Correction:aBIOTECH(2024)5:309-324 https://doi.org/10.1007/s42994-024-00176-2 The article Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza,written by Honggang Dai,Yaxin Fan,Yichao Mei,...Correction:aBIOTECH(2024)5:309-324 https://doi.org/10.1007/s42994-024-00176-2 The article Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza,written by Honggang Dai,Yaxin Fan,Yichao Mei,Ling-Ling Chen,Junxiang Gao,was originally published Online First without Open Access.After publication in volume 5,issue 3,pages 309–324 the authors decided to opt for Open Choice and to make the article an Open Access publication.展开更多
A regulon refers to a group of genes regulated by a transcription factor binding to regulatory motifs to achieve specific biological functions.To infer tissue-specific gene regulons in Arabidopsis,we developed a novel...A regulon refers to a group of genes regulated by a transcription factor binding to regulatory motifs to achieve specific biological functions.To infer tissue-specific gene regulons in Arabidopsis,we developed a novel pipeline named InferReg.InferReg utilizes a gene expression matrix that includes 3400 Arabidopsis transcriptomes to make initial predictions about the regulatory relationships between transcription factors(TFs)and target genes(TGs)using co-expression patterns.It further improves these anticipated interactions by integrating TF binding site enrichment analysis to eliminate false positives that are only supported by expression data.InferReg further trained a graph convolutional network with 133 transcription factors,supported by ChIP-seq,as positive samples,to learn the regulatory logic between TFs and TGs to improve the accuracy of the regulatory network.To evaluate the functionality of InferReg,we utilized it to discover tissue-specific regulons in 5 Arabidopsis tissues:flower,leaf,root,seed,and seedling.We ranked the activities of regulons for each tissue based on reliability using Borda ranking and compared them with existing databases.The results demonstrated that InferReg not only identified known tissue-specific regulons but also discovered new ones.By applying InferReg to rice expression data,we were able to identify rice tissue-specific regulons,showing that our approach can be applied more broadly.We used InferReg to successfully identify important regulons in various tissues of Arabidopsis and Oryza,which has improved our understanding of tissue-specific regulations and the roles of regulons in tissue differentiation and development.展开更多
Glycerol may be converted to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae under anaerobic conditions and glycerol dismutation involves two parallel pathways controlled by the dha regulon. In this study, a fourtee...Glycerol may be converted to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae under anaerobic conditions and glycerol dismutation involves two parallel pathways controlled by the dha regulon. In this study, a fourteen-dimensional nonlinear dynamic system is presented to describe the continuous culture and multiplicity analysis, in which two regulated negative-feedback mechanisms of repression and enzyme inhibition are investigated. The model describing the expression of gene-mRNA-enzyme-product was established according to the repression of the dha regulon by 3-hydroxypropionaldehy (3-HPA). Comparisons between simulated and experimental results indicate that the model can be used to describe the production of 1,3-PD under continuous fermentation. The new model is translated into the corresponding S-system version. The robustness of this model is discussed by using the S-system model and the sensitivity analysis shows that the model is sufficiently robust. The influences of initial glycerol concentration and dilution rate on the biosynthesis of 1,3-PD and the stability of the dha regulon model are investigated. The intracellular concentrations of glycerol, 1,3-PD, 3-HPA, repressor mRNA, repressor, mRNA and protein levels of glycerol dehydratase (GDHt) and 1,3-PD oxydoreductase (PDOR) can be predicted for continuous cultivation. The results of simulation and analysis indicate that 3-HPA accumulation will repress the expression of the dha regulon at the transcriptional level. This model gives new insights into the regulation of glycerol metabolism in K. pneumoniae and explain some of the experimental observations.展开更多
Skeletal muscle regeneration is a complex process where various cell types and cytokines are involved.Single-cell RNA-sequencing (scRNA-seq) provides the opportunity to deconvolute heterogeneous tissue into individual...Skeletal muscle regeneration is a complex process where various cell types and cytokines are involved.Single-cell RNA-sequencing (scRNA-seq) provides the opportunity to deconvolute heterogeneous tissue into individual cells based on their transcriptomic profiles.Recent scRNA-seq studies on mouse muscle regeneration have provided insights to understand the transcriptional dynamics that underpin muscle regeneration.However,a database to investigate gene expression profiling during skeletal muscle regeneration at the single-cell level is lacking.Here,we collected over 105 000 cells at 7 key regenerative time-points and non-injured muscles and developed a database,the Singlecell Skeletal Muscle Regeneration Database (SCSMRD).SCSMRD allows users to search the dynamic expression profiles of genes of interest across different cell types during the skeletal muscle regeneration process.It also provides a network to show the activity of regulons in different cell types at different time points.Pesudotime analysis showed the state changes trajectory of muscle stem cells (MuSCs) during skeletal muscle regeneration.This database is freely available at https://scsmrd.fengs-lab.com.展开更多
The Escherichia coil fadR protein product, a paradigm/ prototypical FadR regulator, positively regulates fabA and fabB, the two critical genes for unsaturated fatty acid （UFA） biosynthesis. However the scenario in t...The Escherichia coil fadR protein product, a paradigm/ prototypical FadR regulator, positively regulates fabA and fabB, the two critical genes for unsaturated fatty acid （UFA） biosynthesis. However the scenario in the other γ- proteobacteria, such as Shewanella with the marine ori- gin, is unusual in that Rodionov and coworkers predicted that only fabA （not fabB） has a binding site for FadR pro- tein. It raised the possibility of fad regulon contraction. Here we report that this is the case. Sequence alignment of the FadR homologs revealed that the N-terminal DNA- binding domain exhibited remarkable similarity, whereas the ligand-accepting motif at C-terminus is relatively-less conserved. The FadR homologue of S. oneidensis （re- ferred to FadR_she） was over-expressed and purified to homogeneity. Integrative evidence obtained by FPLC （fast protein liquid chromatography） and chemical cross. linking analyses elucidated that FadR_she protein can dimerize in solution, whose identity was determined by MALDI-TOF-MS. In vitro data from electrophoretic mobil. ity shift assays suggested that FadR_she is almost functionally-exchangeable/equivalent to E. coil FadR （FadR_ec） in the ability of binding the E. coil fabA （and fabB） promoters. In an agreement with that of E. coil fabA, S. oneidensis fabA promoter bound both FadR_she andFadR_ec, and was disassociated specifically with the FadR regulatory protein upon the addition of long-chain acyI-CoA thioesters. To monitor in vivo effect exerted by FadR on Shewanella fabA expression, the native pro- moter of S. oneidensis fabA was fused to a LacZ reporter gene to engineer a chromosome fabA-lacZtranscriptional fusion in E. coil. As anticipated, the removal of fadR gene gave about 2-fold decrement of Shewanella fabA expression by β-gal activity, which is almost identical to the inhibitory level by the addition of oleate. Therefore, we concluded that fabA is contracted to be the only one member of fad regulon in the context of fatty acid syn- thesis in the marine bacteria Shewanella genus.展开更多
文摘Correction:aBIOTECH(2024)5:309-324 https://doi.org/10.1007/s42994-024-00176-2 The article Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza,written by Honggang Dai,Yaxin Fan,Yichao Mei,Ling-Ling Chen,Junxiang Gao,was originally published Online First without Open Access.After publication in volume 5,issue 3,pages 309–324 the authors decided to opt for Open Choice and to make the article an Open Access publication.
基金supported in part by the National Natural Science Foundation of China(32270712)the Hubei Provincial Natural Science Foundation of China(2019CFA014).
文摘A regulon refers to a group of genes regulated by a transcription factor binding to regulatory motifs to achieve specific biological functions.To infer tissue-specific gene regulons in Arabidopsis,we developed a novel pipeline named InferReg.InferReg utilizes a gene expression matrix that includes 3400 Arabidopsis transcriptomes to make initial predictions about the regulatory relationships between transcription factors(TFs)and target genes(TGs)using co-expression patterns.It further improves these anticipated interactions by integrating TF binding site enrichment analysis to eliminate false positives that are only supported by expression data.InferReg further trained a graph convolutional network with 133 transcription factors,supported by ChIP-seq,as positive samples,to learn the regulatory logic between TFs and TGs to improve the accuracy of the regulatory network.To evaluate the functionality of InferReg,we utilized it to discover tissue-specific regulons in 5 Arabidopsis tissues:flower,leaf,root,seed,and seedling.We ranked the activities of regulons for each tissue based on reliability using Borda ranking and compared them with existing databases.The results demonstrated that InferReg not only identified known tissue-specific regulons but also discovered new ones.By applying InferReg to rice expression data,we were able to identify rice tissue-specific regulons,showing that our approach can be applied more broadly.We used InferReg to successfully identify important regulons in various tissues of Arabidopsis and Oryza,which has improved our understanding of tissue-specific regulations and the roles of regulons in tissue differentiation and development.
基金Supported by the National High Technology Research and Development Program of China (2007AA02Z208)the State Key Development Program for Basic Research of China (2007CB714304)
文摘Glycerol may be converted to 1,3-propanediol (1,3-PD) by Klebsiella pneumoniae under anaerobic conditions and glycerol dismutation involves two parallel pathways controlled by the dha regulon. In this study, a fourteen-dimensional nonlinear dynamic system is presented to describe the continuous culture and multiplicity analysis, in which two regulated negative-feedback mechanisms of repression and enzyme inhibition are investigated. The model describing the expression of gene-mRNA-enzyme-product was established according to the repression of the dha regulon by 3-hydroxypropionaldehy (3-HPA). Comparisons between simulated and experimental results indicate that the model can be used to describe the production of 1,3-PD under continuous fermentation. The new model is translated into the corresponding S-system version. The robustness of this model is discussed by using the S-system model and the sensitivity analysis shows that the model is sufficiently robust. The influences of initial glycerol concentration and dilution rate on the biosynthesis of 1,3-PD and the stability of the dha regulon model are investigated. The intracellular concentrations of glycerol, 1,3-PD, 3-HPA, repressor mRNA, repressor, mRNA and protein levels of glycerol dehydratase (GDHt) and 1,3-PD oxydoreductase (PDOR) can be predicted for continuous cultivation. The results of simulation and analysis indicate that 3-HPA accumulation will repress the expression of the dha regulon at the transcriptional level. This model gives new insights into the regulation of glycerol metabolism in K. pneumoniae and explain some of the experimental observations.
基金supported by the National Natural Science Foundation of China(31972539 and 32102513)the Science,Technology,and Innovation Commission of Shenzhen Municipality,China(JCYJ20180306173644635)+2 种基金the Fundamental Research Funds for the Central Universities,China(G2020KY05109)the Natural Science Basic Research Program of Shaanxi Province,China(2022JQ-644)the Basic Research Programs of Taicang,China(TC2021JC14)。
文摘Skeletal muscle regeneration is a complex process where various cell types and cytokines are involved.Single-cell RNA-sequencing (scRNA-seq) provides the opportunity to deconvolute heterogeneous tissue into individual cells based on their transcriptomic profiles.Recent scRNA-seq studies on mouse muscle regeneration have provided insights to understand the transcriptional dynamics that underpin muscle regeneration.However,a database to investigate gene expression profiling during skeletal muscle regeneration at the single-cell level is lacking.Here,we collected over 105 000 cells at 7 key regenerative time-points and non-injured muscles and developed a database,the Singlecell Skeletal Muscle Regeneration Database (SCSMRD).SCSMRD allows users to search the dynamic expression profiles of genes of interest across different cell types during the skeletal muscle regeneration process.It also provides a network to show the activity of regulons in different cell types at different time points.Pesudotime analysis showed the state changes trajectory of muscle stem cells (MuSCs) during skeletal muscle regeneration.This database is freely available at https://scsmrd.fengs-lab.com.
文摘The Escherichia coil fadR protein product, a paradigm/ prototypical FadR regulator, positively regulates fabA and fabB, the two critical genes for unsaturated fatty acid （UFA） biosynthesis. However the scenario in the other γ- proteobacteria, such as Shewanella with the marine ori- gin, is unusual in that Rodionov and coworkers predicted that only fabA （not fabB） has a binding site for FadR pro- tein. It raised the possibility of fad regulon contraction. Here we report that this is the case. Sequence alignment of the FadR homologs revealed that the N-terminal DNA- binding domain exhibited remarkable similarity, whereas the ligand-accepting motif at C-terminus is relatively-less conserved. The FadR homologue of S. oneidensis （re- ferred to FadR_she） was over-expressed and purified to homogeneity. Integrative evidence obtained by FPLC （fast protein liquid chromatography） and chemical cross. linking analyses elucidated that FadR_she protein can dimerize in solution, whose identity was determined by MALDI-TOF-MS. In vitro data from electrophoretic mobil. ity shift assays suggested that FadR_she is almost functionally-exchangeable/equivalent to E. coil FadR （FadR_ec） in the ability of binding the E. coil fabA （and fabB） promoters. In an agreement with that of E. coil fabA, S. oneidensis fabA promoter bound both FadR_she andFadR_ec, and was disassociated specifically with the FadR regulatory protein upon the addition of long-chain acyI-CoA thioesters. To monitor in vivo effect exerted by FadR on Shewanella fabA expression, the native pro- moter of S. oneidensis fabA was fused to a LacZ reporter gene to engineer a chromosome fabA-lacZtranscriptional fusion in E. coil. As anticipated, the removal of fadR gene gave about 2-fold decrement of Shewanella fabA expression by β-gal activity, which is almost identical to the inhibitory level by the addition of oleate. Therefore, we concluded that fabA is contracted to be the only one member of fad regulon in the context of fatty acid syn- thesis in the marine bacteria Shewanella genus.
