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Lv Y, Han F, Liu M, Zhang T, Cui G, Wang J, Yang Y, Yang YG, Yang W. Characteristics of N 6-methyladenosine Modification During Sexual Reproduction of Chlamydomonas reinhardtii. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:756-768. [PMID: 35550876 PMCID: PMC10787120 DOI: 10.1016/j.gpb.2022.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/12/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii (hereafter Chlamydomonas) possesses both plant and animal attributes, and it is an ideal model organism for studying fundamental processes such as photosynthesis, sexual reproduction, and life cycle. N6-methyladenosine (m6A) is the most prevalent mRNA modification, and it plays important roles during sexual reproduction in animals and plants. However, the pattern and function of m6A modification during the sexual reproduction of Chlamydomonas remain unknown. Here, we performed transcriptome and methylated RNA immunoprecipitation sequencing (MeRIP-seq) analyses on six samples from different stages during sexual reproduction of the Chlamydomonas life cycle. The results show that m6A modification frequently occurs at the main motif of DRAC (D = G/A/U, R = A/G) in Chlamydomonas mRNAs. Moreover, m6A peaks in Chlamydomonas mRNAs are mainly enriched in the 3' untranslated regions (3'UTRs) and negatively correlated with the abundance of transcripts at each stage. In particular, there is a significant negative correlation between the expression levels and the m6A levels of genes involved in the microtubule-associated pathway, indicating that m6A modification influences the sexual reproduction and the life cycle of Chlamydomonas by regulating microtubule-based movement. In summary, our findings are the first to demonstrate the distribution and the functions of m6A modification in Chlamydomonas mRNAs and provide new evolutionary insights into m6A modification in the process of sexual reproduction in other plant organisms.
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Yu F, Qi H, Gao L, Luo S, Njeri Damaris R, Ke Y, Wu W, Yang P. Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:788-804. [PMID: 36775055 PMCID: PMC10787127 DOI: 10.1016/j.gpb.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 12/29/2022] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies. However, the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA, which is an important element for the post-transcriptional regulation of gene expression. To comprehensively profile the N6-methyladenosine (m6A) and N5-methylcytosine (m5C) modifications on RNA, direct RNA sequencing (DRS) using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice. Approximately 94 million reads were generated, with an average length ranging from 619 nt to 1013 nt, and a total of 45,707 transcripts across 34,763 genes were detected. Expression profiles of transcripts at the isoform level were quantified among tissues. Transcriptome-wide mapping of m6A and m5C demonstrated that both modifications exhibited tissue-specific characteristics. The transcripts with m6A modifications tended to be modified by m5C, and the transcripts with modifications presented higher expression levels along with shorter poly(A) tails than transcripts without modifications, suggesting the complexity of gene expression regulation. Gene Ontology analysis demonstrated that m6A- and m5C-modified transcripts were involved in central metabolic pathways related to the life cycle, with modifications on the target genes selected in a tissue-specific manner. Furthermore, most modified sites were located within quantitative trait loci that control important agronomic traits, highlighting the value of cloning functional loci. The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome, improving our understanding of the rice genome.
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Li Y, Sun Y, Yang W, Yang L, Su M, Fang L, Zheng J, Yuan R, Liang W. A novel photoelectrochemical strategy for sequence-spot bispecific analysis of N 6-methyladenosine modification based on proximity ligation-triggered cascade amplification. Anal Chim Acta 2023; 1265:341287. [PMID: 37230570 DOI: 10.1016/j.aca.2023.341287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
N6-methyladenosine (m6A) modification as the most prevalent mammalian RNA internal modification has been considered as the invasive biomarkers in clinical diagnosis and biological mechanism researches. It is still challenged to explore m6A functions due to technical limitations on base- and location-resolved m6A modification. Herein, we firstly proposed a sequence-spot bispecific photoelectrochemical (PEC) strategy based on in situ hybridization mediated proximity ligation assay for m6A RNA characterization with high sensitivity and accuracy. Firstly, the target m6A methylated RNA could be transferred to the exposed cohesive terminus of H1 based on the special self-designed auxiliary proximity ligation assay (PLA) with sequence-spot bispecific recognition. The exposed cohesive terminus of H1 could furtherly trigger the next catalytic hairpin assembly (CHA) amplification and in situ exponential nonlinear hyperbranched hybridization chain reaction for highly sensitive monitoring of m6A methylated RNA. Compared with conventional technologies, the proposed sequence-spot bispecific PEC strategy for m6A methylation of special RNA based on proximity ligation-triggered in situ nHCR performed improved sensitivity and selectivity with a detection limit of 53 fM, providing new insights into highly sensitive monitoring m6A methylation of RNA in bioassay, disease diagnosis and RNA mechanism.
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Sun RX, Zhu HJ, Zhang YR, Wang JN, Wang Y, Cao QC, Ji JD, Jiang C, Yuan ST, Chen X, Liu QH. ALKBH5 causes retinal pigment epithelium anomalies and choroidal neovascularization in age-related macular degeneration via the AKT/mTOR pathway. Cell Rep 2023; 42:112779. [PMID: 37436898 DOI: 10.1016/j.celrep.2023.112779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 05/24/2023] [Accepted: 06/25/2023] [Indexed: 07/14/2023] Open
Abstract
Retinal pigment epithelium (RPE) dysfunction and choroidal neovascularization (CNV) are predominant features of age-related macular degeneration (AMD), with an unclear mechanism. Herein, we show that RNA demethylase α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5) is up-regulated in AMD. In RPE cells, ALKBH5 overexpression associates with depolarization, oxidative stress, disturbed autophagy, irregular lipid homeostasis, and elevated VEGF-A secretion, which subsequently promotes proliferation, migration, and tube formation of vascular endothelial cells. Consistently, ALKBH5 overexpression in mice RPE correlates with various pathological phenotypes, including visual impairments, RPE anomalies, choroidal neovascularization (CNV), and interrupted retinal homeostasis. Mechanistically, ALKBH5 regulates retinal features through its demethylation activity. It targets PIK3C2B and regulates the AKT/mTOR signaling pathway with YTHDF2 as the N6-methyladenosine reader. IOX1, an ALKBH5 inhibitor, suppresses hypoxia-induced RPE dysfunction and CNV progression. Collectively, we demonstrate that ALKBH5 induces RPE dysfunction and CNV progression in AMD via PIK3C2B-mediated activation of the AKT/mTOR pathway. Pharmacological inhibitors of ALKBH5, like IOX1, are promising therapeutic options for AMD.
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Yu B, Liu J, Cai Z, Wang H, Feng X, Zhang T, Ma R, Gu Y, Zhang J. RNA N 6-methyladenosine profiling reveals differentially methylated genes associated with intramuscular fat metabolism during breast muscle development in chicken. Poult Sci 2023; 102:102793. [PMID: 37276703 PMCID: PMC10258505 DOI: 10.1016/j.psj.2023.102793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 06/07/2023] Open
Abstract
Intramuscular fat (IMF) is an important indicator for determining meat quality, and IMF deposition during muscle development is regulated by a complex molecular network involving multiple genes. The N6-methyladenosine (m6A) modification of mRNA plays an important regulatory role in muscle adipogenesis. However, the distribution of m6A and its role in IMF metabolism in poultry has not been reported. In the present study, a transcriptome-wide m6A profile was constructed using methylated RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq) to explore the potential mechanism of regulating IMF deposition in the breast muscle based on the comparative analysis of IMF differences in the breast muscles of 42 (group G), 126 (group S), and 180-days old (group M) Jingyuan chickens. The findings revealed that the IMF content in the breast muscle increased significantly with the increase in the growth days of the Jingyuan chickens (P < 0.05). The m6A peak in the breast muscles of the 3 groups was highly enriched in the coding sequence (CDS) and 3' untranslated regions (3' UTR), which corresponded to the consensus motif RRACH. Moreover, we identified 129, 103, and 162 differentially methylated genes (DMGs) in the breast muscle samples of the G, S, and M groups, respectively. Functional enrichment analyses revealed that DMGs are involved in many physiological activities of muscle fat anabolism. The m6A-induced ferroptosis pathway was identified in breast muscle tissue as a new target for regulating IMF metabolism. In addition, association analysis demonstrated that LMOD2 and its multiple m6A negatively regulated DMGs are potential regulators of IMF differential deposition in muscle. The findings of the present study provide a solid foundation for further investigation into the potential role of m6A modification in regulating chicken fat metabolism.
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Pomaville MM, He C. Advances in targeting RNA modifications for anticancer therapy. Trends Cancer 2023:S2405-8033(23)00059-6. [PMID: 37147166 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] [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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Xiang S, Wang Y, Lei D, Luo Y, Peng D, Zong K, Liu Y, Huang Z, Mo S, Pu X, Zheng J, Wu Z. Donor graft METTL3 gene transfer ameliorates rat liver transplantation ischemia-reperfusion injury by enhancing HO-1 expression in an m 6A-dependent manner. Clin Immunol 2023; 251:109325. [PMID: 37030526 DOI: 10.1016/j.clim.2023.109325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/04/2023] [Indexed: 04/10/2023]
Abstract
Ischemia-reperfusion injury (IRI) is one of the most common complications in liver transplantation. METTL3 regulates inflammation and various cellular stress responses via modulating RNA m6A modification level. Here, the study aimed to investigate the role and mechanism of METTL3 in IRI after rat orthotopic liver transplantation. Firstly, m6A dot blot assay showed that total RNA m6A modification level in grafts was down-regulated, which echoed with the downregulation of METTL3. Furthermore, METTL3 pretreatment in donor significantly reduced liver grafts necrosis formation, apoptosis, improved liver function and depressed the proinflammatory cytokine/chemokine expression. Mechanistically, western blot and immunohistochemical showed that METTL3 inhibited apoptosis via upregulating HO-1. Moreover, MeRIP-qPCR assay revealed that METTL3 promoted HO-1 expression in an m6A-dependent manner. Additionally, METTL3 alleviated primary hepatocytes apoptosis by upregulating HO-1 under hypoxia/reoxygenation condition. Taken together, these results demonstrated that METTL3 exerted a cytoprotective role against IRI via inducing HO-1 in an m6A-dependent manner.
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Cui X, Zheng Y, Zhou Y, Jiang T, Wang S, Cao L, Gao L, Yin H, Ai S. Antibody-free photoelectrochemical strategy for simultaneous detection of methylated RNA, METTL3/METTL14 protein and MazF protein based on enhanced photoactivity of MoSe 2-BiOI nanocomposite. Biosens Bioelectron 2023; 222:115015. [PMID: 36529055 DOI: 10.1016/j.bios.2022.115015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/29/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Taking advantages of the catalytic activity of METTL3/METTL14 protein towards adenine methylation in RNA sequence and the specific digestion activity of MazF protein towards unmethylated RNA sequence containing ACA bases, a novel photoelectrochemical biosensor was constructed for simultaneous detection of RNA methylation, METTL3/METTL14 protein and MazF protein. MoSe2-BiOI nanocomposite was prepared and considered as photoactive material, catalytic hairpin assembly strategy and in situ generation of electron donors catalyzed by polyaspartic acid-loaded alkaline phosphatase technique were employed as signal amplification. Under the optimum conditions, the detection ranges of methylated RNA, METTL3/METTL14 protein and MazF protein were 0.001-50 nM, 0.001-25 ng/μL, and 0.001-10 U/mL, respectively. The corresponding detection limits were 0.46 pM, 0.51 pg/μL and 0.42 U/μL with S/N = 3. In addition, the effect of drugs and composite pollutants on the activities of MazF proteins was assessed, proving the applicability of the developed method in the field of drug screening for MazF-related diseases. Moreover, the effects of pollutants on the activity of METTL3/METTL14 were also preliminarily explored, providing new information on pathogenic mechanism of pollutants.
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Yang F, Zhang A. Involvement of METTL3 in arsenite-induced skin lesions by targeting the SOCS3/STAT3/Krt signaling pathway. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120634. [PMID: 36368553 DOI: 10.1016/j.envpol.2022.120634] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Arsenic is a common environmental pollutant, typically affecting the skin most severely. Recent studies have shown that arsenic's toxicity may be linked to N6-methyladenosine (m6A), an abundant and dynamic epigenetic RNA modification. However, it is not completely understood how m6A contributes to arsenite-induced skin lesions. Herein, it is shown that methyltransferase-like 3 (METTL3) plays a crucial role in the involvement of arsenite-induced skin lesions in an m6A-dependent manner. Using bioinformatic analysis and experimental approaches, we demonstrate that arsenite induces METTL3 upregulation, represses suppressors of cytokine signaling 3 (SOCS3) expression in an m6A- YTH m6A RNA binding protein 2 (YTHDF2)-dependent manner, and leads to the aberrant activation of the Janus kinase (JAK)2/signal transducer and activator of transcription 3(STAT3) signaling pathway. We further found that the activated transcription factor STAT3 binds to the promoter regions of Krt1 and Krt10, promoting their transcription, which ultimately leads to arsenite-induced skin lesions. In conclusion, our study reveals the role of m6A in arsenite-induced skin lesions through the activation of the JAK2/STAT3/Krt signaling axis. The findings provide new insight into the potential molecular mechanisms underlying arsenic toxicity regulation through m6A modification.
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Wang L, Yang C, Shan Q, Zhao M, Yu J, Li YF. Transcriptome-wide profiling of mRNA N 6-methyladenosine modification in rice panicles and flag leaves. Genomics 2023; 115:110542. [PMID: 36535337 DOI: 10.1016/j.ygeno.2022.110542] [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: 09/03/2022] [Revised: 12/01/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
N6-methyladenosine (m6A) modification is essential for plant growth and development. Exploring m6A methylation patterns in rice tissues is fundamental to understanding the regulatory effects of this modification. Here, we profiled the transcriptome-wide m6A landscapes of rice panicles at the booting stage (PB) and flowering stage (PF), and of flag leaves at the flowering stage (LF). The global m6A level differed significantly among the three tissues and was closely associated with the expression of writer and eraser genes. The methylated gene ratio was higher in the flag leaves than in the panicles. Compared with commonly methylated genes, tissue-specific methylated genes showed lower levels of both m6A modification and expression, and a preference for m6A deposition in the coding sequence region. The m6A profiles of the two organs had more distinct differences than the profiles of the same organ at different stages. A negative correlation between m6A levels and gene expression was observed in PF vs. PB but not in PF vs. LF, indicting the complicated regulatory effect of m6A on gene expression. The distinct expression patterns of m6A reader genes in different tissues indicate that readers may affect gene stability through binding. Overall, our findings demonstrated that m6A modification influences tissue function by regulating gene expression. Our findings provide valuable insights on the regulation and biological functions of m6A modifications in rice.
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Li L, Sun Y, Zha W, Li L, Li H. Novel insights into the N 6-methyladenosine RNA modification and phytochemical intervention in lipid metabolism. Toxicol Appl Pharmacol 2022; 457:116323. [PMID: 36427654 DOI: 10.1016/j.taap.2022.116323] [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: 09/10/2022] [Revised: 11/05/2022] [Accepted: 11/17/2022] [Indexed: 11/26/2022]
Abstract
Epitranscriptome (RNA modification) plays a vital role in a variety of biological events. N6-methyladenosine (m6A) modification is the most prevalent mRNA modification in eukaryotic cells. Dynamic and reversible m6A modification affects the plasticity of epitranscriptome, which plays an essential role in lipid metabolism. In this review, we comprehensively delineated the role and mechanism of m6A modification in the regulation of lipid metabolism in adipose tissue and liver, and summarized phytochemicals that improve lipid metabolism disturbance by targeting m6A regulator, providing potential lead candidates for drug therapeutics. Moreover, we discussed the main challenges and possible future directions in this field.
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Timcheva K, Dufour S, Touat-Todeschini L, Burnard C, Carpentier MC, Chuffart F, Merret R, Helsmoortel M, Ferré S, Grézy A, Couté Y, Rousseaux S, Khochbin S, Vourc'h C, Bousquet-Antonelli C, Kiernan R, Seigneurin-Berny D, Verdel A. Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression. Cell Rep 2022; 41:111784. [PMID: 36516773 DOI: 10.1016/j.celrep.2022.111784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/01/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
Heat stress (HS) induces a cellular response leading to profound changes in gene expression. Here, we show that human YTHDC1, a reader of N6-methyladenosine (m6A) RNA modification, mostly associates to the chromatin fraction and that HS induces a redistribution of YTHDC1 across the genome, including to heat-induced heat shock protein (HSP) genes. YTHDC1 binding to m6A-modified HSP transcripts co-transcriptionally promotes expression of HSPs. In parallel, hundreds of the genes enriched in YTHDC1 during HS have their transcripts undergoing YTHDC1- and m6A-dependent intron retention. Later, YTHDC1 concentrates within nuclear stress bodies (nSBs) where it binds to m6A-modified SATIII non-coding RNAs, produced in an HSF1-dependent manner upon HS. These findings reveal that YTHDC1 plays a central role in a chromatin-associated m6A-based reprogramming of gene expression during HS. Furthermore, they support the model where the subsequent and temporary sequestration of YTHDC1 within nSBs calibrates the timing of this YTHDC1-dependent gene expression reprogramming.
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Sun Q, Zhao T, Li B, Li M, Luo P, Zhang C, Chen G, Cao Z, Li Y, Du M, He H. FTO/RUNX2 signaling axis promotes cementoblast differentiation under normal and inflammatory condition. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119358. [PMID: 36084732 DOI: 10.1016/j.bbamcr.2022.119358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/30/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent mRNA modification which plays crucial roles in various biological processes, but its role in cementogenesis remains largely unknown. Here, using time-series transcriptomic analysis, we reveal that mRNA m6A demethylase Fat mass and obesity-associated protein (FTO) is involved in cementogenesis. Knocking down FTO decreases cementoblast differentiation and mineralization in both OCCM-30 cellular model and murine ectopic bone formation model. Mechanistically, we find that FTO directly binds Runt-related transcription factor 2 (Runx2) mRNA, an important cementogenesis factor, thus protecting it from YTH domain-containing family protein 2 (YTHDF2) mediated degradation, when cementoblasts are differentiating. Knocking down YTHDF2 restores the expression of Runx2 in FTO-knockdown cells. Moreover, under inflammatory conditions, TNF-α inhibits cementoblast differentiation and mineralization partly through FTO/RUNX2 axis. Collectively, our study reveals an important regulatory role of FTO/RUNX2 axis in normal and pathological cementogenesis.
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Boo SH, Ha H, Kim YK. m 1A and m 6A modifications function cooperatively to facilitate rapid mRNA degradation. Cell Rep 2022; 40:111317. [PMID: 36070699 DOI: 10.1016/j.celrep.2022.111317] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/25/2022] [Accepted: 08/16/2022] [Indexed: 11/03/2022] Open
Abstract
N6-Methyladenosine (m6A), the most abundant internal mRNA modification, affects multiple steps in gene expression. Mechanistically, the binding of YTHDF2 to m6A on mRNAs elicits rapid mRNA degradation by recruiting several RNA degrading enzymes. Here, we show that N1-methyladenosine (m1A), another type of RNA modification, accelerates rapid m6A RNA degradation. We identify HRSP12 as an RNA-binding protein that recognizes m1A. The binding of HRSP12 to m1A promotes efficient interaction of YTHDF2 with m6A, consequently facilitating endoribonucleolytic cleavage via the RNase P/MRP complex. Transcriptome-wide analyses also reveal that mRNAs harboring both m1A and m6A are downregulated in an HRSP12-dependent manner compared with mRNAs harboring m6A only. Accordingly, a subset of endogenous circular RNAs that harbor m6A and associate with YTHDF2 in an HRSP12-dependent manner is also subjected to m1A-facilitated rapid degradation. Together, our observations provide compelling evidence for crosstalk between different RNA modifications.
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Choi SH, Flamand MN, Liu B, Zhu H, Hu M, Wang M, Sewell J, Holley CL, Al-Hashimi HM, Meyer KD. RBM45 is an m 6A-binding protein that affects neuronal differentiation and the splicing of a subset of mRNAs. Cell Rep 2022; 40:111293. [PMID: 36044854 PMCID: PMC9472474 DOI: 10.1016/j.celrep.2022.111293] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 07/14/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
N6-methyladenosine (m6A) is deposited co-transcriptionally on thousands of cellular mRNAs and plays important roles in mRNA processing and cellular function. m6A is particularly abundant within the brain and is critical for neurodevelopment. However, the mechanisms through which m6A contributes to brain development are incompletely understood. RBM45 acts as an m6A-binding protein that is highly expressed during neurodevelopment. We find that RBM45 binds to thousands of cellular RNAs, predominantly within intronic regions. Rbm45 depletion disrupts the constitutive splicing of a subset of target pre-mRNAs, leading to altered mRNA and protein levels through both m6A-dependent and m6A-independent mechanisms. Finally, we find that RBM45 is necessary for neuroblastoma cell differentiation and that its depletion impacts the expression of genes involved in several neurodevelopmental signaling pathways. Altogether, our findings show a role for RBM45 in controlling mRNA processing and neuronal differentiation, mediated in part by the recognition of methylated RNA. Choi et al. identify RBM45 as an m6A-binding protein enriched in the developing brain. RBM45 binds to thousands of cellular RNAs, primarily within introns, and regulates constitutive splicing of target transcripts. Loss of RBM45 causes altered expression of neurodevelopmental genes and defects in the proliferation and differentiation of neuroblastoma cells.
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Shao Y, Duan X, Zhao X, Lv Z, Li C. Global N 6-methyladenosine methylation analysis reveals the positive correlation between m 6A modification and mRNA abundance during Apostichopus japonicus disease development. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 133:104434. [PMID: 35562078 DOI: 10.1016/j.dci.2022.104434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
N6-methyladenosine (m6A), the most abundant epitranscriptomic modification in eukaryotic messenger RNA (mRNA), plays important roles in regulation of gene expression for fundamental biological processes and diverse physiological functions, including combating with pathogen infection. Here, we were first profile transcriptome-wide m6A sequencing in four stages of skin ulceration syndrome-diseased Apostichopus japonicus following Vibrio splendidus infection, including Control (healthy), Early (small ulcer), Later (extensive ulcer), and Resistant (no ulcer) groups. Our results revealed that three experimental groups were all extensively methylated by m6A and the proportion of the m6A modified genes were also significantly increased to 28.90% (Early), 27.97% (Later), and 29.98% (Resistant) when compared with Control group (15.15%), indicating m6A modification could be induced by V. splendidus infection. Intriguingly, we discovered a positive correlation between the m6A methylation level and mRNA abundance, indicating a positive regulatory role of m6A in sea cucumber gene expression during V. splendidus infection. Moreover, genes with specific and differentially expressed m6A methylation in Later group were both enriched in cell adhesion, while Early and Resistant groups were both mainly involved in DNA conformation change and chromosome organization when compared with Control, suggesting the higher-methylated m6A might serve as "conformational marker" and associated to the initiation of related anti-disease genes transcription in order to improve disease resistance of sea cucumber. Subsequently, we selected the pivotal genes enriched in cell adhesion pathway and found that the IggFc-binding protein (FcGBP) and Fibrocystin-L both had higher levels of m6A methylation and higher level of mRNA expressions in Later group. Conversely, Fibrinogen C domain-containing protein 1 (F1BCD1) gene presented as an antibacterial role in sea cucumber and showed higher mRNA expression and higher m6A methylation in Resistant group and lower mRNA level in Later group. The levels of m6A methylation and mRNA abundance of FcGBP and F1BCD1 genes indicates disease occurrence or disease resistant were also verified by MeRIP-qPCR. Overall, our study presents the first comprehensive characterize of dynamic m6A methylation modification in the different stages of disease in sea cucumber. These data provide an invaluable resource for future studies of function and biological significance of m6A in mRNA in marine invertebrates.
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Sun X, Wang DO, Wang J. Targeted manipulation of m 6A RNA modification through CRISPR-Cas-based strategies. Methods 2022; 203:56-61. [PMID: 35306148 DOI: 10.1016/j.ymeth.2022.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/09/2022] [Accepted: 03/15/2022] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A) is a reversible and prevalent internal modification in RNAs and can be dynamically modulated by methyltransferase and demethylase. Targeted manipulation of m6A RNA modification is critical in studying the functions of specific m6A sites as well as developing molecular therapies through targeting m6A. The CRISPR-Cas systems including CRISPR-Cas9 and CRISPR-Cas13 have been widely used to edit and modify specific nucleotides on DNA and RNA through fusing effective proteins such as enzymes with Cas9/13. Through taking advantage of the m6A methyltransferase and demethylase, a series of CRISPR-Cas-based methods have also been developed to manipulate the m6A methylation at specific RNA sites. This review summarizes the latest CRISPR-Cas13 and Cas9 toolkits for m6A site-specific manipulation, including fundamental components, on-target efficiency, editing window, PAM/PFS requirement, and subcellularly localized targeting as well as potential limitations. We thus aim to provide an overview to assist researchers to choose an optimal tool to manipulate m6A for different purposes and also point out possible optimization strategies.
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Zhou S, Sun Y, Xing Y, Wang Z, Wan S, Yao X, Hua Q, Meng X, Cheng J, Zhong M, Lv K, Kong X. Exenatide ameliorates hydrogen peroxide-induced pancreatic β-cell apoptosis through regulation of METTL3-mediated m 6A methylation. Eur J Pharmacol 2022; 924:174960. [PMID: 35436474 DOI: 10.1016/j.ejphar.2022.174960] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 01/05/2023]
Abstract
Exenatide, a glucagon-like peptide-1 (GLP-1) receptor agonist, is a commonly used hypoglycemic agent in clinical practice; it inhibits reactive oxygen species-induced pancreatic β-cell apoptosis. N6-methyladenosine (m6A) is produced by the methylation of RNA N6 residues and has recently been shown to play a crucial role in the regulation of islet β-cell growth and development. However, the involvement of m6A methylation in the β-cell protective effects of exenatide has not been clarified. In this study, the m6A-methylated RNA content and methyltransferase-like 3 (METTL3) expression levels in NIT-1 cells and primary mouse islets were found to significantly decrease following treatment with hydrogen peroxide (H2O2). Treatment with exenatide induced an increase in m6A content and METTL3 expression in the H2O2-treated NIT-1 cells and islets. Moreover, METTL3 silencing resulted in NIT-1 cell apoptosis under normal culture conditions. METTL3 upregulation significantly ameliorated H2O2-induced apoptosis in NIT-1 cells and primary islets. Furthermore, the anti-apoptotic effects of exenatide were obviously reversed by METTL3 knockdown. In conclusion, these findings suggest that exenatide elicits its anti-apoptotic effects in pancreatic β-cells by promoting m6A methylation through the upregulation METTL3 expression.
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RNA m6A reader YTHDF1 facilitates inflammation via enhancing NLRP3 translation. Biochem Biophys Res Commun 2022; 616:76-81. [PMID: 35649302 DOI: 10.1016/j.bbrc.2022.05.076] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 05/21/2022] [Indexed: 11/20/2022]
Abstract
N6-methyladenosine (m6A) modification of mRNAs is involved in multiple essential biological processes, dynamically regulated by m6A "writers", "erasers", and "readers". Yet, the detailed functional roles of RNA m6A reader proteins, such as YTHDFs, are largely unknown. Herein we show that YTHDF1 promotes pro-inflammatory IL-1β production in macrophages during bacterial infections. YTHDF1 overexpression promotes NLRP3 translation. In vivo knockdown of YTHDF1 facilitates survival in a mouse model of sepsis. Thus, YTHDF1 participates in inflammatory responses and subsequent injuries, serving as a new potential therapeutic target in clinical treatment of inflammatory diseases.
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Fang Z, Mu B, Liu Y, Guo N, Xiong L, Guo Y, Xia A, Zhang R, Zhang H, Yao R, Fan Y, Li L, Yang S, Xiang R. Discovery of a potent, selective and cell active inhibitor of m 6A demethylase ALKBH5. Eur J Med Chem 2022; 238:114446. [PMID: 35597008 DOI: 10.1016/j.ejmech.2022.114446] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/24/2022] [Accepted: 05/05/2022] [Indexed: 02/08/2023]
Abstract
AlkB homolog 5 (ALKBH5) is an RNA m6A demethylase involved in the regulation of genes transcription, translation and metabolism and has been considered as a promising therapeutic target for various human diseases, especially cancers. However, there is still a lack of potent and selective ALKBH5 inhibitors. Herein, we report a new class of ALKBH5 inhibitors containing the 1-aryl-1H-pyrazole scaffold, which were obtained through fluorescence polarization-based screening, structural optimization and structure-activity relationship analysis. Among these compounds, 20m was the most potent one, which showed an IC50 value of 0.021 μM in fluorescence polarization assay. Compound 20m exhibited high selectivity towards ALKBH5 versus FTO as well as other AlkB subfamily members, indicating good selectivity for ALKBH5. Cellular thermal shift assay (CETSA) analysis showed that 20m could efficiently stabilize ALKBH5 in HepG2 cells. Dot blot assay demonstrated that 20m could increase m6A level in intact cells. Collectively, 20m is a potent, selective and cell active ALKBH5 inhibitor and could be used as a versatile chemical probe to explore the biological function of ALKBH5.
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N 6-methyladenosine (m 6A) reader IGF2BP1 accelerates gastric cancer aerobic glycolysis in c-Myc-dependent manner. Exp Cell Res 2022; 417:113176. [PMID: 35489385 DOI: 10.1016/j.yexcr.2022.113176] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/22/2022] [Indexed: 12/19/2022]
Abstract
The N6-methyladenosine (m6A) is involved in the regulation of cell proliferation and metastasis formation in multiple cancers. However, the biological significance of RNA m6A reader IGF2BP1 and the modification of IGF2BP1 itself have not been fully investigated. Here, we analyzed the functions and mechanism of IGF2BP1 in gastric cancer (GC). Results showed that IGF2BP1 upregulated in GC tissue and acted as a predictor of poor prognosis for GC patients. Functionally, IGF2BP1 promoted the migration and aerobic glycolysis of GC cells in vitro. Moreover, IGF2BP1 knockdown repressed the tumor growth in vivo. We also demonstrated that IGF2BP1 directly interacted with c-MYC mRNA via m6A-dependent manner to by stabilize its stability. Overall, these findings demonstrated that m6A reader IGF2BP1 facilitated the carcinogenic of GC in m6A/c-Myc-dependent manner, which might provide critical therapeutic strategy for GC.
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FTO in cancer: functions, molecular mechanisms, and therapeutic implications. Trends Cancer 2022; 8:598-614. [PMID: 35346615 DOI: 10.1016/j.trecan.2022.02.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/06/2022] [Accepted: 02/28/2022] [Indexed: 12/18/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification in mRNA that affects RNA processing, stability, and translation. Discovered as the first RNA m6A demethylase, the fat mass and obesity-associated protein (FTO) is frequently dysregulated and plays important roles in various types of cancers. Targeting FTO holds promising therapeutic significance via suppressing tumor growth, potentiating immunotherapy, and attenuating drug resistance. Here, we review recent advances in our understanding of the functions and underlying molecular mechanisms of FTO in tumor development, cancer stem cell (CSC) self-renewal, microenvironment regulation, immunity, and metabolism and discuss the therapeutic potential of targeting FTO for cancer treatment.
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Control of animal virus replication by RNA adenosine methylation. Adv Virus Res 2022; 112:87-114. [PMID: 35840182 DOI: 10.1016/bs.aivir.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Methylation at the N6-position of either adenosine (m6A) or 2'-O-methyladenosine (m6Am) represents two of the most abundant internal modifications of coding and non-coding RNAs, influencing their maturation, stability and function. Additionally, although less abundant and less well-studied, monomethylation at the N1-position (m1A) can have profound effects on RNA folding. It has been known for several decades that RNAs produced by both DNA and RNA viruses can be m6A/m6Am modified and the list continues to broaden through advances in detection technologies and identification of the relevant methyltransferases. Recent studies have uncovered varied mechanisms used by viruses to manipulate the m6A pathway in particular, either to enhance virus replication or to antagonize host antiviral defenses. As such, RNA modifications represent an important frontier of exploration in the broader realm of virus-host interactions, and this new knowledge already suggests exciting opportunities for therapeutic intervention. In this review we summarize the principal mechanisms by which m6A/m6Am can promote or hinder viral replication, describe how the pathway is actively manipulated by biomedically important viruses, and highlight some remaining gaps in understanding how adenosine methylation of RNA controls viral replication and pathogenesis.
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Su T, Fu L, Kuang L, Chen D, Zhang G, Shen Q, Wu D. Transcriptome-wide m6A methylation profile reveals regulatory networks in roots of barley under cadmium stress. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127140. [PMID: 34523471 DOI: 10.1016/j.jhazmat.2021.127140] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/13/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) pollutants restrict crop yield and food security in long-term agricultural activities. Crops have evolved adaptive strategies under Cd condition, however, the transcriptional regulatory mechanism of Cd-tolerant genes remains to be largely illustrated. In this study, barley roots were exposed to 5 µM CdCl2 for physiological response and transcriptome-wide m6A methylation profile. Cd stress inhibited root growth after 7 d Cd treatment, which is mainly associated with inhibited absorption of Mn. After Cd treatment, 8151 significantly modified m6A sites and 3920 differentially expressed genes were identified. Transcriptome-wide m6A hypermethylation was widely induced by Cd stress and enriched near the stop codon and 3' UTR regions. Among 435 m6A modified DEGs, 319 hypermethylated genes were up-regulated and 84 hypomethylated genes were down-regulated, respectively, indicating a positive correlation of m6A methylation and expression. But well-known Cd transporter genes (HvNramp5, HvIRT1, HvHMA3, etc.) were not modified by m6A methylation, except for ABC transporters. We further found key Cd-responding regulatory genes were positively modulated with m6A methylation, including MAPK, WRKY and MYB members. This study proposed a transcriptional regulatory network of Cd stress response in barley roots, which may provide new insight into gene manipulation of controlling low Cd accumulation for crops.
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Xu K, Zhang Q, Chen M, Li B, Wang N, Li C, Gao Z, Zhang D, Yang L, Xu Z, Li X, Xu H. N 6-methyladenosine modification regulates imatinib resistance of gastrointestinal stromal tumor by enhancing the expression of multidrug transporter MRP1. Cancer Lett 2022; 530:85-99. [PMID: 35032557 DOI: 10.1016/j.canlet.2022.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/23/2021] [Accepted: 01/08/2022] [Indexed: 12/29/2022]
Abstract
N6-methyladenosine (m6A) is a frequently occurring mRNA modification, which regulates mRNA stability, splicing, and translation. However, its role in drug resistance of gastrointestinal stromal tumor (GIST) is not known. Here, we report that m6A modification levels are elevated in imatinib-resistant GIST cells and tissues, and that methyltransferase METTL3 is one of the main protein responsible for this aberrant modification. Increased METTL3 levels contributed to imatinib resistance and worse progression-free survival of GIST patients. Mechanistic studies revealed that METTL3-mediated m6A modification of the 5'UTR of the multidrug transporter MRP1 mRNA promoted drug resistance of GIST by stimulating MRP1 mRNA translation, via binding with YTHDF1 and eEF-1. Further, METTL3 transcription in Imatinib resistant GIST cells was activated by ETV1, leading to the increased m6A methylation of MRP1 mRNA. This is the first report showing a novel regulatory mechanism whereby ETV1, METTL3, and the YTHDF1/eEF-1 complex mediate the translation of MRP1 mRNA in an m6A-dependent manner to regulate the intracellular concentration of imatinib and drug resistance of GIST. These findings highlight MRP1 as a new potential therapeutic target for imatinib resistance of GIST.
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