Genes
·
2021
·Vol. 12
·期 10
·1488
·
IF 4.096
Jizhong Zhao,Hongmei Hu,Sheng Wang,Li Wang,Rui Wang
In living organisms, RNA regulates gene expression, cell migration, differentiation, and cell death. 5-Methylcytosine is a post-transcriptional RNA modification in a wide range of RNA species, including messenger RNAs. The addition of m5C to RNA cytosines is enabled by theNSUNenzyme family, a critical RNA methyltransferase. In this study, natural lysines modified with special groups were synthesized. Through two rounds of positive screening and one round of negative screening, we evaluated and identified theMbPylRS-tRNACUAunnatural lysine substitution system, which specifically recognizes lysine with a defined group. Moreover, non-natural lysine substitution at C271 ofNSUN2active site and the subsequent fluorescent labeling was realized through the click reaction. Then, the function of theNSUN2mutant and its upregulatedCDK1gene as well as its effect on cell proliferation were evaluated. Efficient labeling and regulation ofNSUN2was achieved, laying the basis for further studies on the function and regulatory mechanism of upregulated genes.Keywords:RNA modification;m5C;NSUN enzyme;regulation;labeling
研究领域:
分子生物学
·
细胞生物学
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DOI
PubMed
高影响因子
NUCLEIC ACIDS RESEARCH
·
2022
·Vol. 50
·期 17
·9858-9872
·
IF 19.16
You Xue-Jiao,Zhang Shan,Chen Juan-Juan,Tang Feng,He Jingang,Wang Jie,Qi Chu-Bo,Feng Yu-Qi,Yuan Bi-Feng
RNA molecules harbor diverse modifications that play important regulatory roles in a variety of biological processes. Over 150 modifications have been identified in RNA molecules. N6-methyladenosine (m6A) and 1-methyladenosine (m1A) are prevalent modifications occurring in various RNA species of mammals. Apart from the single methylation of adenosine (m6A and m1A), dual methylation modification occurring in the nucleobase of adenosine, such as N6,N6-dimethyladenosine (m6,6A), also has been reported to be present in RNA of mammals. Whether there are other forms of dual methylation modification occurring in the nucleobase of adenosine other than m6,6A remains elusive. Here, we reported the existence of a novel adenosine dual methylation modification, i.e. 1,N6-dimethyladenosine (m1,6A), in tRNAs of living organisms. We confirmed that m1,6A is located at position 58 of tRNAs and is prevalent in mammalian cells and tissues. The measured level of m1,6A ranged from 0.0049% to 0.047% in tRNAs. Furthermore, we demonstrated that TRMT6/61A could catalyze the formation of m1,6A in tRNAs and m1,6A could be demethylated by ALKBH3. Collectively, the discovery of m1,6A expands the diversity of RNA modifications and may elicit a new tRNA modification-mediated gene regulation pathway.
研究领域:
分子生物学
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表观遗传学
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生物化学
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DOI
PubMed
高影响因子
Genes
·
2023
·Vol. 14
·期 6
·1287
·
IF 3.5
Meng Chu,Yichao Qin,Xiuying Lin,Li Ma,Dehai Deng,Daizhu Lv,Pengcheng Fu,Huan Lin
The coconut (Cocos nuciferaL.) is a commercial crop widely distributed among coastal tropical regions. It provides millions of farmers with food, fuel, cosmetics, folk medicine, and building materials. Among these, oil and palm sugar are representative extracts. However, this unique living species ofCocoshas only been preliminarily studied at molecular levels. Benefiting from the genomic sequence data published in 2017 and 2021, we investigated the transfer RNA (tRNA) modifications and modifying enzymes of the coconut in this survey. An extraction method for the tRNA pool from coconut flesh was built. In total, 33 species of modified nucleosides and 66 homologous genes of modifying enzymes were confirmed using a nucleoside analysis using high-performance liquid chromatography combined with high-resolution mass spectrometry (HPLC-HRMS) and homologous protein sequence alignment. The positions of tRNA modifications, including pseudouridines, were preliminarily mapped using a oligonucleotide analysis, and the features of their modifying enzymes were summarized. Interestingly, we found that the gene encoding the modifying enzyme of 2′-O-ribosyladenosine at the 64th position of tRNA (Ar(p)64) was uniquely overexpressed under high-salinity stress. In contrast, most other tRNA-modifying enzymes were downregulated with mining transcriptomic sequencing data. According to previous physiological studies of Ar(p)64, the coconut appears to enhance the quality control of the translation process when subjected to high-salinity stress. We hope this survey can help advance research on tRNA modification and scientific studies of the coconut, as well as thinking of the safety and nutritional value of naturally modified nucleosides.Keywords:Cocos nucifera;epitranscriptomics;LC-MS/MS;nucleoside misidentification;RNA modification
研究领域:
植物学
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遗传学
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分子生物学
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DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
·
2024
·Vol. 25
·期 8
·4538
·
IF 4.9
Yue Zhu,Yadong Zhang,Yaoqi Jiang,Hongshi Cai,Jianfeng Liang,Hongyu Li,Cheng Wang,Jinsong Hou
Cleft palate only (CPO) is one of the most common craniofacial birth defects. Environmental factors can induce cleft palate by affecting epigenetic modifications such as DNA methylation, histone acetylation, and non-coding RNA. However, there are few reports focusing on the RNA modifications. In this study, all-trans retinoic acid (atRA) was used to simulate environmental factors to induce a C57BL/6J fetal mouse cleft palate model. Techniques such as dot blotting and immunofluorescence were used to find the changes in m6A modification when cleft palate occurs. RNA-seq and KEGG analysis were used to screen for significantly differentially expressed pathways downstream. Primary mouse embryonic palate mesenchymal (MEPM) cells were successfully isolated and used for in vitro experimental verification. We found that an increased m6A methylation level was correlated with suppressed cell proliferation in the palatine process mesenchyme of cleft palate mice. This change is due to the abnormally high expression of m6A methyltransferase METTL14. When using siRNAs and the m6A methyltransferase complex inhibitor SAH to interfere with the expression or function of METTL14, the teratogenic effect of atRA on primary cells was partially alleviated. In conclusion, METTL14 regulates palatal mesenchymal cell proliferation and cycle-related protein expression relies on m6A methylation modification, affecting the occurrence of cleft palate.
CAS / MDL:
研究领域:
发育生物学
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表观遗传学
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分子生物学
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DOI
PubMed
高影响因子
PLANT PHYSIOLOGY
·
2023
·
IF 7.4
Xu Jidi,He Jieqiang,Hu Bichun,Hou Nan,Guo Junxing,Wang Caixia,Li Xuewei,Li Zhongxing,Zhai Jingjing,Zhang Ting,Ma Chuang,Ma Fengwang,Guan Qingmei
Grafting can facilitate better scion performance and is widely used in plants. Numerous studies have studied the involvement of mRNAs, small RNAs, and epigenetic regulations in the grafting process. However, it remains unclear whether the mRNA N6-methyladenosine (m6A) modification participates in the apple (Malus x domestica Borkh.) grafting process. Here, we decoded the landscape of m6A modification profiles in ‘Golden delicious’ (a cultivar, Gd) and Malus prunifolia ‘Fupingqiuzi’ (a unique rootstock with resistance to environmental stresses, Mp), as well as their heterografted and self-grafted plants. Interestingly, global hypermethylation of m6A occurred in both heterografted scion and rootstock compared with their self-grafting controls. Gene Ontology (GO) term enrichment analysis showed that grafting-induced differentially m6A-modified genes were mainly involved in RNA processing, epigenetic regulation, stress response, and development. Differentially m6A-modified genes harboring expression alterations were mainly involved in various stress responses and fatty acid metabolism. Furthermore, grafting-induced mobile mRNAs with m6A and gene expression alterations mainly participated in ABA synthesis and transport (e.g. carotenoid cleavage dioxygenase 1 [CCD1] and ATP-binding cassette G22 [ABCG22]) and abiotic and biotic stress responses, which might contribute to the better performance of heterografted plants. Additionally, the DNA methylome analysis also demonstrated the DNA methylation alterations during grafting. Downregulated expression of m6A methyltransferase gene MdMTA (ortholog of METTL3) in apples induced the global m6A hypomethylation and distinctly activated the expression level of DNA demethylase gene MdROS1 (REPRESSOR OF SILENCING 1) showing the possible association between m6A and 5mC methylation in apples. Our results reveal the m6A modification profiles in the apple grafting process and enhance our understanding of the m6A regulatory mechanism in plant biological processes.
研究领域:
植物生物学
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表观遗传学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
TALANTA
·
2023
·
IF 6.1
Gefei Huang,Feng Zhang,Dongying Xie,Yiming Ma,Pengxi Wang,Guodong Cao,Leijian Chen,Siyi Lin,Zhongying Zhao,Zongwei Cai
Although next-generation sequencing technology has been used to delineate RNA modifications in recent years, the paucity of appropriate converting reactions or specific antibodies impedes the accurate characterization and quantification of numerous RNA modifications, especially when these modifications demonstrate wide variations across developmental stages and cell types. In this study, we developed a high-throughput analytical platform coupling ultra-performance liquid chromatograph (UPLC) with complementary mass spectrometry (MS) to identify and quantify RNA modifications in both synthetic and biological samples. Sixty-four types of RNA modifications, including positional isomers and hypermodified ribonucleosides , were successfully monitored within a 16-min single run of UPLC–MS. Two independent methods to cross-validate the purity of RNA extracted from Caenorhabditis elegans ( C. elegans ) were developed using the coexisting C. elegans and Escherichia coli ( E. coli ) as a surveillance system. To test the validity of the method, we investigated the RNA modification landscape of three model organisms, C. elegans , E. coli , and Arabidopsis thaliana ( A. thaliana ). Both the identity and molarity of modified ribonucleosides markedly varied among the species. Moreover, our platform is not only useful for exploring the dynamics of RNA modifications in response to environmental cues (e.g., cold shock) but can also help with the identification of RNA-modifying enzymes in genetic studies. Cumulatively, our method presents a novel platform for the comprehensive analysis of RNA modifications, which will be of benefit to both analytical chemists involved in biomarker discovery and biologists conducting functional studies of RNA modifications.
研究领域:
生物化学
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分析化学
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分子生物学
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DOI
PubMed
高影响因子
iScience
·
2024
·
IF 4.6
Hui Han,Yucong Sun,Wei Wei,Zixin Huang,Maosheng Cheng,Hongshen Qiu,Juan Wang,Siyi Zheng,Lianlian Liu,Qiang Zhang,Canfeng Zhang,Jieyi Ma,Siyao Guo,Zhaoyu Wang,Zhenpeng Li,Xu Jiang,Shuibin Lin,Qianwen Liu,Shuishen Zhang
Summary Emerging studies have demonstrated the link between RNA modifications and various cancers, while the predictive value and functional mechanisms of RNA modification-related genes (RMGs) in esophageal squamous cell carcinoma (ESCC) remain unclear. Here we established a prognostic signature for ESCC based on five RMGs. The analysis of ESCC clinical samples further verified the prognostic power of the prognostic signature. Moreover, we found that the knockdown of NSUN6 promotes ESCC progression in vitro and in vivo , whereas the overexpression of NSUN6 inhibits the malignant phenotype of ESCC cells. Mechanically, NSUN6 mediated tRNA m 5 C modifications selectively enhance the translation efficiency of CDH1 mRNA in a codon dependent manner. Rescue assays revealed that E-cadherin is an essential downstream target that mediates NSUN6’s function in the regulation of ESCC progression. These findings offer additional insights into the link between ESCC and RMGs, as well as provide potential strategies for ESCC management and therapy.
研究领域:
肿瘤学
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分子生物学
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基因组学
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DOI
PubMed
高影响因子
Chemical Science
·
2021
·Vol. 12
·期 23
·8149-8156
·
IF 9.825
Ming-Yu Cheng,Xue-Jiao You,Jiang-Hui Ding,Yi Dai,Meng-Yuan Chen,Bi-Feng Yuan,Yu-Qi Feng
RNA modifications play critical roles in regulating a variety of physiological processes. Methylation is the most prevalent modification occurring in RNA. Three isomeric cytidine methylation modifications have been reported in RNA, including 3-methylcytidine (m3C), N4-methylcytidine (m4C), and 5-methylcytidine (m5C), in mammals. Aside from the single methylation on the nucleobase of cytidines, dual methylation modifications occurring in both the 2′ hydroxyl of ribose and the nucleobase of cytidines also have been reported, including N4,2′-O-dimethylcytidine (m4Cm) and 5,2′-O-dimethylcytidine (m5Cm). m4Cm has been found in the 16S rRNA of E. coli, while m5Cm has been found in the tRNA of terminal thermophilic archaea and mammals. However, unlike m4Cm and m5Cm, the presumed dual methylation of 3,2′-O-dimethylcytidine (m3Cm) has never been discovered in living organisms. Thus, the presence of m3Cm in RNA remains an open question. In the current study, we synthesized m3Cm and established a liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) method to determine the dimethylation of cytidines, m3Cm, m4Cm and m5Cm. Under optimized analytical conditions, m3Cm, m4Cm and m5Cm can be clearly distinguished. Using the method, we discovered the existence of m3Cm in the RNA of mammals. The identified m3Cm is a novel modification that hasn't been reported in the three-domain system, including archaea, bacteria, and eukaryotes. We confirmed that m3Cm mainly existed in the small RNA (<200 nt) of mammals. In addition, we identified, for the first time, the presence of m4Cm in the 18S rRNA of mammalian cells. The stable isotope tracing monitored by mass spectrometry demonstrated that S-adenosyl-L-methionine was a methyl donor for all three dimethylations of cytidines in RNA. The discovery of m3Cm broadens the diversity of RNA modifications in living organisms. In addition, the discovery of m3Cm and m4Cm in mammals opens new directions in understanding RNA modification-mediated RNA processing and gene expression regulation.
研究领域:
分子生物学
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生物化学
·
RNA生物学
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DOI
PubMed
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
·
2025
·
IF 11.3
Run Ling,Xin Yin,Liyao Ma,Yan Zhang,Yidan Ma,Rufei Gao,Yanqing Geng,Xinyi Mu,Xuemei Chen,Fangfang Li,Junlin He
Decabromodiphenyl ethane (DBDPE) is a brominated flame retardant widely used for its high flame retardancy and low bioavailability. However, DBDPE exhibits bioaccumulative potential. The placental vasculature, critical for the exchange between maternal and fetal circulation, is susceptible to environmental factors. We aimed to understand the potential toxicity of DBDPE to the placental vasculature. Gestational CD-1 mice and human umbilical vein endothelial cells (HUVECs) were exposed to 0, 0.5, 5, 50 mg/kg·bw·day or 0, 6.25, 12.5, 25, 50 μmol/L DBDPE, respectively. DBDPE exposure impaired placental angiogenesis and inhibited the proliferation and invasion of HUVECs by activating the endothelial-to-mesenchymal transition (EndMT) through the TGF-β1/Smad pathway, in vivo and in vitro . DBDPE upregulated the transcription factor TWIST2 and mRNA acetyltransferase NAT10. Knockdown or overexpression of TWIST2 reversed the vascular dysfunction and EndMT mechanism. DBDPE facilitated the recruitment of NAT10 by TWIST2, promoting N4-acetylcytidine (ac4C) RNA modifications and stabilizing the TGF-β1 mRNA. NAT10 inhibition rescued the effects caused by DBDPE. These findings uncover molecular mechanisms linking DBDPE exposure to adverse pregnancy outcomes, highlighting potential risks to pregnant women.
研究领域:
毒理学
·
生殖生物学
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分子生物学
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环境健康
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细胞生物学
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RNA修饰
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发育生物学
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产品关联
DOI
PubMed
高影响因子
Chemical Science
·
2020
·Vol. 11
·期 7
·1878-1891
·
IF 9.346
Qing-Yun Cheng,Jun Xiong,Cheng-Jie Ma,Yi Dai,Jiang-Hui Ding,Fei-Long Liu,Bi-Feng Yuan,Yu-Qi Feng
The discovery of dynamic and reversible modifications in messenger RNA (mRNA) is opening new directions in RNA modification-mediated regulation of biological processes. Methylation is the most prevalent modification occurring in mRNA and the methyl group is mainly decorated in the adenine, cytosine, and guanine base or in the 2′-hydroxyl group of ribose. However, methylation of the uracil base (5-methyluridine, m5U) has not been discovered in mRNA of eukaryotes. In the current study, we established a method of N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide p-toluenesulfonate (CMCT) labelling coupled with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) analysis for the sensitive determination of uridine modifications in RNA. Our results demonstrated that the detection sensitivities of uridine modifications in RNA increased up to 1408 fold upon CMCT labelling. Using the developed method, we identified the distinct existence of m5U in mRNA of various mammalian cells and tissues. In addition, the stable isotope tracing monitored by mass spectrometry revealed that the methyl group of m5U originated from S-adenosyl-L-methionine (SAM). Our study expanded the list of modifications occurring in mRNA of mammals. Future work on transcriptome-wide mapping of m5U will further uncover the functional roles of m5U in mRNA of mammals.
研究领域:
分子生物学
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生物化学
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表观遗传学
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产品关联
DOI
PubMed
高影响因子
eLife
·
2025
·
IF 0
Chong Zhang,Zuoyan Zhang,Yueyi Wu,Yuchen Wu,Jing Cheng,Kaizhi Luo,Zhidi Li,Manman Zhang,Jian Wang,Xuesen Zhang,Yangling Li
Non-small cell lung cancer (NSCLC) is the most common subtype of lung cancer, and the prognosis is poor due to distant metastasis. Thus, there is an urgent need to discover novel therapeutic targets and strategies to overcome metastasis. A series of in vitro and in vivo phenotype experiments were performed to investigate the role of phosphodiesterase 1A (PDE1A) in NSCLC. The RNA binding protein immunoprecipitation (RIP) assay, messenger RNA (mRNA) stability assay, and LC-MS/MS were performed to investigate the molecular mechanisms of PDE1A in NSCLC progression. PDE1A has been shown to promote metastasis and epithelial-mesenchymal transition (EMT) progression of NSCLC. In addition, NSCLC cells overexpressing PDE1A promoted angiogenesis by regulating exosome release. IL-6/JAK/STAT3 signaling pathway was highly enriched in PDE1A-coexpressed genes, and PDE1A promoted NSCLC metastasis by activating the STAT3 pathway. GO enrichment analysis of PDE1A-interacting genes showed that PDE1A might interact with YTHDF2 and participate in m6A-containing RNA binding. The binding between PDE1A and YTHDF2 was verified, and PDE1A regulated the STAT3 pathway by interacting with YTHDF2. The mechanism of the YTHDF2/PDE1A complex in regulating the STAT3 pathway was predicted by overlapping YTHDF2-interacting RNAs and genes coexpressed with YTHDF2 and STAT3. The interactions between YTHDF2 and target mRNAs were predicted, and there were three predicted targets of YTHDF2 with high scores: NRF2, SOCS2, and MET. Indeed, PDE1A interacted with YTHDF2, destabilized SOCS2, and activated the STAT3 pathway. Mechanistic data uncover a novel PDE1A/YTHDF2/STAT3 axis driving NSCLC metastasis and suggest potential therapeutic strategies for metastatic disease.
研究领域:
癌症生物学
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分子生物学
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细胞生物学
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生物化学
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信号转导
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RNA生物学
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肿瘤学
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产品关联
DOI
PubMed
INFECTION GENETICS AND EVOLUTION
·
2021
·
IF 3.342
Congshan Liu,Jianping Cao,Haobing Zhang,Jianhai Yin
RNA modifications, as one of epigenetic mechanisms, are important and conserved mechanisms for maintaining the homeostasis of organisms. Little is known about RNA modifications in Echinococcus granulosus, an obligate parasite that inhabits mammals and gives rise to a huge public health and economic impact. Here, we focused on the RNA modification characteristics of E. granulosus for the first time by using mass spectrometry (UPLC-MS/MS) to qualitatively and quantitatively analyze 47 types of RNA modifications in E. granulosus total RNA. Furthermore, the E. granulosus homologs of writer enzymes preforming RNA modifications were identified, and their gene expression pattern at different developmental stages were analyzed by bioinformatics analysis. Finally, 23 types of RNA modifications were found in E. granulosus cysts total RNA, of which m 1 A, Ψ and m 5 C are the most abundant. The homologs of writer enzymes involved in these modifications were identified in the E. granulosus genome, with the dynamic gene expression during the different parasitic developmental stages. This work confirms that E. granulosus retains the conserved RNA modification mechanism during evolution, suggesting the important role of RNA modification in regulating its development and parasitic process. Moreover, the differences of amino acid sequences of RNA modification writer enzymes between parasite and host make it possible to use these enzymes as the candidate drug targets in the follow-up in-depth researches.
研究领域:
寄生虫学
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分子生物学
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基因组学
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DOI
PubMed
高影响因子
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