BACKGROUND Ulcerative colitis(UC)is a complicated disease caused by the interaction between genetic and environmental factors that affects mucosal homeostasis and triggers an inappropriate immune response.Single-cell ...BACKGROUND Ulcerative colitis(UC)is a complicated disease caused by the interaction between genetic and environmental factors that affects mucosal homeostasis and triggers an inappropriate immune response.Single-cell RNA sequencing(scRNA-seq)can be used to rapidly obtain the precise gene expression patterns of thousands of cells in the intestine,analyze the characteristics of cells with the same phenotype,and provide new insights into the growth and development of intestinal organs,the clonal evolution of cells,and immune cell changes.These findings can provide new ideas for the diagnosis and treatment of intestinal diseases.To identify clinical phenotypes and biomarkers that can predict the response of UC patients to specific therapeutic drugs and thus aid the diagnosis and treatment of UC.METHODS Using the Gene Expression Omnibus(GEO)database,we analyzed peripheral blood cell subtypes of patients with UC by scRNA-seq combined with bulk RNA sequencing(RNA-seq)to reveal the core genes of UC.We then combined weighted gene correlation network analysis(WGCNA)and least absolute shrinkage and selection operator(LASSO)analysis to reveal diagnostic markers of UC.RESULTS After processing the scRNA-seq data,we obtained data from approximately 24340 cells and identified 17 cell types.Through intercellular communication analysis,we selected monocyte marker genes as the candidate gene set for the prediction model.Construction of a WGCNA coexpression network identified RhoB,cathepsin D(CTSD)and zyxin(ZYX)as core genes.Immune infiltration analysis showed that these three core genes were strongly correlated with immune cells.Functional enrichment analysis showed that the differentially expressed genes were closely related to immune and inflammatory responses,which are associated with many challenges in the diagnosis and treatment of UC.CONCLUSION Through scRNA-seq analysis,LASSO diagnostic model building and WGCNA,we identified RhoB,CTSD and ZYX as core genes of UC that are closely related to monocyte infiltration that may serve as diagnostic markers and molecular targets for UC therapeutic intervention.展开更多
Alternative polyadenylation(APA)plays important roles in modulating mRNA stability,translation,and subcellular localization,and contributes extensively to shaping eukaryotic transcriptome complexity and proteome diver...Alternative polyadenylation(APA)plays important roles in modulating mRNA stability,translation,and subcellular localization,and contributes extensively to shaping eukaryotic transcriptome complexity and proteome diversity.Identification of poly(A)sites(pAs)on a genomewide scale is a critical step toward understanding the underlying mechanism of APA-mediated gene regulation.A number of established computational tools have been proposed to predict pAs from diverse genomic data.Here we provided an exhaustive overview of computational approaches for predicting pAs from DNA sequences,bulk RNA sequencing(RNA-seq)data,and single-cell RNA sequencing(scRNA-seq)data.Particularly,we examined several representative tools using bulk RNA-seq and scRNA-seq data from peripheral blood mononuclear cells and put forward operable suggestions on how to assess the reliability of pAs predicted by different tools.We also proposed practical guidelines on choosing appropriate methods applicable to diverse scenarios.Moreover,we discussed in depth the challenges in improving the performance of pA prediction and benchmarking different methods.Additionally,we highlighted outstanding challenges and opportunities using new machine learning and integrative multi-omics techniques,and provided our perspective on how computational methodologies might evolve in the future for non-30 untranslated region,tissuespecific,cross-species,and single-cell pA prediction.展开更多
Prezygotic isolation is important for successful fertilization in rice, significantly affecting yield. This study focused on F_(5:6) generation plants derived from inter-subspecific crosses(Nipponbare × KDML105) ...Prezygotic isolation is important for successful fertilization in rice, significantly affecting yield. This study focused on F_(5:6) generation plants derived from inter-subspecific crosses(Nipponbare × KDML105) with low(LS) and high seed-setting rates(HS), in which normal pollen fertility was observed. However, LS plants showed a reduced number of pollen grains adhering to the stigma and fewer pollen tubes reaching the ovules at 4-5 h post-pollination, compared with HS plants. Bulked segregant RNA-Seq analysis of pollinated pistils from the HS and LS groups revealed 249 and 473 differentially expressed genes(DEGs), respectively. Kyoto Encyclopedia of Genes and Genomes analysis of the HS and LS-specific DEGs indicated enrichment in metabolic pathways, pentose and glucuronate interconversions, and flavonoid biosynthesis. Several of these DEGs exhibited co-expression with pollen development genes and formed extensive clusters of co-expression networks. Compared with LS pistils, enzyme genes controlling pectin degradation, such as OsPME35 and OsPLL9, showed similar expression patterns, with higher levels in HS pistils pre-pollination. Os02g0467600, similar to cinnamate 4-hydroxylase gene(CYP73), involved in flavonoid biosynthesis, displayed higher expression in HS pistils post-pollination. Our findings suggest that OsPME35, OsPLL9, and Os02g0467600 contribute to prezygotic isolation by potentially modifying the stigma cell wall(OsPME35 and OsPLL9) and controlling later processes such as pollen-stigma adhesion(Os02g0467600) genes. Furthermore, several DEGs specific to HS and LS were co-localized with QTLs and functional genes associated with spikelet fertility. These findings provide valuable insights for further research on rice spikelet fertility, ultimately contributing to the development of high-yielding rice varieties.展开更多
The lifetime of G. biloba is very long, and its growth is relatively slow. However, little is known about growth-related genes in this species. We combined mRNA sequencing (RNA-Seq) with bulked segregant analysis (BSA...The lifetime of G. biloba is very long, and its growth is relatively slow. However, little is known about growth-related genes in this species. We combined mRNA sequencing (RNA-Seq) with bulked segregant analysis (BSA) to fine map significant agronomic trait genes by developing polymorphism molecular markers at the transcriptome level. In this study, transcriptome sequencing of high growth (GD) and low growth (BD) samples of G. biloba half-sib families was performed. After assembling the clean reads, 601 differential expression genes were detected and 513 of them were assigned functional annotations. Single nucleotide polymorphism (SNP) analysis identified SNPs associated with 119 genes in the GD and BD groups;58 of these genes were annotated. Two Homeobox-leucine zipper protein genes were up-regulated in the GD group compared with the BD group;therefore, these are very likely related to high growth of G. biloba. This study provides molecular level data that could be used for seed selection of high growth G. biloba half-sib families for future breeding programs.展开更多
基金Supported by the National Natural Science Foundation of China,No.81873253 and 81704009the Shanghai Natural Science Foundation,No.22ZR1458800+1 种基金the Hongkou District Health Committee,No.HKZK2020A01the Xinglin Scholar Program of Shanghai University of Traditional Chinese Medicine,Shanghai University of Traditional Chinese Medicine 2020 Document No.23.
文摘BACKGROUND Ulcerative colitis(UC)is a complicated disease caused by the interaction between genetic and environmental factors that affects mucosal homeostasis and triggers an inappropriate immune response.Single-cell RNA sequencing(scRNA-seq)can be used to rapidly obtain the precise gene expression patterns of thousands of cells in the intestine,analyze the characteristics of cells with the same phenotype,and provide new insights into the growth and development of intestinal organs,the clonal evolution of cells,and immune cell changes.These findings can provide new ideas for the diagnosis and treatment of intestinal diseases.To identify clinical phenotypes and biomarkers that can predict the response of UC patients to specific therapeutic drugs and thus aid the diagnosis and treatment of UC.METHODS Using the Gene Expression Omnibus(GEO)database,we analyzed peripheral blood cell subtypes of patients with UC by scRNA-seq combined with bulk RNA sequencing(RNA-seq)to reveal the core genes of UC.We then combined weighted gene correlation network analysis(WGCNA)and least absolute shrinkage and selection operator(LASSO)analysis to reveal diagnostic markers of UC.RESULTS After processing the scRNA-seq data,we obtained data from approximately 24340 cells and identified 17 cell types.Through intercellular communication analysis,we selected monocyte marker genes as the candidate gene set for the prediction model.Construction of a WGCNA coexpression network identified RhoB,cathepsin D(CTSD)and zyxin(ZYX)as core genes.Immune infiltration analysis showed that these three core genes were strongly correlated with immune cells.Functional enrichment analysis showed that the differentially expressed genes were closely related to immune and inflammatory responses,which are associated with many challenges in the diagnosis and treatment of UC.CONCLUSION Through scRNA-seq analysis,LASSO diagnostic model building and WGCNA,we identified RhoB,CTSD and ZYX as core genes of UC that are closely related to monocyte infiltration that may serve as diagnostic markers and molecular targets for UC therapeutic intervention.
基金This work was supported by the National Natural Science Foundation of China(Grant No.61871463 to XW)the Natural Science Foundation of Fujian Province of China(Grant No.2020J01047 to CY).
文摘Alternative polyadenylation(APA)plays important roles in modulating mRNA stability,translation,and subcellular localization,and contributes extensively to shaping eukaryotic transcriptome complexity and proteome diversity.Identification of poly(A)sites(pAs)on a genomewide scale is a critical step toward understanding the underlying mechanism of APA-mediated gene regulation.A number of established computational tools have been proposed to predict pAs from diverse genomic data.Here we provided an exhaustive overview of computational approaches for predicting pAs from DNA sequences,bulk RNA sequencing(RNA-seq)data,and single-cell RNA sequencing(scRNA-seq)data.Particularly,we examined several representative tools using bulk RNA-seq and scRNA-seq data from peripheral blood mononuclear cells and put forward operable suggestions on how to assess the reliability of pAs predicted by different tools.We also proposed practical guidelines on choosing appropriate methods applicable to diverse scenarios.Moreover,we discussed in depth the challenges in improving the performance of pA prediction and benchmarking different methods.Additionally,we highlighted outstanding challenges and opportunities using new machine learning and integrative multi-omics techniques,and provided our perspective on how computational methodologies might evolve in the future for non-30 untranslated region,tissuespecific,cross-species,and single-cell pA prediction.
基金supported by the Agricultural Research Development Agency of Thailand (Grant No.PRP6405030280)Research Promotion fund for International and Educational Excellence, Thailand (Grant No.08/2562)。
文摘Prezygotic isolation is important for successful fertilization in rice, significantly affecting yield. This study focused on F_(5:6) generation plants derived from inter-subspecific crosses(Nipponbare × KDML105) with low(LS) and high seed-setting rates(HS), in which normal pollen fertility was observed. However, LS plants showed a reduced number of pollen grains adhering to the stigma and fewer pollen tubes reaching the ovules at 4-5 h post-pollination, compared with HS plants. Bulked segregant RNA-Seq analysis of pollinated pistils from the HS and LS groups revealed 249 and 473 differentially expressed genes(DEGs), respectively. Kyoto Encyclopedia of Genes and Genomes analysis of the HS and LS-specific DEGs indicated enrichment in metabolic pathways, pentose and glucuronate interconversions, and flavonoid biosynthesis. Several of these DEGs exhibited co-expression with pollen development genes and formed extensive clusters of co-expression networks. Compared with LS pistils, enzyme genes controlling pectin degradation, such as OsPME35 and OsPLL9, showed similar expression patterns, with higher levels in HS pistils pre-pollination. Os02g0467600, similar to cinnamate 4-hydroxylase gene(CYP73), involved in flavonoid biosynthesis, displayed higher expression in HS pistils post-pollination. Our findings suggest that OsPME35, OsPLL9, and Os02g0467600 contribute to prezygotic isolation by potentially modifying the stigma cell wall(OsPME35 and OsPLL9) and controlling later processes such as pollen-stigma adhesion(Os02g0467600) genes. Furthermore, several DEGs specific to HS and LS were co-localized with QTLs and functional genes associated with spikelet fertility. These findings provide valuable insights for further research on rice spikelet fertility, ultimately contributing to the development of high-yielding rice varieties.
文摘The lifetime of G. biloba is very long, and its growth is relatively slow. However, little is known about growth-related genes in this species. We combined mRNA sequencing (RNA-Seq) with bulked segregant analysis (BSA) to fine map significant agronomic trait genes by developing polymorphism molecular markers at the transcriptome level. In this study, transcriptome sequencing of high growth (GD) and low growth (BD) samples of G. biloba half-sib families was performed. After assembling the clean reads, 601 differential expression genes were detected and 513 of them were assigned functional annotations. Single nucleotide polymorphism (SNP) analysis identified SNPs associated with 119 genes in the GD and BD groups;58 of these genes were annotated. Two Homeobox-leucine zipper protein genes were up-regulated in the GD group compared with the BD group;therefore, these are very likely related to high growth of G. biloba. This study provides molecular level data that could be used for seed selection of high growth G. biloba half-sib families for future breeding programs.
