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学者姓名：张玉
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Abstract ：
Drought is a critical risk factor that impacts rice growth and yields. Previous studies have focused on the regulatory roles of individual transcription factors in response to drought stress. However, there is limited understanding of multi-factor stresses gene regulatory networks and their mechanisms of action. In this study, we utilised data from the JASPAR database to compile a comprehensive dataset of transcription factors and their binding sites in rice, Arabidopsis, and barley genomes. We employed the PyTorch framework for machine learning to develop a nine-layer convolutional deep neural network TFBind. Subsequently, we obtained rice RNA-seq and ATAC-seq data related to abiotic stress from the public database. Utilising integrative analysis of WGCNA and ATAC-seq, we effectively identified transcription factors associated with open chromatin regions in response to drought. Interestingly, only 81% of the transcription factors directly bound to the opened genes by testing with TFBind model. By this approach we identified 15 drought-responsive transcription factors corresponding to open chromatin regions of targets, which enriched in the terms related to protein transport, protein allocation, nitrogen compound transport. This approach provides a valuable tool for predicting TF-TAG-opened modules during biological processes.
Keyword ：
ATAC-seq ATAC-seq drought responsive TF-TAG modules drought responsive TF-TAG modules neural networks neural networks rice rice WGCNA WGCNA
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| GB/T 7714 | Liu, Jingpeng , Shi, Ximiao , Zhang, Zhitai et al. Deep Neural Network-Mining of Rice Drought-Responsive TF-TAG Modules by a Combinatorial Analysis of ATAC-Seq and RNA-Seq [J]. | PLANT CELL AND ENVIRONMENT , 2025 , 48 (7) : 5217-5235 . |
| MLA | Liu, Jingpeng et al. "Deep Neural Network-Mining of Rice Drought-Responsive TF-TAG Modules by a Combinatorial Analysis of ATAC-Seq and RNA-Seq" . | PLANT CELL AND ENVIRONMENT 48 . 7 (2025) : 5217-5235 . |
| APA | Liu, Jingpeng , Shi, Ximiao , Zhang, Zhitai , Cen, Xuexiang , Lin, Lixian , Wang, Xiaowei et al. Deep Neural Network-Mining of Rice Drought-Responsive TF-TAG Modules by a Combinatorial Analysis of ATAC-Seq and RNA-Seq . | PLANT CELL AND ENVIRONMENT , 2025 , 48 (7) , 5217-5235 . |
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【目的】探究水稻AP2/ERF转录因子在叶片衰老中的功能及其受miRNA和组蛋白修饰调控的转录机制。【方法】在全基因组水平对水稻(Oryza sativa)AP2/ERF家族成员及其上游靶向的miRNAs进行鉴定和生物信息学分析。对miRNA及其靶基因在水稻叶片衰老过程中的表达谱进行分析。通过RT-qPCR检测该家族成员及miRNAs在水稻叶片衰老过程中的互作关系。【结果】在水稻中共有155个AP2/ERF基因，所有成员启动子都含有光响应元件，大多数基因都具有茉莉酸(jasmonic acid, JA)、脱落酸(abscisic acid, ABA)和厌氧诱导顺式作用元件。预测到45个miRNAs靶向调控水稻AP2/ERF家族的58个成员。鉴定出一系列在水稻叶片衰老过程中呈显著负相关的miRNA-靶基因对，暗示这些miRNAs可能通过抑制AP2/ERF基因的表达，参与水稻叶片衰老过程的调控。同时，发现4个AP2/ERF基因的表达量及其组蛋白H3K9ac富集水平随水稻叶片的衰老持续上升，说明这些基因表达同时受到H3K9ac修饰调控。【结论】在水稻叶片衰老过程中AP2/ERF基因的转录受其相应靶向的miRNAs和组蛋白H3K9ac修饰的影响。
Keyword ：
AP2/ERF转录因子 AP2/ERF转录因子 H3K9ac修饰 H3K9ac修饰 miRNA调控 miRNA调控 叶片衰老 叶片衰老 水稻 水稻 表观遗传修饰 表观遗传修饰
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| GB/T 7714 | 蒋鑫 , 陈重先 , 刘梦兰 et al. 水稻AP2/ERF转录因子家族及其相应miRNAs在叶片衰老中的表达 [J]. | 福建农林大学学报(自然科学版) , 2024 , 53 (02) : 159-168 . |
| MLA | 蒋鑫 et al. "水稻AP2/ERF转录因子家族及其相应miRNAs在叶片衰老中的表达" . | 福建农林大学学报(自然科学版) 53 . 02 (2024) : 159-168 . |
| APA | 蒋鑫 , 陈重先 , 刘梦兰 , 黄丹丹 , 李伟 , 缪颖 et al. 水稻AP2/ERF转录因子家族及其相应miRNAs在叶片衰老中的表达 . | 福建农林大学学报(自然科学版) , 2024 , 53 (02) , 159-168 . |
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The color of flowers is one of the main characteristics adopted for plants to attract pollinators to ensure the reproductive success of the plant, they are also important in their ornamental appeal in Narcissus plant. In this study, we identified a NtMYB12 locus encoding an R2R3-MYB transcription factor. Comparative transcriptome analysis of loss- and gain- of NtMYB12 tissue relative to wild-type narcissus showed NtMYB12 was mainly involved in flavonol and phenylpropanoid metabolic pathways. Biochemical evidences of dual-luciferase activity and chromatin immunoprecipitation assay supported that MYB12 directly bound to promoters of NtFLS, NtLAR, and NtDFR that were cloned by genome walking assay, and activated NtFLS and NtLAR expression but repressed NtDFR expression. More interestingly, NtMYB12 can interact with NtbHLH1 and NtWD40-1 proteins via R3 domain that were selected by transcriptome-based WGCNA and confirmed by yeast two hybrid, bimolecular fluorescence complementation and coimmunoprecipitation assay. Interaction of NtMYB12 with NtbHLH1 and NtWD40-1 forming MYB-bHLH-WD40 triplex specially activated NtDFR and NtANS expression and promoted (pro)anthocyanin accumulation, while NtMYB12 alone activated NtFLS and NtLAR expression and accumulated flavonols, but repressed NtDFR expression. These results indicated that NtMYB12 alone or NtMYB12-bHLH1-WD40-1 triplex requires for competition of metabolism fluxes between flavonol and (pro)anthocyanin biosynthesis.
Keyword ：
Flavonol biosynthesis Flavonol biosynthesis MBW triplex MBW triplex Narcissus tazetta Narcissus tazetta NtMYB12 NtMYB12 Proanthocyanin biosynthesis Proanthocyanin biosynthesis
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| GB/T 7714 | Yang, Jingwen , Wu, Xi , Aucapina, Cristina belen et al. NtMYB12 requires for competition between flavonol and (pro)anthocyanin biosynthesis in Narcissus tazetta tepals [J]. | MOLECULAR HORTICULTURE , 2023 , 3 (1) . |
| MLA | Yang, Jingwen et al. "NtMYB12 requires for competition between flavonol and (pro)anthocyanin biosynthesis in Narcissus tazetta tepals" . | MOLECULAR HORTICULTURE 3 . 1 (2023) . |
| APA | Yang, Jingwen , Wu, Xi , Aucapina, Cristina belen , Zhang, Deyu , Huang, Jiazhi , Hao, Ziyuan et al. NtMYB12 requires for competition between flavonol and (pro)anthocyanin biosynthesis in Narcissus tazetta tepals . | MOLECULAR HORTICULTURE , 2023 , 3 (1) . |
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Plant senescence is the last stage of plant development and a type of programmed cell death, occurring at a predictable time and cell. It involves the functional conversion from nutrient assimilation to nutrient remobilization, which substantially impacts plant architecture and plant biomass, crop quality, and horticultural ornamental traits. In past two decades, DNA damage was believed to be a main reason for cell senescence. Increasing evidence suggests that the alteration of epigenetic information is a contributing factor to cell senescence in organisms. In this review, we summarize the current research progresses of epigenetic and epitranscriptional mechanism involved in cell senescence of plant, at the regulatory level of DNA methylation, histone methylation and acetylation, chromatin remodeling, non-coding RNAs and RNA methylation. Furthermore, we discuss their molecular genetic manipulation and potential application in agriculture for crop improvement. Finally we point out the prospects of future research topics.
Keyword ：
cell senescence of plant cell senescence of plant chromatin remodeling chromatin remodeling crop improvement crop improvement DNA methylation DNA methylation epigenetic manipulation epigenetic manipulation histone modifications histone modifications non-coding RNAs non-coding RNAs RNA methylation RNA methylation
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| GB/T 7714 | Zhang, Yu , Huang, Dongmei , Miao, Ying . Epigenetic control of plant senescence and cell death and its application in crop improvement [J]. | FRONTIERS IN PLANT SCIENCE , 2023 , 14 . |
| MLA | Zhang, Yu et al. "Epigenetic control of plant senescence and cell death and its application in crop improvement" . | FRONTIERS IN PLANT SCIENCE 14 (2023) . |
| APA | Zhang, Yu , Huang, Dongmei , Miao, Ying . Epigenetic control of plant senescence and cell death and its application in crop improvement . | FRONTIERS IN PLANT SCIENCE , 2023 , 14 . |
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Transcription factor NtMYB1 targeting the promoters of NtNCED1/2 and activating their transcription redirects metabolic flux of abscisic acid and & beta;-carotene biosynthesis, regulating petal senescence and leaf yellowing in Narcissus . Chinese narcissus (Narcissus tazetta var. chinensis cv. 'Jingzhanyuntai') is one of the 10 most famous traditional flowers of China, having a beautiful and highly ornamental flower with a rich fragrance. However, the flower longevity affects its commercial appeal. While petal senescence in Narcissus is ethylene-independent and abscisic acid-dependent, the regulatory mechanism has yet to be determined. In this study, we identified a R2R3-MYB gene (NtMYB1) from Narcissus tazetta and generated oeNtMYB1 and Ntmyb1 RNA interference mutants in Narcissus as well as an oeNtMYB1 construct in Arabidopsis. Overexpressing NtMYB1 in Narcissus or Arabidopsis led to premature leaf yellowing, an elevated level of total carotenoid, a reduced level of chlorophyll b, and a decrease in photosystem II fluorescence (Fv/Fm). A dual-luciferase assay and chromatin immunoprecipitation-quantitative PCR revealed that NtMYB1 directly binds to the promoter of NtNCED1 or NtNCED2 and activates NtNCED1/2 gene expression both in vitro and in vivo. Moreover, overexpressing NtMYB1 accelerated abscisic acid biosynthesis, up-regulated the content of zeatin and abscisic acid, and down-regulated the level of & beta;-carotene and gibberellin A1, leading to petal senescence and leaf yellowing in Narcissus. This study revealed a regulatory process that is fundamentally different between non-photosynthetic organs and leaves.
Keyword ：
ABA biosynthesis ABA biosynthesis metabolic flux metabolic flux Narcissus Narcissus NtMYB1 NtMYB1 NtNCED NtNCED tepal senescence tepal senescence
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| GB/T 7714 | Yang, Jingwen , Huang, Jiazhi , Wu, Xi et al. NtMYB1 and NtNCED1/2 control abscisic acid biosynthesis and tepal senescence in Chinese narcissus (Narcissus tazetta) [J]. | JOURNAL OF EXPERIMENTAL BOTANY , 2023 , 74 (21) : 6505-6521 . |
| MLA | Yang, Jingwen et al. "NtMYB1 and NtNCED1/2 control abscisic acid biosynthesis and tepal senescence in Chinese narcissus (Narcissus tazetta)" . | JOURNAL OF EXPERIMENTAL BOTANY 74 . 21 (2023) : 6505-6521 . |
| APA | Yang, Jingwen , Huang, Jiazhi , Wu, Xi , Xu, Yun , Gu, Zheng , Chen, Yajue et al. NtMYB1 and NtNCED1/2 control abscisic acid biosynthesis and tepal senescence in Chinese narcissus (Narcissus tazetta) . | JOURNAL OF EXPERIMENTAL BOTANY , 2023 , 74 (21) , 6505-6521 . |
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Drought is the main abiotic stress that constrains sugarcane growth and production. To understand the molecular mechanisms that govern drought stress, we performed a comprehensive comparative analysis of physiological changes and transcriptome dynamics related to drought stress of highly drought-resistant (ROC22, cultivated genotype) and weakly drought-resistant (Badila, wild genotype) sugarcane, in a time-course experiment (0 h, 4 h, 8 h, 16 h and 32 h). Physiological examination reviewed that ROC22, which shows superior drought tolerance relative to Badila, has high performance photosynthesis and better anti-oxidation defenses under drought conditions. The time series dataset enabled the identification of important hubs and connections of gene expression networks. We identified 36,956 differentially expressed genes (DEGs) in response to drought stress. Of these, 15,871 DEGs were shared by the two genotypes, and 16,662 and 4423 DEGs were unique to ROC22 and Badila, respectively. Abscisic acid (ABA)-activated signaling pathway, response to water deprivation, response to salt stress and photosynthesis-related processes showed significant enrichment in the two genotypes under drought stress. At 4 h of drought stress, ROC22 had earlier stress signal transduction and specific up-regulation of the processes response to ABA, L-proline biosynthesis and MAPK signaling pathway-plant than Badila. WGCNA analysis used to compile a gene regulatory network for ROC22 and Badila leaves exposed to drought stress revealed important candidate genes, including several classical transcription factors: NAC87, JAMYB, bHLH84, NAC21/22, HOX24 and MYB102, which are related to some antioxidants and trehalose, and other genes. These results provide new insights and resources for future research and cultivation of drought-tolerant sugarcane varieties.
Keyword ：
drought resistant drought resistant sugarcane sugarcane transcription factor transcription factor transcriptome transcriptome WGCNA WGCNA
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| GB/T 7714 | Li, Peiting , Lin, Pingping , Zhao, Zhenli et al. Gene Co-Expression Analysis Reveals Transcriptome Divergence between Wild and Cultivated Sugarcane under Drought Stress [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2022 , 23 (1) . |
| MLA | Li, Peiting et al. "Gene Co-Expression Analysis Reveals Transcriptome Divergence between Wild and Cultivated Sugarcane under Drought Stress" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 23 . 1 (2022) . |
| APA | Li, Peiting , Lin, Pingping , Zhao, Zhenli , Li, Zihong , Liu, Yanming , Huang, Chaohua et al. Gene Co-Expression Analysis Reveals Transcriptome Divergence between Wild and Cultivated Sugarcane under Drought Stress . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2022 , 23 (1) . |
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Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice. Genome-wide H3K9 acetylation level increases with age-dependent senescence in rice flag leaf, and the density and breadth of H3K9ac positively correlate with transcript elongation and expression of many genes involved in a complex metabolism-mediated senescence network.
Keyword ：
Aging Aging flag leaf flag leaf rice rice senescence associated genes senescence associated genes transcriptome transcriptome
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| GB/T 7714 | Zhang, Yu , Li, Yanyun , Zhang, Yuanyuan et al. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice [J]. | JOURNAL OF EXPERIMENTAL BOTANY , 2022 . |
| MLA | Zhang, Yu et al. "Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice" . | JOURNAL OF EXPERIMENTAL BOTANY (2022) . |
| APA | Zhang, Yu , Li, Yanyun , Zhang, Yuanyuan , Zhang, Zeyu , Zhang, Deyu , Wang, Xiaonan et al. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice . | JOURNAL OF EXPERIMENTAL BOTANY , 2022 . |
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Cross talking between natural senescence and cell death in response to pathogen attack is an interesting topic; however, its action mechanism is kept open. In this study, 33 OsWRKY genes were obtained by screening with leaf aging procedure through RNA-seq dataset, and 11 of them were confirmed a significant altered expression level in the flag leaves during aging by using the reverse transcript quantitative PCR (RT-qPCR). Among them, the OsWRKY2, OsWRKY14, OsWRKY26, OsWRKY69, and OsWRKY93 members exhibited short-term alteration in transcriptional levels in response to Magnaporthe grisea infection. The CRISPR/Cas9-edited mutants of five genes were developed and confirmed, and a significant sensitivity to M. oryzae infection was observed in CRISPR OsWRKY93-edited lines; on the other hand, a significant resistance to M. oryzae infection was shown in the enhanced expression OsWRKY93 plants compared to mock plants; however, enhanced expression of other four genes have no significant affection. Interestingly, ROS accumulation was also increased in OsWRKY93 enhanced plants after flg22 treatment, compared with the controls, suggesting that OsWRKY93 is involved in PAMP-triggered immune response in rice. It indicated that OsWRKY93 was involved in both flag leaf senescence and in response to fungi attack.
Keyword ：
biotic stress biotic stress flag leaf flag leaf OsWRKY93 OsWRKY93 rice rice senescence senescence
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| GB/T 7714 | Li, Yanyun , Liao, Shuting , Mei, Pengying et al. OsWRKY93 Dually Functions Between Leaf Senescence and in Response to Biotic Stress in Rice [J]. | FRONTIERS IN PLANT SCIENCE , 2021 , 12 . |
| MLA | Li, Yanyun et al. "OsWRKY93 Dually Functions Between Leaf Senescence and in Response to Biotic Stress in Rice" . | FRONTIERS IN PLANT SCIENCE 12 (2021) . |
| APA | Li, Yanyun , Liao, Shuting , Mei, Pengying , Pan, Yueyun , Zhang, Yu , Zheng, Xiangzi et al. OsWRKY93 Dually Functions Between Leaf Senescence and in Response to Biotic Stress in Rice . | FRONTIERS IN PLANT SCIENCE , 2021 , 12 . |
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A total of 16 OsS40 genes of Oryza sativa were identified in our previous work, but their functions remain unclear. In this study, 13 OsS40 members were knocked out using the CRISPR/cas9 gene-editing technology. After screening phenotype characterization of CRISPR/Cas9 mutants compared to WT, five oss40s mutants exhibited a stay-green phenotype at 30 days after heading. Moreover, increased grain size and grain weight occurred in the oss40-1, oss40-12, and oss40-14 lines, while declined grain weight appeared in the oss40-7 and oss40-13 mutants. The transcript levels of several senescence-associated genes (SAGs), chlorophyll degradation-related genes (CDGs), as well as WRKY members were differentially decreased in the five stay-green oss40s mutants compared to WT. Five oss40 mutants also exhibited a stay-green phenotype when the detached leaves were incubated under darkness for 4 days. OsSWEET4 and OsSWEET1b were significantly upregulated, while OsSWEET1a and OsSWEET13 were significantly downregulated in both oss40-7 and oss40-14 compared to WT. Furthermore, these five OsS40 displayed strong transcriptional activation activity and were located in the nucleus. Most of the OsS40 genes were downregulated in the oss40-1, oss40-7, and oss40-12 mutants, but upregulated in the oss40-13 and oss40-14 mutants, indicating coordinated regulation among OsS40 members. These results suggest that OsS40-1, OsS40-7, OsS40-12, OsS40-13, and OsS40-14 are senescence-associated genes, involved in the senescence and carbon allocation network by modulating other OsS40 members, SWEET member genes, and senescence-related gene expression.
Keyword ：
Cas9 edited mutants Cas9 edited mutants CRISPR CRISPR gene expression network gene expression network leaf senescence leaf senescence OsS40 gene family OsS40 gene family rice rice
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| GB/T 7714 | Habiba , Xu, Jiaxuan , Gad, Ahmed G. et al. Five OsS40 Family Members Are Identified as Senescence-Related Genes in Rice by Reverse Genetics Approach [J]. | FRONTIERS IN PLANT SCIENCE , 2021 , 12 . |
| MLA | Habiba et al. "Five OsS40 Family Members Are Identified as Senescence-Related Genes in Rice by Reverse Genetics Approach" . | FRONTIERS IN PLANT SCIENCE 12 (2021) . |
| APA | Habiba , Xu, Jiaxuan , Gad, Ahmed G. , Luo, Yuling , Fan, Chunlan , Uddin, Junaite Bin Gias et al. Five OsS40 Family Members Are Identified as Senescence-Related Genes in Rice by Reverse Genetics Approach . | FRONTIERS IN PLANT SCIENCE , 2021 , 12 . |
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BackgroundAPETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, few studies concerning AP2/ERF genes in sugarcane which are the most critical sugar and energy crops worldwide.ResultsA total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV), and four Soloist genes. These genes were unevenly distributed on 32 chromosomes. The structural analysis of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum had a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflected their similarity. Multiple cis-regulatory elements (CREs) present in the SsAP2/ERF promoter were related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to sugarcane adaptation to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different development stages. In ten sugarcane samples, 39 SsAP2/ERFs were not expressed, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under dehydration stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3h of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in the responses to ABA and GA-associated dehydration stress. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes played an essential role in dehydration and salt stress responses of S. spontaneum.ConclusionsIn this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.
Keyword ：
Abiotic stress Abiotic stress AP2 AP2 ERF gene ERF gene Sugarcane Sugarcane Transcription factor Transcription factor
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| GB/T 7714 | Li, Peiting , Chai, Zhe , Lin, Pingping et al. Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane (Saccharum spontaneum L.) [J]. | BMC GENOMICS , 2020 , 21 (1) . |
| MLA | Li, Peiting et al. "Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane (Saccharum spontaneum L.)" . | BMC GENOMICS 21 . 1 (2020) . |
| APA | Li, Peiting , Chai, Zhe , Lin, Pingping , Huang, Chaohua , Huang, Guoqiang , Xu, Liangnian et al. Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane (Saccharum spontaneum L.) . | BMC GENOMICS , 2020 , 21 (1) . |
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