Transcriptomics is one of the most developed fields in the post-genomic era.Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specif...Transcriptomics is one of the most developed fields in the post-genomic era.Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specific physiological condition,including messenger RNA,transfer RNA,ribosomal RNA,and other non-coding RNAs.Transcriptomics focuses on the gene expression at the RNA level and offers the genome-wide information of gene structure and gene function in order to reveal the molecular mechanisms involved in specific biological processes.With the development of next-generation high-throughput sequencing technology,transcriptome analysis has been progressively improving our understanding of RNA-based gene regulatory network.Here,we discuss the concept,history,and especially the recent advances in this inspiring field of study.展开更多
以栽培2个月的黄参为试材,设置对照(土壤相对含水量70%~80%)和适度干旱胁迫(土壤相对含水量55%~60%)处理,利用高通量转录组测序BGISEQ-500平台,对测序结果进行基因功能注释、差异表达基因(DEGs,differentially expressed genes)筛选。...以栽培2个月的黄参为试材,设置对照(土壤相对含水量70%~80%)和适度干旱胁迫(土壤相对含水量55%~60%)处理,利用高通量转录组测序BGISEQ-500平台,对测序结果进行基因功能注释、差异表达基因(DEGs,differentially expressed genes)筛选。结果表明:(1)获得的68193条Unigene中,分别有34230(50.20%)、34170(50.11%)、31727(46.53%)、27701(40.62%)、27092(39.73%)和22793(33.42%)个Unigene分别被分配到NCBI非冗余蛋白(NR)、eggNOG(基因的进化谱系,Evolutionary genealogy of genes:Non-supervised Orthologous Groups)、基因本体(Gene ontology,GO)、Pfam(Protein family)、SwissProt(Reviewed protein sequence database)和KEGG(Kyoto encyelopedia of genes and genomes)六大功能数据库。(2)DEGs分析显示,黄参块状根和叶中分别有10674个和13402个DEGs;GO富集结果表明,根和叶中的DEGs功能部位中的分布基本一致,主要富集在生物过程、DNA的复制和翻译调控、氧化还原过程、蛋白质磷酸化、防御响应等;KEGG富集分析表明,根中DEGs显著富集在苯丙烷类生物合成、半乳糖代谢、半胱氨酸和甲硫氨酸代谢、淀粉和蔗糖代谢、植物-病原菌相互作用、植物激素信号转导等途径,叶中DEGs则主要富集在半乳糖代谢、淀粉和蔗糖代谢、苯丙烷类生物合成、戊糖、葡萄糖醛酸转换、植物激素信号转导等途径,说明淀粉和蔗糖代谢、半乳糖代谢、苯丙烷类生物合成途径、植物激素信号转导途径在黄参应对干旱胁迫中起重要作用。干旱胁迫影响黄参不同器官中差异基因的表达,为解析黄参耐受干旱的生物学途径、黄参药效成分的生物合成和分子机制提供了理论依据。展开更多
Alternative polyadenylation(APA)contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases.Singlecell RNA sequencing(scRNA-seq)has enabled...Alternative polyadenylation(APA)contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases.Singlecell RNA sequencing(scRNA-seq)has enabled the profiling of APA at the single-cell level;however,the spatial information of cells is not preserved in scRNA-seq.Alternatively,spatial transcriptomics(ST)technologies provide opportunities to decipher the spatial context of the transcriptomic landscape.Pioneering studies have revealed potential spatially variable genes and/or splice isoforms;however,the pattern of APA usage in spatial contexts remains unappreciated.In this study,we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatially barcoded ST data.APA sites were identified and quantified from the ST data.In particular,an imputation model based on the k-nearest neighbors algorithm was designed to recover APA signals,and then APA genes with spatial patterns of APA usage variation were identified.By analyzing wellestablished ST data of the mouse olfactory bulb(MOB),we presented a detailed view of spatial APA usage across morphological layers of the MOB.We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers.By extending this analysis to two additional replicates of the MOB ST data,we observed that the spatial APA patterns of several genes were reproducible among replicates.stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution.This toolkit is available at https://github.com/BMILAB/stAPAminer and https://ngdc.cncb.ac.cn/biocode/tools/BT007320.展开更多
Tension wood(TW)is a specialized xylem tissue formed in angiosperm trees under gravitational stimulus or mechanical stresses(e.g.,bending).The genetic regulation that underlies this important mechanism remains poorly ...Tension wood(TW)is a specialized xylem tissue formed in angiosperm trees under gravitational stimulus or mechanical stresses(e.g.,bending).The genetic regulation that underlies this important mechanism remains poorly understood.Here,we used laser capture microdissection of stem xylem cells coupled with full transcriptome RNA-sequencing to analyze TW formation in Populus trichocarpa.After tree bending,PtrLBD39 was the most significantly induced transcription factor gene;it has a phylogenetically paired homolog,PtrLBD22.CRISPR-based knockout of PtrLBD39/22 severely inhibited TW formation,reducing cellulose and increasing lignin content.Transcriptomic analyses of CRISPR-based PtrLBD39/22 double mutants showed that these two genes regulate a set of TW-related genes.Chromatin immunoprecipitation sequencing(ChIP-seq)was used to identify direct targets of PtrLBD39.We integrated transcriptomic analyses and ChIP-seq assays to construct a transcriptional regulatory network(TRN)mediated by PtrLBD39.In this TRN,PtrLBD39 directly regulates 26 novel TW-responsive transcription factor genes.Our work suggests that PtrLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus.展开更多
Understanding the complexity of biological systems requires a comprehensive analysis of their cell populations.Ideally,this should be done at the single cell level,because bulk analysis of the full population obscured...Understanding the complexity of biological systems requires a comprehensive analysis of their cell populations.Ideally,this should be done at the single cell level,because bulk analysis of the full population obscured many critical details due to artifacts introduced by averaging.However,this has been technically challenging due to the cumbersome procedure,low throughput,and high costs of performing analysis on a single-cell basis.Excitingly,technical improvements in single-cell RNA sequencing are making it economically practical to profile the transcriptomics of large populations of cells at the single-cell level,and have yielded numerous results that address important biological and medical questions.Further development of the technology and data analysis will significantly benefit the biomedical field by unraveling the function of individual cells in their microenvironments and modeling their transcriptional dynamics.展开更多
基金supported by grants from the National Natural Science Foundation of China(31271318)Natural Science Foundation of Guangdong(S2012010008912)Foundation of Key Laboratory of Plant Resources Conservation and Sustainable Utilization,South China Botanical Garden,Chinese Academy of Sciences
文摘Transcriptomics is one of the most developed fields in the post-genomic era.Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specific physiological condition,including messenger RNA,transfer RNA,ribosomal RNA,and other non-coding RNAs.Transcriptomics focuses on the gene expression at the RNA level and offers the genome-wide information of gene structure and gene function in order to reveal the molecular mechanisms involved in specific biological processes.With the development of next-generation high-throughput sequencing technology,transcriptome analysis has been progressively improving our understanding of RNA-based gene regulatory network.Here,we discuss the concept,history,and especially the recent advances in this inspiring field of study.
文摘以栽培2个月的黄参为试材,设置对照(土壤相对含水量70%~80%)和适度干旱胁迫(土壤相对含水量55%~60%)处理,利用高通量转录组测序BGISEQ-500平台,对测序结果进行基因功能注释、差异表达基因(DEGs,differentially expressed genes)筛选。结果表明:(1)获得的68193条Unigene中,分别有34230(50.20%)、34170(50.11%)、31727(46.53%)、27701(40.62%)、27092(39.73%)和22793(33.42%)个Unigene分别被分配到NCBI非冗余蛋白(NR)、eggNOG(基因的进化谱系,Evolutionary genealogy of genes:Non-supervised Orthologous Groups)、基因本体(Gene ontology,GO)、Pfam(Protein family)、SwissProt(Reviewed protein sequence database)和KEGG(Kyoto encyelopedia of genes and genomes)六大功能数据库。(2)DEGs分析显示,黄参块状根和叶中分别有10674个和13402个DEGs;GO富集结果表明,根和叶中的DEGs功能部位中的分布基本一致,主要富集在生物过程、DNA的复制和翻译调控、氧化还原过程、蛋白质磷酸化、防御响应等;KEGG富集分析表明,根中DEGs显著富集在苯丙烷类生物合成、半乳糖代谢、半胱氨酸和甲硫氨酸代谢、淀粉和蔗糖代谢、植物-病原菌相互作用、植物激素信号转导等途径,叶中DEGs则主要富集在半乳糖代谢、淀粉和蔗糖代谢、苯丙烷类生物合成、戊糖、葡萄糖醛酸转换、植物激素信号转导等途径,说明淀粉和蔗糖代谢、半乳糖代谢、苯丙烷类生物合成途径、植物激素信号转导途径在黄参应对干旱胁迫中起重要作用。干旱胁迫影响黄参不同器官中差异基因的表达,为解析黄参耐受干旱的生物学途径、黄参药效成分的生物合成和分子机制提供了理论依据。
基金supported by the National Natural Science Foundation of China(Grant Nos.T2222007 to Xiaohui Wu,61573296 to Guoli Ji,and 81901287 to Shuting Xia)the Suzhou City People’s Livelihood Science and Technology Project,China(Grant No.SYS2020086 to Shuting Xia).
文摘Alternative polyadenylation(APA)contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases.Singlecell RNA sequencing(scRNA-seq)has enabled the profiling of APA at the single-cell level;however,the spatial information of cells is not preserved in scRNA-seq.Alternatively,spatial transcriptomics(ST)technologies provide opportunities to decipher the spatial context of the transcriptomic landscape.Pioneering studies have revealed potential spatially variable genes and/or splice isoforms;however,the pattern of APA usage in spatial contexts remains unappreciated.In this study,we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatially barcoded ST data.APA sites were identified and quantified from the ST data.In particular,an imputation model based on the k-nearest neighbors algorithm was designed to recover APA signals,and then APA genes with spatial patterns of APA usage variation were identified.By analyzing wellestablished ST data of the mouse olfactory bulb(MOB),we presented a detailed view of spatial APA usage across morphological layers of the MOB.We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers.By extending this analysis to two additional replicates of the MOB ST data,we observed that the spatial APA patterns of several genes were reproducible among replicates.stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution.This toolkit is available at https://github.com/BMILAB/stAPAminer and https://ngdc.cncb.ac.cn/biocode/tools/BT007320.
基金This work was supported by the National Key Research and Development Program of China(no.2016YFD0600106)We also acknowledge financial support from the National Natural Science Foundation of China(grant nos.32001332 and 32001331)+1 种基金the Fundamental Research Funds for the Central Universities of China(grant nos.2572018CL01 and 2572018CL02)the Heilongjiang Touyan Innovation Team Program(Tree Genetics and Breeding Innovation Team).
文摘Tension wood(TW)is a specialized xylem tissue formed in angiosperm trees under gravitational stimulus or mechanical stresses(e.g.,bending).The genetic regulation that underlies this important mechanism remains poorly understood.Here,we used laser capture microdissection of stem xylem cells coupled with full transcriptome RNA-sequencing to analyze TW formation in Populus trichocarpa.After tree bending,PtrLBD39 was the most significantly induced transcription factor gene;it has a phylogenetically paired homolog,PtrLBD22.CRISPR-based knockout of PtrLBD39/22 severely inhibited TW formation,reducing cellulose and increasing lignin content.Transcriptomic analyses of CRISPR-based PtrLBD39/22 double mutants showed that these two genes regulate a set of TW-related genes.Chromatin immunoprecipitation sequencing(ChIP-seq)was used to identify direct targets of PtrLBD39.We integrated transcriptomic analyses and ChIP-seq assays to construct a transcriptional regulatory network(TRN)mediated by PtrLBD39.In this TRN,PtrLBD39 directly regulates 26 novel TW-responsive transcription factor genes.Our work suggests that PtrLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus.
基金This work was supported by the Harvard Materials Research Science and Engineering Center(NSF DMR-1420570)National Science Foundation(DMR-1708729)+1 种基金National Institutes of Health(P01HL120839)Harvard-Suzhou Industrial Park Research and engineering innovation initiative grant,and National Natural Science Foundation of China(81372496).
文摘Understanding the complexity of biological systems requires a comprehensive analysis of their cell populations.Ideally,this should be done at the single cell level,because bulk analysis of the full population obscured many critical details due to artifacts introduced by averaging.However,this has been technically challenging due to the cumbersome procedure,low throughput,and high costs of performing analysis on a single-cell basis.Excitingly,technical improvements in single-cell RNA sequencing are making it economically practical to profile the transcriptomics of large populations of cells at the single-cell level,and have yielded numerous results that address important biological and medical questions.Further development of the technology and data analysis will significantly benefit the biomedical field by unraveling the function of individual cells in their microenvironments and modeling their transcriptional dynamics.
