CELL
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2025
·
IF 42.5
Shaoqian Ma,Yantao Hong,Junhan Chen,Jingzhao Xu,Xiaohua Shen
Understanding cell diversification from a common genome in metazoans requires single-cell transcriptional analysis. We introduce single-cell full-length EU-labeled nascent RNA sequencing (scFLUENT-seq), a single-cell nascent RNA sequencing method using brief 10-min metabolic labeling to capture genome-wide transcription. Surprisingly, individual cells—from splenic lymphocytes to pluripotent stem cells—transcribe only ∼0.02%–3.1% of the genome, versus >80% in bulk, revealing limited genome engagement and profound cell-type and cell-to-cell heterogeneity. Intergenic transcription, especially from heterochromatin, is pervasive and stochastic. Promoter-associated antisense and genic transcription rarely co-occur in the same cell. Proximal intergenic transcription involves both gene readthrough and independent initiation, while distal intergenic transcription is largely independent of neighboring genes and correlates with increased transcriptional diversity, a hallmark of cellular plasticity. Although global RNA synthesis and turnover are coupled in bulk, individual mRNA transcription and decay are poorly coordinated in single cells, suggesting noise-buffering mechanisms. Overall, scFLUENT-seq uncovers complex coding and noncoding transcriptional dynamics that underlie single-cell heterogeneity and state transitions.
研究领域:
分子生物学
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基因组学
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发育生物学
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干细胞生物学
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表观遗传学
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DOI
PubMed
高影响因子
Frontiers in Genetics
·
2023
·
IF 3.7
Bin Wang,Yukun Wang,Xiao Yuan,Yuanyuan Jiang,Yunna Zhu,Xinmiao Kang,Jinming He,Yanhui Xiao
Planting aromatic plant might be a promising strategy for safely utilizing heavy metal (HM)-contaminated soils, as HMs in essential oil could be completely excluded using some special technologies with ease. Clove basil ( Ocimum gratissimum L.) is an important aromatic plant used in essential oil production. Improving cadmium (Cd) tolerance in clove basil can increase its production and improve the utilization efficiency of Cd-contaminated soils. However, the lack of genomic information on clove basil greatly restricts molecular studies and applications in phytoremediation. In this study, we demonstrated that high levels of Cd treatments (0.8, 1.6 and 6.5 mg/L) significantly impacted the growth and physiological attributes of clove basil. Cd contents in clove basil tissues increased with treatment concentrations. To identify Cd stress-responsive genes, we conducted a comparative transcriptomic analysis using seedlings cultured in the Hoagland’s solution without Cd ion (control) or containing 1.6 mg/L CdCl 2 (a moderate concentration of Cd stress for clove basil seedlings). A total of 104.38 Gb clean data with high-quality were generated in clove basil under Cd stress through Illumina sequencing. More than 1,800 differential expressed genes (DEGs) were identified after Cd treatment. The reliability and reproducibility of the transcriptomic data were validated through qRT-PCR analysis and Sanger sequencing. KEGG classification analysis identified the “MAPK signaling pathway,” “plant hormone signal transduction” and “plant-pathogen interaction” as the top three pathways. DEGs were divided into five clusters based on their expression patterns during Cd stress. The functional annotation of DEGs indicated that downregulated DEGs were mainly involved in the “photosynthesis system,” whereas upregulated DEGs were significantly assigned to the “MAPK signaling pathway” and “plant-pathogen interaction pathway.” Furthermore, we identified a total of 78 transcription factors (TFs), including members of bHLH, WRKY, AP2/ERF, and MYB family. The expression of six bHLH genes, one WRKY and one ERF genes were significantly induced by Cd stress, suggesting that these TFs might play essential roles in regulating Cd stress responses. Overall, our study provides key genetic resources and new insights into Cd adaption mechanisms in clove basil.
研究领域:
植物学
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环境科学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
PLANT CELL TISSUE AND ORGAN CULTURE
·
2021
·Vol. 147
·期 2
·389-404
·
IF 2.711
Shi Min,Hua Qiang,Kai Guoyin
Phenolic acids and tanshinones are important bioactive components with multiple pharmacological properties accumulated in traditional Chinese medicinal plant Salvia miltiorrhiza . Abscisic acid (ABA) is effective to enhance the content of the two compounds in S. miltiorrhiza , while the regulation mechanism remains unknown. Deep transcriptome profile of S. miltiorrhiza hairy roots treated with ABA was conducted. Totally, 42,710 unigenes with the average length of 1,157 bp were obtained from de novo assembly from about 2.81 billion produced clean reads, of which 27,641 unigenes (64.72%) were successfully annotated. Unigenes encoding key enzymes such as PAL, TAT, C4H, RAS, CYP98A14, GGPPS expressed significantly higher than that in control. Candidate laccases showing similar expression with RAS and CYP98A14 in phenolic acid biosynthesis and potential P450 unigenes involved in tanshinone biosynthesis genes were screened out. Furthermore, transcription factor (TF) profiles revealed that 1,250 TFs representing 35 families were identified, of which MYB, AP2/ERF, bHLH and bZIP were most abundant. The present study provided a comprehensive transcriptional expression profile affected by ABA, which will help underly the biosynthesis and regulation mechanism.
研究领域:
植物科学
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分子生物学
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药理学
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转录组学
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产品关联
DOI
高影响因子
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
·
2020
·
IF 4.192
Da Li,Cun-Yu Li,Ci-Jie Hu,Yu-Si Yang,Chen Lin,Dong Zhao,Qing-Sheng Li,Jian-Hui Ye,Xin-Qiang Zheng,Yue-Rong Liang,Jian-Liang Lu
Amino acids are very important for oolong tea brisk-smooth mouthfeel which is mainly associated with bruising and withering treatment (BWT). In this study, metabolome and transcriptome analyses were performed to comprehensively investigate the changes in abundance of amino acids and the expression pattern of relevant genes during BWT of oolong tea manufacturing. Levels of most amino acids increased during BWT in the leaves harvested from 4 cultivars, while expression of the relevant function genes responsible for synthesis and transformation of amino acids up-regulated accordingly. Upstream hub genes including receptor-like protein kinase IKU2, serine/threonine-protein kinase PBL11, MYB transcription factor MYB2, ethylene-responsive transcription factor ERF114, WRKY transcription factor WRKY71, aspartate aminotransferase AATC, UDP-glycosyltransferase U91D1, and 4-hydroxy-4-methyl-2-oxoglutarate aldolase 2 RRAA2, were predicted to be involved in regulation of the function genes expression and the amino acids metabolism through weighted gene coexpression network analysis. A modulation mechanism for accumulation of amino acids during BWT was also proposed. These findings give a deep insight into the metabolic reprogramming mechanism of amino acids during BWT of oolong tea.
研究领域:
植物学
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分子生物学
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茶叶科学
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植物代谢
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DOI
PubMed
高影响因子
Jove-Journal of Visualized Experiments
·
2019
·
IF 1.108
Yafeng Zhang,Xun Liao,Peihua Luo,Kui Peng,Wenyi Ye,Tengxiang Lian,Qibin Ma,Hai Nian
In plant mitochondria, some steady-state transcripts have 5' triphosphate derived from transcription initiation (primary transcripts), while the others contain 5' monophosphate generated post-transcriptionally (processed transcripts). To discriminate between the two types of transcripts, several strategies have been developed, and most of them depend on presence/absence of 5' triphosphate. However, the triphosphate at primary 5' termini is unstable, and it hinders a clear discrimination of the two types of transcripts. To systematically differentiate and map the primary and processed transcripts stably accumulated in maize mitochondrion, we have developed a circular RT-PCR (cRT-PCR)-based strategy by combining cRT-PCR, RNA 5' polyphoshpatase treatment, quantitative RT-PCR (RT-qPCR), and Northern blot. As an improvement, this strategy includes an RNA normalization step to minimize the influence of unstable 5' triphosphate.In this protocol, the enriched mitochondrial RNA is pre-treated by RNA 5' polyphosphatase, which converts 5' triphsophate to monophosphate. After circularization and reverse transcription, the two cDNAs derived from 5' polyphosphatase-treated and non-treated RNAs are normalized by maize 26S mature rRNA, which has a processed 5' end and is insensitive to 5' polyphosphatase. After normalization, the primary and processed transcripts are discriminated by comparing cRT-PCR and RT-qPCR products obtained from the treated and non-treated RNAs. The transcript termini are determined by cloning and sequencing of the cRT-PCR products, and then verified by Northern blot.By using this strategy, most steady-state transcripts in maize mitochondrion have been determined. Due to the complicated transcript pattern of some mitochondrial genes, a few steady-state transcripts were not differentiated and/or mapped, though they were detected in a Northern blot. We are not sure whether this strategy is suitable to discriminate and map the steady-state transcripts in other plant mitochondria or in plastids.
研究领域:
植物学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
LWT-FOOD SCIENCE AND TECHNOLOGY
·
2025
·
IF 6.6
Mingzheng Duan,Ting Jiang,Xi Wang,Kangjian Song,Xu Xiao,Xiaoting Fu,Sijiu He,Jieming Feng,Muhammad Junaid Rao,Hengcui Guo
Strawberries ( Fragaria × ananassa ) are prized for bioactive flavonoids and anthocyanins, contributing to antioxidant capacity and health benefits. However, decades of breeding for yield and shelf-life have eroded their phytochemical diversity. To explore this trade-off, we compared wild strawberries ( Fragaria nilgerrensis , HM) with three cultivated varieties (pink-FY, red-RF, white-DX) using integrated LC-MS/MS metabolomics and transcriptomics. Wild HM strawberries contained twice the vitamin C (134.2 mg/100g), 2.5× more total flavonoids (138.7 mg/100g), and higher antioxidant activity (367 μg Trolox/g) than commercial varieties. In contrast, red-fruited RF showed abundant anthocyanins (pelargonidin-3-glucoside 6.6% abundance), while the wild HM genotype accumulated higher levels of flavonoids, with neohesperidin, lonicerin, hyperin and ternatumoside II collectively representing 20.9% of total flavonoids - concentrations 3-169 times greater than those observed in the three commercial varieties (FY, RF, DX). Transcriptomic analysis (RNA-seq, Illumina HiSeq 2500) revealed distinct MYB transcription factor associations: FxaYL_611g0111200 (MYB66) showed strong positive correlation with anthocyanin biosynthesis in RF (r=0.92, **p<0.005 ), while FxaYL_242g0472670 (MYB44-like) was significantly associated with HM's unique antioxidant flavonoid profile (r=0.96, ***p<0.0001 ). These regulatory relationships were corroborated by hierarchical clustering demonstrating varietal-specific expression patterns and principal component analysis (82.6% variance explained), collectively providing molecular targets for enhancing nutritional quality in strawberry breeding programs.
研究领域:
植物科学
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食品化学
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分子生物学
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营养学
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代谢组学
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产品关联
DOI
高影响因子
Plants-Basel
·
2025
·Vol. 14
·期 14
·2094
·
IF 4.1
Feixiong Zheng,Zhangting Xu,Xiaoji Deng,Xiaoyuan Wang,Yiming Sun,Xiaoxia Shen,Zhenming Yu
Flavonoids are key bioactive compounds in plants that play important defense roles against abiotic stress and are involved in plant growth and development. Methyl jasmonate (MeJA) is a significant growth regulator that promotes the accumulation of flavonoids in a variety of plants, but the effect of MeJA inHedera helixremains poorly understood. In the present study, the flavonoid content was significantly increased after MeJA treatment and peaked at 6 h post-treatment. A total of 31,931 genes were identified using transcriptome, and 6484 DEGs were identified at 6 h post-treatment. Through GO and KEGG enrichment analysis, it was shown that DEGs were primarily enriched in phenylpropanoid biosynthesis pathways. Based on the putative transcription factors derived from DEGs, growth-regulating factor (GRF), a transcription factor potentially linking MeJA signaling to flavonoid accumulation and participating in plant growth and stress responses, was further identified. A total of 20 Hh-GRFd genes were identified on the whole genome level and clustered into five phylogenetic groups with conserved subfamily characteristics. Abundant MeJA-responsive cis-elements were presented in the promoter regions ofHhGRF1-HhGRF20. They exhibited a tissue-specific expression variation, andHhGRF10was dominantly expressed in leaves ofH. helix. Notably,HhGRF10exhibited MeJA-induced expression that correlated temporally with flavonoid accumulation, suggesting thatHhGRF10might play a potential role in promoting flavonoid biosynthesis, and overexpression and knockout assay substantiated this conclusion. The finding provides the first transcriptome-wide resource for flavonoid biosynthesis inH. helixand identifies the candidate GRF-mediated regulator for flavonoid accumulation.
研究领域:
植物学
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遗传学
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生物化学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
·
2018
·Vol. 19
·期 8
·2364
·
IF 3.687
Xiwu Qi,Hailing Fang,Xu Yu,Dongbei Xu,Li Li,Chengyuan Liang,Hongfei Lu,Weilin Li,Yin Chen,Zequn Chen
Mentha canadensisL. has important economic value for its abundance in essential oils. Menthol is the main component ofM. canadensisessential oils, which is certainly the best-known monoterpene for its simple structure and wide applications. However, the regulation of menthol biosynthesis remains elusive inM. canadensis. In this study, transcriptome sequencing ofM. canadensiswith MeJA treatment was applied to illustrate the transcriptional regulation of plant secondary metabolites, especially menthol biosynthesis. Six sequencing libraries were constructed including three replicates for both control check (CK) and methyl jasmonate (MeJA) treatment and at least 8 Gb clean bases was produced for each library. After assembly, a total of 81,843 unigenes were obtained with an average length of 724 bp. Functional annotation indicated that 64.55% of unigenes could be annotated in at least one database. Additionally, 4430 differentially expressed genes (DEGs) with 2383 up-regulated and 2047 down-regulated transcripts were identified under MeJA treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that “Monoterpenoid biosynthesis” was one of the most significantly enriched pathways in metabolism. Subsequently, DEGs involved in JA signal transduction, transcription factors, and monoterpene biosynthesis were analyzed. 9 orthologous genes involved in menthol biosynthesis were also identified. This is the first report of a transcriptome study ofM. canadensisand will facilitate the studies of monoterpene biosynthesis in the genusMentha.Keywords:Mentha canadensisL.;transcriptome sequencing;JA signaling;transcription factors;menthol biosynthesis
研究领域:
植物生物学
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分子生物学
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生物信息学
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产品关联
DOI
PubMed
高影响因子
PHYTOMEDICINE
·
2023
·
IF 7.9
Xiangyun Li,Taoli Sun,Jiaqin Liu,Shanshan Wei,Yuanying Yang,Jian Liu,Bikui Zhang,Wenqun Li
Background Doxorubicin (Dox), a chemotherapeutic agent known for its efficacy, has been associated with the development of severe cardiotoxicity, commonly referred to as doxorubicin-induced cardiotoxicity (DIC). The role and mechanism of action of phloretin (Phl) in cardiovascular diseases are well-established; however, its specific function and underlying mechanism in the context of DIC have yet to be fully elucidated. Objective This research aimed to uncover the protective effect of Phl against DIC in vivo and in vitro , while also providing a comprehensive understanding of the underlying mechanisms involved. Methods DIC cell and murine models were established. The action targets and mechanism of Phl against DIC were comprehensively examined by systematic network pharmacology, molecular docking, transcriptomics technologies, transcription factor (TF) prediction, and experimental validation. Results Phl relieved Dox-induced cell apoptosis in vitro and in vivo . Through network pharmacology analysis, a total of 554 co-targeted genes of Phl and Dox were identified. Enrichment analysis revealed several key pathways including the PI3K-Akt signaling pathway, Apoptosis, and the IL-17 signaling pathway. Protein-protein interaction (PPI) analysis identified 24 core co-targeted genes, such as Fos, Jun, Hif1a, which were predicted to bind well to Phl based on molecular docking. Transcriptomics analysis was performed to identify the top 20 differentially expressed genes (DEGs), and 202 transcription factors (TFs) were predicted for these DEGs. Among these TFs, 10 TFs (Fos, Jun, Hif1a, etc.) are also the co-targeted genes, and 3 TFs (Fos, Jun, Hif1a) are also the core co-targeted genes. Further experiments validated the finding that Phl reduced the elevated levels of Hif3a (one of the top 20 DEGs) and Fos (one of Hif3a's predicted TFs) induced by Dox. Moreover, the interaction between Fos protein and the Hif3a promoter was confirmed through luciferase reporter assays. Conclusion Phl actively targeted and down-regulated the Fos protein to inhibit its binding to the promoter region of Hif3a, thereby providing protection against DIC.
研究领域:
药理学
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分子生物学
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心血管疾病
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肿瘤学
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产品关联
DOI
PubMed
高影响因子
Plants-Basel
·
2025
·Vol. 14
·期 1
·133
·
IF 4.1
Wang Yu,Xiangru Zhou,Jinhao Meng,Hongwei Xu,Xiaofu Zhou
The depletion of the ozone layer has resulted in elevated ultraviolet-B (UV-B) radiation levels, posing a significant risk to terrestrial plant growth.Rhododendron chrysanthumPall. (R. chrysanthum), adapted to high-altitude and high-irradiation environments, has developed unique adaptive mechanisms. This study exposedR. chrysanthumto UV-B radiation for two days, with an 8 h daily treatment, utilizing metabolomic and transcriptomic analyses to explore the role of WRKY transcription factors in the plant’s UV-B stress response and their regulation of flavonoid synthesis. UV-B stress resulted in a significant decrease in rETR and Ik and a significant increase in 1-qP. These chlorophyll fluorescence parameters indicate that UV-B stress impaired photosynthesis inR. chrysanthum. Faced with the detrimental impact of UV-B radiation,R. chrysanthumis capable of mitigating its effects by modulating its flavonoid biosynthetic pathways to adapt positively to the stress. This study revealed changes in the expression of 113 flavonoid-related metabolites and 42 associated genes, with WRKY transcription factors showing significant correlation with these alterations. WRKY transcription factors can influence the expression of key enzyme genes in the flavonoid metabolic pathway, thereby affecting metabolite production. A theoretical reference for investigating plant stress physiology is provided in this work, which also offers insights into the stress responses of alpine plants under adverse conditions.
研究领域:
植物学
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分子生物学
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环境科学
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产品关联
DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
·
2021
·Vol. 22
·期 24
·13502
·
IF 5.924
Yue Zhang,Zhen Zeng,Yubing Yong,Yingmin Lyu
In lily reproduction, the mechanism of formation of bulbs has been a hot topic. However, studies on stem bulblet formation are limited. Stem bulblets, formed in the leaf axils of under- and above-ground stems, provide lilies with a strong capacity for self-propagation. First, we showed that above-ground stem bulblets can be induced by spraying 100 mg/L 6-BA on the LA hybrid lily ‘Aladdin’, with reduced endogenous IAA and GA4and a higher relative content of cytokinins. Then, expression patterns of three potential genes (twoKNOTTED1-like homeobox (KNOX) and one partialBEL1-like homeobox (BELL)), during stem bulblet formation from our previous study, were determined by RT-qPCR, presenting a down-up trend inKNOXs and a rising tendency inBELL. The partialBELLgene was cloned by RACE fromL. ‘Aladdin’ and denotedLaBEL1. Physical interactions of LaKNOX1-LaBEL1 and LaKNOX1-LaKNOX2 were confirmed by yeast two-hybrid and bimolecular fluorescence complementation assays. Furthermore, hormonal regulatory patterns of single LaKNOX1, LaKNOX2, LaBEL1, and their heterodimers, were revealed in transgenicArabidopsis, suggesting that the massive mRNA accumulations ofLaKNOX1,LaKNOX2andLaBEL1genes during stem bulblet formation could cause the dramatic relative increase of cytokinins and the decline of GAs and IAA. Taken together, a putative model was proposed that LaKNOX1 interacts with LaKNOX2 and LaBEL1 to regulate multiple phytohormones simultaneously for an appropriate hormonal homeostasis, which suggests their potential role in stem bulblet formation inL. ‘Aladdin’.Keywords:KNOX transcription factor;BELL transcription factor;interaction;phytohormone;bulblet formation;LA hybrid lily
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
FOOD CHEMISTRY
·
2020
·
IF 6.306
Wanbao Ouyang,Xin Liu,Yanling Wang,Zhibing Huang,Xiujiang Li
Monascus , which is traditionally used in various Asian industries, produces several secondary metabolites during the fermentation process, including citrinin, a toxin whose impact limits the development of the Monascus industry. We have previously found that the addition of 2.0 g/L genistein to Monascus medium reduces citrinin production by approximately 80%. Here, we explored the molecular mechanisms whereby genistein affects citrinin production. We sequenced the Monascus genome and performed transcriptome analysis on genistein-treated and -untreated groups. Comparison between the two groups showed 378 downregulated and 564 upregulated genes. Among the latter, we further examined the genes related to citrinin biosynthesis and quantified them using quantitative real-time polymerase chain reaction (qRT-PCR). Genes orf5 , pksCT , orf3 , orf1 , orf6 , and ctnE were significantly downregulated, demonstrating that genistein addition indeed affects citrinin synthesis. Our results may lay the groundwork for substantial improvements in the Monascus fermentation industry.
研究领域:
微生物学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）