TOXICOLOGY AND APPLIED PHARMACOLOGY
·
2022
·
IF 4.46
Shaoxiong Chen,Zhanbing Sun,Weihua Deng,Guilan Li,Xiuli Liu,Zhaohui Zhang
Beryllium and its compounds can cause pulmonary interstitial fibrosis through mechanisms that are not yet clear. Long non-coding RNA (lncRNA) is implicated in various diseases. The molecular toxicity of beryllium sulfate (BeSO 4 ) was investigated through the RNA-seq analysis of the lncRNA and mRNA whole-transcriptome of BeSO 4 -treated 16HBE cells. A total of 1014 lncRNAs (535 upregulated and 479 downregulated) and 4035 mRNAs (2224 upregulated and 1811 downregulated) were found to be significantly dysregulated (|logFC| ≥> 2.0, p < 0.05) in the BeSO 4 -treated groups when compared with the control group. Five differentially expressed lncRNAs and mRNAs were verified by qRT-PCR. KEGG analysis showed that lncRNA regulates the ECM receiver interaction and PI3K/AKT signaling pathways, etc. In addition, H19:17, lnc-C5orf13–1:1, lnc-CRYAA-17:1, lnc-VSTM5–1:11, and lnc-THSD7A-7:1 may regulate BeSO 4 -induced 16HBE cytotoxicity through ceRNA mechanism. The results of this study will provide some theoretical support for the study of the toxic mechanism of beryllium and its compounds.
研究领域:
毒理学
·
分子生物学
·
基因组学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
ANALYTICAL CHEMISTRY
·
2025
·
IF 6.7
Haozhi Song,Zhayila Reheman,Ying Fang,Haodong Jiang,Ranran Hou,Ying Shi,Yunxuan Weng,Xing Li,Ling Liu
Cellular targets can be imaged using biosensors composed of RNA. However, current RNA-based sensors encounter several challenges, including low brightness, poor photostability, slow response kinetics, and green background noise. In addition, these sensors are often limited to detecting cellular single rather than multiple targets, or are unable to image targets within subcellular compartments. To address these issues, we develop a novel RNA-based sensor by using RhoBAST fluorogenic RNA aptamer to detect various small molecules and Ca2+ in living cells. Importantly, RhoBAST-based sensors exhibit high red fluorescence intensity, robust photostability, and fast activation kinetics compared to previous fluorescent sensors. With these advantageous performances, we also create an orthogonal sensor for the simultaneous subcellular imaging of multiple small molecules. Together, we provide a highly bright, stable, and rapidly responsive red fluorescent sensor composed of RNA for sensing subcellular multiple targets in living mammalian cells.
研究领域:
分子生物学
·
生物成像
·
RNA适配体技术
·
细胞生物学
·
荧光传感
✓ 已验证
产品关联
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
·
生物化学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
TALANTA
·
2023
·
IF 6.1
Yaqi Hu,Fang Bao,Siyuan Fu,Shiyuan Feng,Jinfeng Miao,Peng Miao,Yuanyuan Xu
Coronaviruses are highly infectious and pose a serious threat to human and animal healths. In this work, a facile electrochemical method based on Exonuclease III (Exo III) catalyzed digestion and silver deposition is developed for coronavirus RNA analysis. A magnetic separation procedure is performed to specifically identify target sequence and release single-stranded DNA modified gold nanoparticles (AuNPs). The nanoparticles can thus be immobilized at a screen-printed electrode and catalyze silver deposition for signal readout. This method allows sensitive analysis of PEDV and SARS-CoV-2 RNAs in the concentration range from 1 to 1000 nM with the limits of detection as low as 0.47 nM and 0.17 nM, respectively. Good specificities are demonstrated. Thus, the proposed method may have great potential use in the applications of coronaviruses analysis.
研究领域:
生物医学工程
·
分子生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
Nature Protocols
·
2025
·
IF 16
Xu Ziye,Wang Yuting,Cai Wenjie,Chen Yu,Wang Yongcheng
Bacteria colonize nearly every part of the human body and various environments, displaying remarkable diversity. Traditional population-level transcriptomics measurements provide only average population behaviors, often overlooking the heterogeneity within bacterial communities. To address this limitation, we have developed a droplet-based, high-throughput single-microorganism RNA sequencing method (smRandom-seq) that offers highly species specific and sensitive gene detection. Here we detail procedures for microbial sample preprocessing, in situ preindexed cDNA synthesis, in situ poly(dA) tailing, droplet barcoding, ribosomal RNA depletion and library preparation. The main smRandom-seq workflow, including sample processing, in situ reactions and library construction, takes ~2 days. This method features enhanced RNA coverage, reduced doublet rates and minimized ribosomal RNA contamination, thus enabling in-depth analysis of microbial heterogeneity. smRandom-seq is compatible with microorganisms from both laboratory cultures and complex microbial community samples, making it well suited for constructing single-microorganism transcriptomic atlases of bacterial strains and diverse microbial communities. This Protocol requires experience in molecular biology and RNA sequencing techniques, and it holds promising potential for researchers investigating bacterial resistance, microbiome heterogeneity and host–microorganism interactions.
研究领域:
微生物学
·
分子生物学
·
基因组学
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产品关联
DOI
PubMed
高影响因子
Molecular Medicine Reports
·
2015
·Vol. 12
·期 5
·6656-6662
·
IF 1.554
Chengfei Zheng,Hui Niu,Ming Li,Hongkun Zhang,Zhenggang Yang,Lu Tian,Ziheng Wu,Donglin Li,Xudong Chen
Aortic aneurysm is a cardiovascular condition with a serious risk of mortality and the dismal prognosis of any type of major cardiovascular disease. The present study found that tissues from aortic aneurysm patients and hypoxic aortic smooth muscle cells showed aberrant high expression of the cyclic RNA hsa‑circ‑000595, as demonstrated by polymerase chain reaction array screening. Knockdown of hsa‑circ‑000595 resulted in a decreased apoptotic rate of human aortic smooth muscle cells. Furthermore, it was determined that miR‑19a is a target of hsa‑circ‑000595. The results of the present study laid an epigenetic foundation for exploring the underlying mechanisms of the development of aortic aneurysm.
研究领域:
心血管疾病
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分子生物学
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表观遗传学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
Science China-Chemistry
·
2020
·Vol. 63
·期 4
·546-553
·
IF 6.356
Li Junwei,Yuan Dandan,Zheng Xiangjiang,Zhang Xinyue,Li Xuemei,Zhang Shusheng
Conventional cancer combination therapy usually involves systemic delivery of anticancer drugs which may lead to the destruction of normal cells and physiological toxicity due to the lack of targeting ability and toxicity of drug carriers. In the present study, a triple combination nanosystem of gene therapy, chemotherapy and phototherapy delivered by multifunctional RNA nanohydrogels (RNA NHs) was established. By taking the advantages of DNA nanotechnology and rolling circle transcription (RCT), three lung cancer inhibitor microRNA (let-7a, microRNA 34a, microRNA 145) hairpins were integrated in one RNA NH nanoparticle, leading to the simultaneous silencing of three targeted mRNAs. Meanwhile, RNA NH carried doxorubicin (DOX, a chemotherapy drug) as well as 5,10,15,20-tetrakis (1-methylpyridinium-4-yl) porphyrin (TMPyP4, a photosensitizer) and delivered these drugs to cancer cells. It was demonstrated that lung cancer inhibitor microRNAs integrated in RNA NHs, DOX and TMPyP4 could play a synergistic anti-cancer role in multi-drug resistance cancer cells. Under the action of aptamer sequence S6 that was modified with cholesterol, the resulting RNA NHs were condensed to feasible size without the assistance of polyelectrolyte condensation reagents and showed cancer-specific cellular targeting. Subsequently, thousands of copies of miRNA together with chemotherapy drug as well as photosensitizer were delivered to cancer cells specifically, and an ideal synergistic treatment effect was achieved in vivo , thus playing a combined role of gene therapy, chemotherapy and phototherapy. Through this study, it can be concluded that the triple combination therapy nanosystem can overcome the multidrug resistance caused by the malfunction of genes in chemotherapy and shows a great potential in the field of multifunctional synergistic cancer treatment.
研究领域:
纳米技术
·
癌症研究
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分子生物学
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药学
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生物医学工程
✓ 已验证
产品关联
DOI
高影响因子
Cell Host & Microbe
·
2023
·
IF 30.3
Chao Liu,Rui Wang,Jie Li,Feiyue Cheng,Xian Shu,Huiwei Zhao,Qiong Xue,Haiying Yu,Aici Wu,Lingyun Wang,Sushu Hu,Yihan Zhang,Jun Yang,Hua Xiang,Ming Li
CRISPR RNAs (crRNAs) and Cas proteins work together to provide prokaryotes with adaptive immunity against genetic invaders like bacteriophages and plasmids. However, the coordination of crRNA production and cas expression remains poorly understood. Here, we demonstrate that widespread modulatory mini-CRISPRs encode cas-regulating RNAs (CreRs) that mediate autorepression of type I-B, I-E, and V-A Cas proteins, based on their limited complementarity to cas promoters. This autorepression not only reduces autoimmune risks but also responds to changes in the abundance of canonical crRNAs that compete with CreR for Cas proteins. Furthermore, the CreR-guided autorepression of Cas proteins can be alleviated or even subverted by diverse bacteriophage anti-CRISPR (Acr) proteins that inhibit Cas effectors, which, in turn, promotes the generation of new Cas proteins. Our findings reveal a general RNA-guided autorepression paradigm for diverse Cas effectors, shedding light on the intricate self-coordination of CRISPR-Cas and its transcriptional counterstrategy against Acr proteins.
研究领域:
分子生物学
·
微生物学
·
遗传学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
BIOCHEMISTRY
·
2018
·
IF 2.997
Qianwei Zhao,Wen Yang,Tong Qin,Zhen Huang
RNA is a key player in the cellular central dogma, including RNA transcription and protein synthesis. However, it is unknown whether RNA can directly interfere with DNA synthesis. Recently, we have found in vitro that while binding to DNA polymerase nonspecifically, RNA can transform DNA polymerase to display a moonlighting activity, dNTP phosphatase, in turn interfering with DNA synthesis. This phosphatase activity removes the γ-phosphate from dNTPs (generating dNDPs) and subsequently removes the β-phosphate from the formed dNDPs (generating dNMPs), confirmed by the noncleavable α,β-CH2-dGTP and β,γ-CH2-dGTP analogues. We also found that dGTP is the best substrate for the phosphatase, and the dNTP phosphatase activity is sensitive to the reaction medium. In addition, we have revealed that RNA can tune the activity of closely related proteins and give rise to new catalytic functions with subtle differences. Moreover, we have demonstrated in vitro that at the lower dNTP level, this phosphatase can directly inhibit DNA synthesis by dNTP depletion, though the phosphatase activity is 690-fold slower than the polymerase activity. Our observation in vitro suggests a plausible strategy for RNA to directly interfere with DNA polymerase and DNA synthesis in vivo.
研究领域:
分子生物学
·
生物化学
✓ 已验证
DOI
PubMed
高影响因子
ACS Applied Bio Materials
·
2019
·
IF 0
Jiantao Yu,Jing Li,Shiyao Zhai,Li Lin,Kui Wang,Bin Tang,Hong Meng,Leilei Tian
Polymerization of small interfering RNA (siRNA) has been demonstrated as a promising strategy to improve siRNA delivery, which will change the low-charge and rigid properties of single siRNA and enhance its electrostatic interactions with cationic polymers. For such polymerization strategy, a major breakthrough is still needed to fully eliminate chemical processes and further improve the nanocomplex-forming ability of polymerized siRNAs. Herein, the extremely strong interaction between the DNA product of rolling circle amplification (RCA) and linear poly(ether imide) (PEI) has been disclosed; accordingly, a stable nanocomplex is formed just at its charge neutralization point, which benefits from the high molecular weight of the RCA product (>3 000 000 Da). In addition, as the sequence of the RCA product is determined by the cyclic template, the programmable nature of DNA can simplify the optimization process and maximize the hybridization efficiency between RCA and sticky siRNAs, realizing a superior siRNA polymerization efficiency. Depending on these two effects, the RCA DNA is utilized as a cocarrier material to organize siRNA polymerization and substantially reduce the usage amount of PEI, which greatly improves RNAi efficiency of PEI/RCA-siRNA polyplex both in vitro and in vivo, providing evidence that RCA DNA is a promising material to promote the RNAi-based therapeutics.
研究领域:
分子生物学
·
纳米医学
·
治疗开发
✓ 已验证
产品关联
DOI
PubMed
SEPARATION AND PURIFICATION TECHNOLOGY
·
2021
·
IF 7.312
Yunhai Fu,Qingmei Chen,Li Jia
Isolation of high-quality DNA is one of the essential steps in the field of molecular biology. Before DNA isolation, ribonuclease A (RNase) has to be introduced to degrade RNA. However, RNase needs to be stored at low temperature, and the conditions for the degradation of RNA need to be strictly controlled. In the study, graphene oxide functionalized magnetic particles (GO-MPs) were prepared and used for RNA removal. GO-MPs demonstrate good environmental stability. The RNA removing process by GO-MPs can be finished in 10 min at room temperature. Also, GO-MPs exhibit good selectivity toward RNA over double-stranded DNA. Next, the spherical and core–shell structure poly(3,4-dihydroxy-L-phenylalanine) functionalized MPs (polyDOPA-MPs) were prepared and used for the purification of DNA. The DNA adsorption and release can be realized by adjusting the pH value of solutions. It is worth emphasizing that the condition for RNA removal by GO-MPs is the same as that for DNA adsorption by polyDOPA-MPs, which ensures the effective connection between the two steps. The feasibility of the MPs-based protocol was verified by the successful extraction of genomic DNA from Escherichia coli DH5α and genetically modified corn. The results suggest that the protocol would provide a promising platform for RNase-free RNA removal and DNA purification from bacteria and plant seeds.
研究领域:
分子生物学
·
纳米技术
·
生物技术
·
基因组学
✓ 已验证
产品关联
DOI
高影响因子
MOLECULES
·
2023
·Vol. 28
·期 14
·5496
·
IF 4.6
Ting Li,Chaoyue Yang,Houkang Cao,Siyi Mo,Bo Li,Zhipeng Huang,Ruobing Zhang,Jianzhao Wu,Kefeng Zhang,Ya Gao
Bergenin (BER), a natural component of polyphenols, has a variety of pharmacological activities, especially in improving drug metabolism, reducing cholestasis, anti-oxidative stress and inhibiting inflammatory responses. The aim of this study was to investigate the effects of BER on liver injury induced by isonicotinic acid hydrazide (INH) and rifampicin (RIF) in mice. The mice model of liver injury was established with INH (100 mg/kg)+RIF (100 mg/kg), and then different doses of BER were used to intervene. The pathological morphology and biochemical indicators of mice were detected. Meanwhile, RNA sequencing was performed to screen the differentially expressed genes and signaling pathways. Finally, critical differentially expressed genes were verified by qRT-PCR and Western blot. RNA sequencing results showed that 707 genes were significantly changed in the INH+RIF group compared with the Control group, and 496 genes were significantly changed after the BER intervention. These differentially expressed genes were mainly enriched in the drug metabolism, bile acid metabolism, Nrf2 pathway and TLR4 pathway. The validation results of qRT-PCR and Western blot were consistent with the RNA sequencing. Therefore, BER alleviated INH+RIF-induced liver injury in mice. The mechanism of BER improving INH+RIF-induced liver injury was related to regulating drug metabolism enzymes, bile acid metabolism, Nrf2 pathway and TLR4 pathway.Keywords:bergenin;isonicotinic acid hydrazide;rifampicin;liver injury;RNA sequencing
研究领域:
药理学
·
分子生物学
·
毒理学
✓ 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）