in m6A levels in the transcriptome. The reduction of m6A in the transcriptome can be attributed to the decreased expression of METTL3 and METTL14. Therefore, we conclude that SETD2-mediated m6A modifications are crucial for glioma oncogenesis.
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Affiliation(s)
- Subhadra Kumari
- Human Molecular Genetics (HMG) Lab., Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Mandakini Singh
- RNA Biology Lab., Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Santosh Kumar
- RNA Biology Lab., Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Srinivasan Muthuswamy
- Human Molecular Genetics (HMG) Lab., Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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40
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Wang Z, Ge P, Zhou XL, Shui KM, Geng H, Yang J, Chen JY, Wang J. nASAP: A Nascent RNA Profiling Data Analysis Platform. J Mol Biol 2023; 435:168142. [PMID: 37356907 DOI: 10.1016/j.jmb.2023.168142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 04/19/2023] [Accepted: 04/30/2023] [Indexed: 06/27/2023]
Abstract
Although nascent RNA profiling data are widely used in transcriptional regulation studies, the development and standardization of data processing pipeline lags far behind RNA-seq. We are filling this gap by establishing the nASAP web server (https://grobase.top/nasap/) to provide practical quality evaluation and comprehensive analysis of nascent RNA datasets. In nASAP, four customized analysis modules are provided, including i) quality assessment, which summarizes the sequencing statistics, mapping ratio, and evaluates RNA integrity and mRNA contamination; ii) quantification analysis for mRNAs, lncRNAs and eRNAs; iii) pausing analysis across the whole genome based on sequencing reads distribution; and iv) network analysis to better understand the gene regulatory mechanism by obtaining annotated enhancer-promoter interactomes. The nASAP is user-friendly and outperforms the existing pipeline for quality control of nascent RNA profiling data. We anticipate that nASAP, which eases both basic and advanced analysis of nascent RNA data, will be extremely useful in various fields.
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Affiliation(s)
- Zhi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Peng Ge
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiao-Long Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kun-Ming Shui
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huichao Geng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jie Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Jin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; NJU Advanced Institute for Life Sciences (NAILS), Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Nanjing University, Nanjing 210023, China.
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41
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Kong Y, Yu J, Ge S, Fan X. Novel insight into RNA modifications in tumor immunity: Promising targets to prevent tumor immune escape. Innovation (N Y) 2023; 4:100452. [PMID: 37485079 PMCID: PMC10362524 DOI: 10.1016/j.xinn.2023.100452] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/23/2023] [Indexed: 07/25/2023] Open
Abstract
An immunosuppressive state is a typical feature of the tumor microenvironment. Despite the dramatic success of immune checkpoint inhibitor (ICI) therapy in preventing tumor cell escape from immune surveillance, primary and acquired resistance have limited its clinical use. Notably, recent clinical trials have shown that epigenetic drugs can significantly improve the outcome of ICI therapy in various cancers, indicating the importance of epigenetic modifications in immune regulation of tumors. Recently, RNA modifications (N6-methyladenosine [m6A], N1-methyladenosine [m1A], 5-methylcytosine [m5C], etc.), novel hotspot areas of epigenetic research, have been shown to play crucial roles in protumor and antitumor immunity. In this review, we provide a comprehensive understanding of how m6A, m1A, and m5C function in tumor immunity by directly regulating different immune cells as well as indirectly regulating tumor cells through different mechanisms, including modulating the expression of immune checkpoints, inducing metabolic reprogramming, and affecting the secretion of immune-related factors. Finally, we discuss the current status of strategies targeting RNA modifications to prevent tumor immune escape, highlighting their potential.
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Affiliation(s)
- Yuxin Kong
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200001, China
| | - Jie Yu
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200001, China
| | - Shengfang Ge
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200001, China
| | - Xianqun Fan
- Department of Ophthalmology, Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200001, China
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Li Y, Yi Y, Lv J, Gao X, Yu Y, Babu S, Bruno I, Zhao D, Xia B, Peng W, Zhu J, Chen H, Zhang L, Cao Q, Chen K. Low RNA stability signifies increased post-transcriptional regulation of cell identity genes. Nucleic Acids Res 2023; 51:6020-6038. [PMID: 37125636 PMCID: PMC10325912 DOI: 10.1093/nar/gkad300] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023] Open
Abstract
Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g. by super-enhancers and broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m6A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains and their associated genes. METTL3 binding intensity is positively correlated with RNA m6A methylation and negatively correlated with RNA stability of cell identity genes, probably due to co-transcriptional m6A modifications promoting RNA decay. Nanopore direct RNA-sequencing showed that METTL3 knockdown has a stronger effect on RNA m6A and mRNA stability for cell identity genes. Our data suggest a run-and-brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression.
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Affiliation(s)
- Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yi
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jie Lv
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yu
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sahana Suresh Babu
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Ivone Bruno
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Dongyu Zhao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Bo Xia
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC 20052, USA
| | - Jun Zhu
- Systems Biology Center, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Hong Chen
- Vascular Biology Program, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
- Broad Institute of MIT and Harvard, Boston, MA 02115, USA
- Dana-Farber/Harvard Cancer Center, Boston, MA 02115, USA
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43
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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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Khorkova O, Stahl J, Joji A, Volmar CH, Zeier Z, Wahlestedt C. Long non-coding RNA-targeting therapeutics: discovery and development update. Expert Opin Drug Discov 2023; 18:1011-1029. [PMID: 37466388 DOI: 10.1080/17460441.2023.2236552] [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: 03/14/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023]
Abstract
INTRODUCTION lncRNAs are major players in regulatory networks orchestrating multiple cellular functions, such as 3D chromosomal interactions, epigenetic modifications, gene expression and others. Due to progress in the development of nucleic acid-based therapeutics, lncRNAs potentially represent easily accessible therapeutic targets. AREAS COVERED Currently, significant efforts are directed at studies that can tap the enormous therapeutic potential of lncRNAs. This review describes recent developments in this field, particularly focusing on clinical applications. EXPERT OPINION Extensive druggable target range of lncRNA combined with high specificity and accelerated development process of nucleic acid-based therapeutics open new prospects for treatment in areas of extreme unmet medical need, such as genetic diseases, aggressive cancers, protein deficiencies, and subsets of common diseases caused by known mutations. Although currently wide acceptance of lncRNA-targeting nucleic acid-based therapeutics is impeded by the need for parenteral or direct-to-CNS administration, development of less invasive techniques and orally available/BBB-penetrant nucleic acid-based therapeutics is showing early successes. Recently, mRNA-based COVID-19 vaccines have demonstrated clinical safety of all aspects of nucleic acid-based therapeutic technology, including multiple chemical modifications of nucleic acids and nanoparticle delivery. These trends position lncRNA-targeting drugs as significant players in the future of drug development, especially in the area of personalized medicine.
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Affiliation(s)
- Olga Khorkova
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Zane Zeier
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
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Mu M, Li X, Dong L, Wang J, Cai Q, Hu Y, Wang D, Zhao P, Zhang L, Zhang D, Cheng S, Tan L, Wu F, Shi YG, Xu W, Shi Y, Shen H. METTL14 regulates chromatin bivalent domains in mouse embryonic stem cells. Cell Rep 2023; 42:112650. [PMID: 37314930 DOI: 10.1016/j.celrep.2023.112650] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 04/11/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
METTL14 (methyltransferase-like 14) is an RNA-binding protein that partners with METTL3 to mediate N6-methyladenosine (m6A) methylation. Recent studies identified a function for METTL3 in heterochromatin in mouse embryonic stem cells (mESCs), but the molecular function of METTL14 on chromatin in mESCs remains unclear. Here, we show that METTL14 specifically binds and regulates bivalent domains, which are marked by trimethylation of histone H3 lysine 27 (H3K27me3) and lysine 4 (H3K4me3). Knockout of Mettl14 results in decreased H3K27me3 but increased H3K4me3 levels, leading to increased transcription. We find that bivalent domain regulation by METTL14 is independent of METTL3 or m6A modification. METTL14 enhances H3K27me3 and reduces H3K4me3 by interacting with and probably recruiting the H3K27 methyltransferase polycomb repressive complex 2 (PRC2) and H3K4 demethylase KDM5B to chromatin. Our findings identify an METTL3-independent role of METTL14 in maintaining the integrity of bivalent domains in mESCs, thus indicating a mechanism of bivalent domain regulation in mammals.
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Affiliation(s)
- Mandi Mu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinze Li
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Dong
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jin Wang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qingqing Cai
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yajun Hu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Duanduan Wang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peng Zhao
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lei Zhang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Daixuan Zhang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Siyi Cheng
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Tan
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China
| | - Feizhen Wu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yujiang Geno Shi
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenqi Xu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.
| | - Yang Shi
- Ludwig Institute for Cancer Research, Oxford Branch, Oxford University, Oxford, UK.
| | - Hongjie Shen
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.
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Abstract
Chemical modifications on mRNA represent a critical layer of gene expression regulation. Research in this area has continued to accelerate over the last decade, as more modifications are being characterized with increasing depth and breadth. mRNA modifications have been demonstrated to influence nearly every step from the early phases of transcript synthesis in the nucleus through to their decay in the cytoplasm, but in many cases, the molecular mechanisms involved in these processes remain mysterious. Here, we highlight recent work that has elucidated the roles of mRNA modifications throughout the mRNA life cycle, describe gaps in our understanding and remaining open questions, and offer some forward-looking perspective on future directions in the field.
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Affiliation(s)
- Wendy V Gilbert
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA;
| | - Sigrid Nachtergaele
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA;
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Chen Q, Zeng Y, Kang J, Hu M, Li N, Sun K, Zhao Y. Enhancer RNAs in transcriptional regulation: recent insights. Front Cell Dev Biol 2023; 11:1205540. [PMID: 37266452 PMCID: PMC10229774 DOI: 10.3389/fcell.2023.1205540] [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: 04/14/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023] Open
Abstract
Enhancers are a class of cis-regulatory elements in the genome that instruct the spatiotemporal transcriptional program. Last decade has witnessed an exploration of non-coding transcripts pervasively transcribed from active enhancers in diverse contexts, referred to as enhancer RNAs (eRNAs). Emerging evidence unequivocally suggests eRNAs are an important layer in transcriptional regulation. In this mini-review, we summarize the well-established regulatory models for eRNA actions and highlight the recent insights into the structure and chemical modifications of eRNAs underlying their functions. We also explore the potential roles of eRNAs in transcriptional condensates.
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Affiliation(s)
- Qi Chen
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yaxin Zeng
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jinjin Kang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Minghui Hu
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Nianle Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
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Kaye EG, Nelson GM, Zomer HD, Roy D, Joseph II, Adelman K, Reddi PP. RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539879. [PMID: 37215034 PMCID: PMC10197597 DOI: 10.1101/2023.05.08.539879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Male germ cell development requires precise regulation of gene activity in a cell-type and stage-specific manner, with perturbations in gene expression during spermatogenesis associated with infertility. Here, we use steady-state, nascent and single-cell RNA sequencing strategies to comprehensively characterize gene expression across male germ cell populations, to dissect the mechanisms of gene control and provide new insights towards therapy. We discover a requirement for pausing of RNA Polymerase II (Pol II) at the earliest stages of sperm differentiation to establish the landscape of gene activity across development. Accordingly, genetic knockout of the Pol II pause-inducing factor NELF in immature germ cells blocks differentiation to mature spermatids. Further, we uncover unanticipated roles for Pol II pausing in the regulation of meiosis during spermatogenesis, with the presence of paused Pol II associated with double strand break formation by SPO11, and disruption of SPO11 expression in germ cells lacking NELF.
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Affiliation(s)
- Emily G. Kaye
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Geoffrey M. Nelson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Helena D. Zomer
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois, 61802, USA
| | - Debarun Roy
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois, 61802, USA
| | - Irene Infancy Joseph
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois, 61802, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Prabhakara P. Reddi
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois, 61802, USA
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Liu Y, Yang D, Liu T, Chen J, Yu J, Yi P. N6-methyladenosine-mediated gene regulation and therapeutic implications. Trends Mol Med 2023; 29:454-467. [PMID: 37068987 DOI: 10.1016/j.molmed.2023.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/11/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023]
Abstract
N6-methyladenosine (m6A) RNA methylation is the most abundant form of mRNA modification in eukaryotes and is at the front line of biological and biomedical research. This dynamic and reversible m6A RNA modification determines the fates of modified RNA molecules at the post-transcriptional level, affecting almost all important biological processes. Notably, m6A is also involved in chromatin and transcriptional regulation, while m6A dysregulation is implicated in various diseases. Here, we review current knowledge of post-transcriptional and transcriptional regulatory mechanisms involving m6A modification. We also discuss their involvement in the occurrence and development of diseases, including cancer, as well as potential theranostic targets, in hope of facilitating the translation of preclinical findings to the clinic.
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Affiliation(s)
- Yujiao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Dan Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Tao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Los Angeles, CA 91010, USA
| | - Jianhua Yu
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA.
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China.
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Abstract
N6-Methyladenosine (m6A) is one of the most abundant modifications of the epitranscriptome and is found in cellular RNAs across all kingdoms of life. Advances in detection and mapping methods have improved our understanding of the effects of m6A on mRNA fate and ribosomal RNA function, and have uncovered novel functional roles in virtually every species of RNA. In this Review, we explore the latest studies revealing roles for m6A-modified RNAs in chromatin architecture, transcriptional regulation and genome stability. We also summarize m6A functions in biological processes such as stem-cell renewal and differentiation, brain function, immunity and cancer progression.
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Affiliation(s)
- Konstantinos Boulias
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA
| | - Eric Lieberman Greer
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA.
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