Journal of Translational Medicine
·
2024
·Vol. 22
·期 1
·1-19
·
IF 6.1
Wang Runze,Xue Wei,Kan Feifei,Zhang Huiying,Wang Di,Wang Lei,Wang Jianwen
Background Diabetic retinopathy (DR) is the leading cause of blinding eye disease among working adults and is primarily attributed to the excessive proliferation of microvessels, which leads to vitreous hemorrhage and retinal traction, thereby significantly impairing patient vision. NSUN2-mediated RNA m 5 C methylation is implicated in various diseases, and in this investigation, we focused on elucidating the impact of NSUN2 on the regulation of the expression of the downstream gene MUC1, specifically through RNA m 5 C methylation, on the progression of DR. Method Utilizing Microarray analysis, we examined patient vitreous fluid to pinpoint potential therapeutic targets for DR. Differential expression of NSUN2 was validated through qRT-PCR, Western blot, and immunofluorescence in human tissue, animal tissue, and cell model of DR. The relationship between NSUN2 and DR was explored in vitro and in vivo through gene knockdown and overexpression. Various techniques, such as MeRIP-qPCR and dot blot, were applied to reveal the downstream targets and mechanism of action of NSUN2. Results The levels of both NSUN2 and RNA m 5 C methylation were significantly elevated in the DR model. Knockdown of NSUN2 mitigated DR lesion formation both in vitro and in vivo. Mechanistically, NSUN2 promoted MUC1 expression by binding to the RNA m 5 C reader ALYREF. Knockdown of ALYREF resulted in DR lesion alterations similar to those observed with NSUN2 knockdown. Moreover, MUC1 overexpression successfully reversed a series of DR alterations induced by NSUN2 silencing. Conclusions NSUN2 regulates the expression of MUC1 through ALYREF-mediated RNA m 5 C methylation, thereby regulating the progression of DR and providing a new option for the treatment of DR in the future.
研究领域:
眼科学
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分子生物学
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表观遗传学
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DOI
高影响因子
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
·
2020
·
IF 4.192
Xiaojing Yang,Yukun Feng,Zhengyu Zhang,Hui Wang,Weiwei Li,Dan Ohtan Wang,Ying Peng,Jiang Zheng
Methyleugenol (ME) is a ubiquitous component in spices and other culinary herbal products. A prevailing theory in ME toxicity is its ability to be metabolically activated by P450 enzymes and sulfotransferases, which initiates sequential reactions of the resulting metabolites with functional biomolecules. The present study aimed at a potential interaction between the reactive metabolites of ME and RNA. Cultured mouse primary hepatocytes were incubated with ME followed by RNA extraction and NaOH and alkaline phosphatase-based RNA hydrolysis. Three adenosine adducts were detected in the hydrolytic mixture by LC–MS/MS. The same adenosine adducts were also detected in hepatic tissues harvested from ME-treated mice. These three adducts were chemically synthesized and structurally characterized by 1H NMR. Additionally, two guanosine adducts and one cytidine adduct were detected in the in vivo samples. These results provided solid evidence that the reactive metabolites of ME attacked RNA, resulting in RNA adduction.
研究领域:
毒理学
·
分子生物学
✓ 已验证
DOI
PubMed
高影响因子
ACS Nano
·
2023
·
IF 17.1
Dou Wang,Xuedong Wang,Feidi Ye,Jin Zou,Jiuxin Qu,Xingyu Jiang
Conventional nucleic acid detection technologies usually rely on amplification to improve sensitivity, which has drawbacks, such as amplification bias, complicated operation, high requirements for complex instruments, and aerosol pollution. To address these concerns, we developed an integrated assay for the enrichment and single molecule digital detection of nucleic acid based on a CRISPR/Cas13a and microwell array. In our design, magnetic beads capture and concentrate the target from a large volume of sample, which is 100 times larger than reported earlier. The target-induced CRISPR/Cas13a cutting reaction was then dispersed and limited to a million individual femtoliter-sized microwells, thereby enhancing the local signal intensity to achieve single-molecule detection. The limit of this assay for amplification-free detection of SARS-CoV-2 is 2 aM. The implementation of this study will establish a “sample-in-answer-out” single-RNA detection technology without amplification and improve the sensitivity and specificity while shortening the detection time. This research has broad prospects in clinical application.
研究领域:
生物技术
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分子生物学
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诊断方法
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产品关联
DOI
PubMed
高影响因子
Science China-Chemistry
·
2019
·Vol. 63
·期 3
·404-410
·
IF 6.085
Lu Shasha,Wang Shuang,Zhao Jiahui,Sun Jian,Yang Xiurong
RNA-cleaving DNAzymes possess important roles in DNAzymes and have been widely used in the biosensors, DNA nanomachines owing to their ion-specific dependence. However, there are still challenges in constructing universal but versatile stimuli-responsive strategies of RNA-cleaving DNAzymes. Herein, a stimuli-responsive strategy for RNA-cleaving DNAzyme is proposed by the artful design of hairpin nanostructure, in which the activities of DNAzyme (Pb 2+ -dependent DNAzyme as a model) in the hairpin’s loop are pH-regulated by using the triplex stem as the “lock”. Upon introducing the “key”, pH values, the DNAzyme will be activated and fragment the substrate of it in the presence of Pb 2+ , accompanied by the turn-on of the fluorescence quenched by fluorescence resonance energy transfer (FRET). The regulation ability of pH can be controlled by the length and sequence of the triplex stem, and the wide pH regulation range may be helpful for the application of DNAzymes in biological medicine delivery systems.
研究领域:
生物化学
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纳米技术
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生物传感器
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分子生物学
✓ 已验证
产品关联
DOI
高影响因子
LANGMUIR
·
2022
·
IF 4.331
Yani Ma,Yao Chen,Feixia Peng,Xueqin Ding
A phenylpropyl guanidinium magnetic ionic liquid (PGMIL) was designed and prepared to extract RNA from complex samples. The properties of PGMIL were characterized by a vibrating sample magnetometer, Fourier transform infrared spectrometer, thermogravimetric analyzer, transmission electron microscope, and scanning electron microscope. Through single-factor analysis, the factors affecting the RNA extraction process, such as PGMIL volume, temperature, extraction time, and pH, were systematically investigated. The ability of PGMIL to selectively extract RNA was investigated by a NanoDrop. Under the optimized conditions, the extraction efficiency of RNA can reach 81.9 ± 1.9%. The proposed extraction method has been demonstrated with the extraction of RNA from a series of complex sample matrices, including a metal ion mixture and medicinal yeast. After extraction, the retained RNA could be readily recovered by simply using Tris–HCl buffer, with a recovery rate of 68.11 ± 2.45%. Regeneration studies have shown that the extraction efficiency of PGMIL did not change significantly after using 4 times. This study provides a green, rapid, and environmental friendly extraction method for the selective extraction of RNA.
研究领域:
生物化学
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分析化学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
Frontiers in Bioengineering and Biotechnology
·
2024
·
IF 4.3
He Wei,Zhang Xinya,Zou Yangxiaoyu,Li Ji,Chang Le,He Yu-Cai,Jin Qiuheng,Ye Jianren
Introduction: Circular RNAs (circRNAs) are endogenous noncoding RNAs (ncRNAs) with transcriptional lengths ranging from hundreds to thousands. circRNAs have attracted attention owing to their stable structure and ability to treat complicated diseases. Our objective was to create a one-step reaction for circRNA synthesis using wild-type T7 RNA polymerase as the catalyst. However, T7 RNA polymerase is thermally unstable, and we streamlined circRNA synthesis via consensus and folding free energy calculations for hotspot selection. Because of the thermal instability, the permuted intron and exon (PIE) method for circRNA synthesis is conducted via tandem catalysis with a transcription reaction at a low temperature and linear RNA precursor cyclization at a high temperature.Methods: To streamline the process, a multisite mutant T7 RNA polymerase (S430P, N433T, S633P, F849I, F880Y, and G788A) with significantly improved thermostability was constructed, and G788A was used.Results: The resulting mutant exhibited stable activity at 45°C for over an hour, enabling the implementation of a one-pot transcription and cyclization reaction. The simplified circRNA production process demonstrated an efficiency comparable to that of the conventional two-step reaction, with a cyclization rate exceeding 95% and reduced production of immunostimulatory dsRNA byproducts.
研究领域:
分子生物学
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生物化学
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合成生物学
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产品关联
DOI
PubMed
高影响因子
CHEMICO-BIOLOGICAL INTERACTIONS
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2022
·
IF 5.168
Weiwei Li,Ting Cheng,Tingting Jiang,Mengyue Zhou,Bowen Gong,Guode Zhao,Jing Li,Rong Tan,Xiaojing Yang,Kandarp Joshi,Ying Peng,Maosheng Cheng,Ting Liu,Dan Ohtan Wang,Jiang Zheng
Pyrrolizidine alkaloids (PAs) are among the most significant hepatotoxins widely distributed in plant species. Incidence of liver injuries caused by PAs has been reported worldwide, and the reactive metabolites of PAs are known to play a critical role in causing the hepatotoxicity. To better understand the toxicity-induction mechanisms, we explored the interactions of PA metabolites with cellular RNA molecules, and examined their effects on the biochemical and metabolic properties of hepatic RNAs. After exposure to retrorsine, adduction on adenosine and guanosine were detected in mouse liver microsomal incubations, cultured mouse primary hepatocytes, and mouse liver tissues. NMR analysis showed that the exocyclic amino group participated in the adduction. We found drastically altered properties and metabolism of the adducted RNA such as reverse-transcriptability, translatability, and RNase-susceptibility. In addition, endogenous modification of N 6 -methyladenosine (m6A) was remarkably reduced.
研究领域:
毒理学
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分子生物学
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药理学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
PLoS One
·
2016
·Vol. 11
·期 10
·e0163340
·
IF 3.057
Hong Zhou,Yapei Wang,Qiongying Lv,Juan Zhang,Qing Wang,Fei Gao,Haoli Hou,Hao Zhang,Wei Zhang,Lijia Li
The ribosomal RNA (rRNA) gene encodes rRNA for protein synthesis. Aberrant expression of the rRNA gene has been generally observed in tumor cells and levels of its promoter methylation as an epigenetic regulator affect rRNA gene transcription. The possible relationship between expression and promoter methylation of rDNA has not been examined in human clinical cervical cancer. Here we investigate rRNA gene expression by quantitative real time PCR, and promoter methylation levels by HpaII/MspI digestion and sodium bisulfite sequencing in the development of human cervical cancer. We find that indeed rRNA levels are elevated in most of cervical intraepithelial neoplasia (CIN) specimens as compared with non-cancer tissues. The rDNA promoter region in cervical intraepithelial neoplasia (CIN) tissues reveals significant hypomethylation at cytosines in the context of CpG dinucleotides, accompanied with rDNA chromatin decondensation. Furthermore treatment of HeLa cells with the methylation inhibitor drug 5-aza-2’-deoxycytidine (DAC) demonstrates the negative correlation between the expression of 45S rDNA and the methylation level in the rDNA promoter region. These data suggest that a decrease in rDNA promoter methylation levels can result in an increase of rRNA synthesis in the development of human cervical cancer.
研究领域:
分子生物学
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肿瘤学
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表观遗传学
✓ 已验证
DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
·
2018
·
IF 3.247
Na Zhang,Yahui zhou,Qingxin Yuan,Yao Gao,Yan Wang,Xingyun Wang,Xianwei Cui,Pengfei Xu,Chenbo Ji,Xirong Guo,Lianghui You,Nan Gu,Yu Zeng
T2DM is a global health problem that seriously lowers the quality of life and insulin resistance makes a considerable contribution to the pathophysiology of T2DM. Long noncoding RNAs (lncRNAs) have emerged as important regulators in glucose and lipid metabolism. However, comprehensive analysis of lncRNAs in db/db mice skeletal muscle and their potential roles involved in skeletal muscle insulin resistance (IR) remains poorly characterized. Here, we identified 331 lncRNAs, 172 upregulated and 159 downregulated (|fold change|>2, q<0.05), differentially expressed in db/db mice skeletal muscle. Gene Ontology analysis, Pathway analysis and Gene Set Enrichment Analysis of network gene expression revealed the potential functions of dysregulated lncRNAs may involve skeletal muscle function, fatty acid metabolism and the PPAR signaling pathway. In addition, differentially expressed lncRNAs were verified in skeletal muscle from the widely known IR mouse models ( db/db and ob/ob mice). Further validation of lncRNAs in C2C12 myotubes exposed with various concentrations of palmitate uncovered that lncRNAs were responsive to palmitate exposure at the high concentrations (0.5mM and 0.75mM). Coexpression analysis revealed the key lncRNA-mRNA interactions and indicated a potential regulatory role of lncRNAs. Moreover, we characterized two candidate lncRNAs Gm15441 and 3110045C21Rik by a comprehensive examination of their genomic context and validated their expression with neighboring genes (Txnip and Ddr2) by the Spearman correlation analysis. Collectively, these findings improve our understanding of lncRNAs that mediate skeletal muscle insulin resistance in diabetes and represent potential molecular therapeutic targets to improve insulin sensitivity and associated metabolic diseases.
研究领域:
分子生物学
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代谢疾病
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遗传学
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产品关联
DOI
PubMed
高影响因子
Journal of Materials Chemistry B
·
2018
·Vol. 6
·期 26
·4380-4384
·
IF 4.776
Guanghan Li,Yong Liu,Jie Niu,Meishan Pei,Weiying Lin
RNA plays a central role in controlling cellular functions. Research of the content and distribution of RNA in living cells is of great significance to both biochemistry and biomedicine. However, ratiometric fluorescent probes for the detection of RNA in the cytoplasm and nucleoli are still rarely reported. We herein present the first example of a novel ratiometric fluorescent composite nanomaterial by using graphene quantum dots (GQDs) and a fluorescent probe molecule for the sensitive and selective detection of RNA. HVC-6 was selected as the detection group. The fluorescence was excited at 365 nm and the fluorescence emission at 470 and 610 nm increased gradually with the addition of RNA. The fluorescence intensity ratio of I610/I470 displayed a linear response to RNA. Furthermore, the developed nanomaterial HVC-6@GQDs showed potential for utilization as a fluorescent RNA probe in living cells.
研究领域:
生物化学
·
生物医学
·
纳米材料科学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
ANALYTICA CHIMICA ACTA
·
2025
·
IF 6
Mimi Li,Lina Wang,Yue Hu,Yi Liu,Shuang Xu,Kexing Peng,Chenghong Li,Hui Huang,Lichao Fang,Lulu Li,Huamin Liu,Xiaolong Wang,Junsong Zheng
Sensitive and efficient detection of RNA methylation sites is considered an integral part of epigenetic assessment. Contrary to previous studies on the detection of RNA m5C or m6A methylation alone, this study innovatively designed a biosensor capable of detecting RNA m5C or m6A methylation at the same time. Substances with specific electrochemical reactions such as ferrocene (FC) or methylene blue (MB) were modified onto the hairpin probe. When the hairpin probe was activated under specific conditions, it triggered a dendritic nonlinear hybridization chain reaction (HCR), which resulted in signal amplification. Gold (Au) and iron tetraoxide (Fe 3 O 4 ) composite nanomaterials were employed as the linking materials: the carboxylated ends of Fe 3 O 4 were connected to an antibody that specifically recognizes the m5C and m6A methylation sites, while Au nanoparticle ends adhering to the carboxylated Fe 3 O 4 surface are connected to the HCR enhanced signal amplifier. The m5C antibody was linked to Fc-containing HCR amplification products by this material, and similarly, the m6A antibody was linked to MB-containing amplifiers. Thus, the dandelion complex, a multifunctional body with methyl recognition and signal amplification, was formed. The capture probe immobilized on the surface of the gold electrode by Au–S recognized the target RNA sequence by base complementary pairing. Upon addition of the dandelion complex, due to its multi-functionality, the amplified signals were carried to the electrode by the antigen-antibody recognition mechanism, generating a current signal. The positions and heights of the current signal peaks enabled rapid determination of target RNA methyl modification sites and their abundance. The detection limits of this biosensor for RNA m5C and m6A were 4.68 × 10 −16 M and 1.10 × 10 −15 M, respectively, and the linear range was from 10 −15 mol/L to 10 −8 mol/L. The sensor developed in this study has the advantages of cost-effectiveness, ease of fabrication, and fast response time, and has the potential to be promoted for RNA methylation detection.
研究领域:
分子生物学
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生物传感技术
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表观遗传学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
Frontiers in Physiology
·
2025
·
IF 3.4
Senyue Liu,Qiang Li,Yongqiang Deng,Zhongwei Wang,Yang Feng,Han Zhao,Zhongmeng Zhao,Lu Zhang,Yuanliang Duan,Zhipeng Huang,Jian Zhou,Chengyan Mou
Understanding how distinct brain regions of Leiocassis longirostris molecularly adapt to heat stress is vital for improving aquaculture sustainability and guiding conservation strategies in a warming climate. To elucidate the region-specific molecular mechanisms underlying heat stress responses in the brain of L. longirostris , we exposed L. longirostris to acute heat stress (32°C) for 24 h and performed RNA-seq and WGCNA on five brain regions (OB: olfactory bulb, FB: pituitary, hypothalamus, forebrain, MB: mesencephalon, CB: cerebellum, and SC: spinal cord). The results showed that, after heat stress, the FB region significantly activated the ER stress pathway, and the abnormal proteins were synergically cleared by HSP-mediated UPR (such as Hsp70, Hsp90, IRE1α, Perk, ATF6) and UPS-mediated ERAD (such as UBE2, UBE3, TRIM63). Meanwhile, the SC region showed marked downregulation of lipid metabolism and PPAR signaling pathway, suggesting energy conservation as a compensatory strategy. WGCNA further highlighted the FB as the hub for ER stress and the SC for metabolic suppression. In conclusion, our study suggests that distinct brain regions of L. longirostris adopt different strategies under heat stress, in which the FB region mediates protein quality control and the SC region drives metabolic inhibition. These findings highlight the adaptation strategies of the L. longirostris brain to heat stress and provides a potential target for improving its survival under global warming.
研究领域:
分子生物学
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神经科学
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水产养殖学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）