Actinobacillus pleuropneumoniae(APP)is the major pathogen of porcine contagious pleuropneumoniae(PCP).The QseB/QseC two-component system(TCS)consists of the regulator QseB and the kinase QseC,which relates to quorum s...Actinobacillus pleuropneumoniae(APP)is the major pathogen of porcine contagious pleuropneumoniae(PCP).The QseB/QseC two-component system(TCS)consists of the regulator QseB and the kinase QseC,which relates to quorum sensing(QS)and virulence in some bacteria.Here,we investigated the role of QseB/QseC in apf gene cluster(apfABCD)expression of APP.Our results have showed that QseB/QseC TCS can potentially regulate the expression of apf gene cluster.The△qseBC,△apfA,△apfB,△apfC and△apfD strains are more sensitive to acidic and osmotic stressful conditions,and exhibite lower biofilm formation ability than wild-type(WT)strain,whereas the complemented strains show similar phenotype to the wr strain.In additon,the mutants have defective antiphagocytosis,adhesion and invasion when they come into contact with the host cells.In experimental animal models of infection,mice infected with△qseBC,△apfA,△apfB,△apfC and △apfD strains showed lower mortality and bacterial loads in the lung and the blood than those infected with wr strain.In conclusion,our results suggest that QseB/QseC TCS contributes to stress resistance,biofilm formation,phagocytosis,adhesion,invasion and virulence by downregulating expression of apf gene cluster in A.pleuropneumoniae.展开更多
Divergently-paired genes(DPGs)are minimal co-transcriptional units of clustered genes,representing over 10%of human genes.Our previous studies have shown that vertebrate DPGs are highly conserved compared to those fro...Divergently-paired genes(DPGs)are minimal co-transcriptional units of clustered genes,representing over 10%of human genes.Our previous studies have shown that vertebrate DPGs are highly conserved compared to those from invertebrates.Three critical questions remain:(1)which DPGs are conserved across vertebrates,especially among mammals and primates?(2)to what extent and precision do these paired promoters share their sequences mechanistically and stringently?and(3)how are human DPGs distributed over selected primate lineages,and what are their possible biological functional consequences?There are 1399 human DPGs(approximately 12%of all human protein-coding genes),of which 1136,1118,925,and 830 human DPGs show conservation when compared to selected primates,mammals,avians,and fish,respectively.DPGs are not only functionally enriched toward direct protein–DNA interactions and cell cycle synchronization,but also exhibit lineage association,narrow in principle toward synchronization of certain core molecular mechanisms and cellular processes.Second,the inter-transcription start site(inter-TSS)distances affect both co-expression strength and disparity between the two genes of a DPG.Finally,among primates,human-associated DPGs exhibit diversification in their co-expression patterns and gene duplication events,and are obviously involved in neural development.Comparing high-quality human reference genomes from European(T2T-CHM13)and Chinese(T2T-YAO)populations,we identified 55 and 357 DPGs unique to the former and the latter,respectively.Our findings offer novel insights into the regulatory characteristics between neighboring genes and their structure–function selection among functionally conserved gene clusters.展开更多
As explored by biologists, there is a real and emerging need to identify co-regulated gene clusters, which include both positive and negative regulated gene clusters. However, the existing pattern-based and tendency-b...As explored by biologists, there is a real and emerging need to identify co-regulated gene clusters, which include both positive and negative regulated gene clusters. However, the existing pattern-based and tendency-based clustering approaches are only designed for finding positive regulated gene clusters. In this paper, a new subspace clustering model called g-Cluster is proposed for gene expression data. The proposed model has the following advantages： 1） find both positive and negative co-regulated genes in a shot, 2） get away from the restriction of magnitude transformation relationship among co-regulated genes, and 3） guarantee quality of clusters and significance of regulations using a novel similarity measurement gCode and a user-specified regulation threshold δ, respectively. No previous work measures up to the task which has been set. Moreover, MDL technique is introduced to avoid insignificant g-Clusters generated. A tree structure, namely GS-tree, is also designed, and two algorithms combined with efficient pruning and optimization strategies to identify all qualified g-Clusters. Extensive experiments are conducted on real and synthetic datasets. The experimental results show that 1） the algorithm is able to find an amount of co-regulated gene clusters missed by previous models, which are potentially of high biological significance, and 2） the algorithms are effective and efficient, and outperform the existing approaches.展开更多
Our goal is to decipher which DNA sequences are required for tissue-specific expression of epididymal genes. At least 6 epididymis-specific lipocalin genes are known. These are differently regulated and regionalized i...Our goal is to decipher which DNA sequences are required for tissue-specific expression of epididymal genes. At least 6 epididymis-specific lipocalin genes are known. These are differently regulated and regionalized in the epididymis. Lipocalin 5 （Lcn5 or mE-RABP） and Lipocalin 8 （Lcn8 or mEP17） are homologous genes belonging to the epididymis-specific lipocalin gene cluster. Both the 5 kb promoter fragment of the Lcn5 gene and the 5.3 kb promoter fragment of the Lcn8 gene can direct transgene expression in the epididymis （Lcn5 to the distal caput and Lcn8 to the initial segment）, indicating that these promoter fragments contain important cis-regulatory element（s） for epididymisspecific gene expression. To define further the fragments regulating gene expression, the Lcn5 promoter was examined in transgenic mice and immortalized epididymal cell lines. After serial deletion, the 1.8 kb promoter fragment of the Lcn5 gene was sufficient for tissue-specific and region-specific gene expression in transgenic mice. Transient transfection analysis revealed that a transcription factor forkhead box A2 （Foxa2） interacts with androgen receptor and binds to the 100 bp fragment of the Lcn5 promoter between 1.2 kb and 1.3 kb and that Foxa2 expression inhibits androgen-dependent induction of the Lcn5 promoter activity. Immunohistochemistry indicated a restricted expression of Foxa2 in the epididymis where endogenous Lcn5 gene expression is suppressed and that the Foxa2 inhibition of the Lcn5 promoter is consistent with the lack of expression of Lcn5 in the corpus and cauda. Our approach provides a basic strategy for further analysis of the epididymal lipocalin gene regulation and flexible control of epididymal function. （Asian J Androl 2007 July; 9： 515-521）展开更多
BACKGROUND Statistics indicate that the incidence of Crohn’s disease(CD)is rising in many countries.The poor understanding on the pathological mechanism has limited the development of effective therapy against this d...BACKGROUND Statistics indicate that the incidence of Crohn’s disease(CD)is rising in many countries.The poor understanding on the pathological mechanism has limited the development of effective therapy against this disease.Previous studies showed that long noncoding RNAs(lncRNAs)could be involved in autoimmune diseases including CD,but the detailed molecular mechanisms remain unclear.AIM To identify the differentially expressed lncRNAs in the intestinal mucosa associated with CD,and to characterize their pathogenic role(s)and related mechanisms.METHODS The differential expression of lncRNAs was screened by high-throughput RNA sequencing,and the top candidate genes were validated in an expanded cohort by real-time PCR.The regulatory network was predicted by bioinformatic software and competitive endogenous RNA analysis,and was characterized in Caco-2 and HT-29 cell culture using methods of cell transfection,real-time PCR,Western blotting analysis,flow cytometry,and cell migration and invasion assays.Finally,these findings were confirmed in vivo using a CD animal model.RESULTS The 3'end of lncRNACNN3-206 and the 3’UTR of Caspase10 contain highaffinity miR212 binding sites.lncRNACNN3-206 expression was found to be significantly increased in intestinal lesions of CD patients.Activation of the lncRNACNN3-206-miR-212-Caspase10 regulatory network led to increased apoptosis,migration and invasion in intestinal epithelial cells.Knockdown of lncRNACNN3-206 expression alleviated intestinal mucosal inflammation and tissue damage in the CD mouse model.CONCLUSION lncRNACNN3-206 may play a key role in CD pathogenesis.lncRNACNN3-206 could be a therapeutic target for CD treatment.展开更多
Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under ...Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern geneediting platforms. In particular, clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.展开更多
The common approach to find co-regulated genes is to cluster genes based on gene expression. However, due to the limited information present in any dataset, genes in the same cluster might be co-expressed but not nece...The common approach to find co-regulated genes is to cluster genes based on gene expression. However, due to the limited information present in any dataset, genes in the same cluster might be co-expressed but not necessarily co-regulated. In this paper, we propose to integrate known transcription factor binding site information and gene expression data into a single clustering scheme. This scheme will find clusters of co-regulated genes that are not only expressed similarly under the measured conditions, but also share a regulatory structure that may explain their common regulation. We demonstrate the utility of this approach on a microarray dataset of yeast grown under different nutrient and oxygen limitations. Our integrated clustering method not only unravels many regulatory modules that are consistent with current biological knowledge, but also provides a more profound understanding of the underlying process. The added value of our approach, compared with the clustering solely based on gene expression, is its ability to uncover clusters of genes that are involved in more specific biological processes and are evidently regulated by a set of transcription factors.展开更多
禾谷镰刀菌复合种(Fusarium graminearum species complex,FGSC)引起的赤霉病是小麦生产上危害最为严重的病害之一。赤霉病除了造成减产外,感病籽粒中含有多种镰刀菌毒素,如单端孢霉烯族的呕吐毒素,可引起人畜中毒和重大疾病,给食品安...禾谷镰刀菌复合种(Fusarium graminearum species complex,FGSC)引起的赤霉病是小麦生产上危害最为严重的病害之一。赤霉病除了造成减产外,感病籽粒中含有多种镰刀菌毒素,如单端孢霉烯族的呕吐毒素,可引起人畜中毒和重大疾病,给食品安全构成严重威胁。过去20年,随着禾谷镰刀菌全基因组序列的公布和遗传转化体系的成熟,禾谷镰刀菌Fusarium graminearum的功能基因组学的研究取得了较大进展,单端孢霉烯族毒素的产生、调控机制及网络研究成为热点。本文综述国内外单端孢霉烯族毒素的生物合成和分子调控机制,包括合成基因簇及决定不同产毒化学型的基因、产毒调控元件、环境因子调控产毒的分子机制,可为小麦抗赤霉病的育种提供新思路,为新型药剂的研发提供分子靶标,为赤霉病的持续防控和毒素污染的有效治理提供理论依据。展开更多
基金supported by grants from the Technique Innovation Program of Hubei Province(No.2018ABA108)the National Pig Industry Technology System(No.CARS-35).
文摘Actinobacillus pleuropneumoniae(APP)is the major pathogen of porcine contagious pleuropneumoniae(PCP).The QseB/QseC two-component system(TCS)consists of the regulator QseB and the kinase QseC,which relates to quorum sensing(QS)and virulence in some bacteria.Here,we investigated the role of QseB/QseC in apf gene cluster(apfABCD)expression of APP.Our results have showed that QseB/QseC TCS can potentially regulate the expression of apf gene cluster.The△qseBC,△apfA,△apfB,△apfC and△apfD strains are more sensitive to acidic and osmotic stressful conditions,and exhibite lower biofilm formation ability than wild-type(WT)strain,whereas the complemented strains show similar phenotype to the wr strain.In additon,the mutants have defective antiphagocytosis,adhesion and invasion when they come into contact with the host cells.In experimental animal models of infection,mice infected with△qseBC,△apfA,△apfB,△apfC and △apfD strains showed lower mortality and bacterial loads in the lung and the blood than those infected with wr strain.In conclusion,our results suggest that QseB/QseC TCS contributes to stress resistance,biofilm formation,phagocytosis,adhesion,invasion and virulence by downregulating expression of apf gene cluster in A.pleuropneumoniae.
基金supported by the National Key R&D Program of China(Grant No.2023YFC2605700 to Wenming Zhao)the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDB38050300 to Wenming Zhao).
文摘Divergently-paired genes(DPGs)are minimal co-transcriptional units of clustered genes,representing over 10%of human genes.Our previous studies have shown that vertebrate DPGs are highly conserved compared to those from invertebrates.Three critical questions remain:(1)which DPGs are conserved across vertebrates,especially among mammals and primates?(2)to what extent and precision do these paired promoters share their sequences mechanistically and stringently?and(3)how are human DPGs distributed over selected primate lineages,and what are their possible biological functional consequences?There are 1399 human DPGs(approximately 12%of all human protein-coding genes),of which 1136,1118,925,and 830 human DPGs show conservation when compared to selected primates,mammals,avians,and fish,respectively.DPGs are not only functionally enriched toward direct protein–DNA interactions and cell cycle synchronization,but also exhibit lineage association,narrow in principle toward synchronization of certain core molecular mechanisms and cellular processes.Second,the inter-transcription start site(inter-TSS)distances affect both co-expression strength and disparity between the two genes of a DPG.Finally,among primates,human-associated DPGs exhibit diversification in their co-expression patterns and gene duplication events,and are obviously involved in neural development.Comparing high-quality human reference genomes from European(T2T-CHM13)and Chinese(T2T-YAO)populations,we identified 55 and 357 DPGs unique to the former and the latter,respectively.Our findings offer novel insights into the regulatory characteristics between neighboring genes and their structure–function selection among functionally conserved gene clusters.
基金This work is supported by the National Grand Fundamental Research 973 Program of China （Grant No. 2006CB303103） and the National Natural Science Foundation of China under Grants No. 60573089, No. 60273079 and No. 60473074.
文摘As explored by biologists, there is a real and emerging need to identify co-regulated gene clusters, which include both positive and negative regulated gene clusters. However, the existing pattern-based and tendency-based clustering approaches are only designed for finding positive regulated gene clusters. In this paper, a new subspace clustering model called g-Cluster is proposed for gene expression data. The proposed model has the following advantages： 1） find both positive and negative co-regulated genes in a shot, 2） get away from the restriction of magnitude transformation relationship among co-regulated genes, and 3） guarantee quality of clusters and significance of regulations using a novel similarity measurement gCode and a user-specified regulation threshold δ, respectively. No previous work measures up to the task which has been set. Moreover, MDL technique is introduced to avoid insignificant g-Clusters generated. A tree structure, namely GS-tree, is also designed, and two algorithms combined with efficient pruning and optimization strategies to identify all qualified g-Clusters. Extensive experiments are conducted on real and synthetic datasets. The experimental results show that 1） the algorithm is able to find an amount of co-regulated gene clusters missed by previous models, which are potentially of high biological significance, and 2） the algorithms are effective and efficient, and outperform the existing approaches.
文摘Our goal is to decipher which DNA sequences are required for tissue-specific expression of epididymal genes. At least 6 epididymis-specific lipocalin genes are known. These are differently regulated and regionalized in the epididymis. Lipocalin 5 （Lcn5 or mE-RABP） and Lipocalin 8 （Lcn8 or mEP17） are homologous genes belonging to the epididymis-specific lipocalin gene cluster. Both the 5 kb promoter fragment of the Lcn5 gene and the 5.3 kb promoter fragment of the Lcn8 gene can direct transgene expression in the epididymis （Lcn5 to the distal caput and Lcn8 to the initial segment）, indicating that these promoter fragments contain important cis-regulatory element（s） for epididymisspecific gene expression. To define further the fragments regulating gene expression, the Lcn5 promoter was examined in transgenic mice and immortalized epididymal cell lines. After serial deletion, the 1.8 kb promoter fragment of the Lcn5 gene was sufficient for tissue-specific and region-specific gene expression in transgenic mice. Transient transfection analysis revealed that a transcription factor forkhead box A2 （Foxa2） interacts with androgen receptor and binds to the 100 bp fragment of the Lcn5 promoter between 1.2 kb and 1.3 kb and that Foxa2 expression inhibits androgen-dependent induction of the Lcn5 promoter activity. Immunohistochemistry indicated a restricted expression of Foxa2 in the epididymis where endogenous Lcn5 gene expression is suppressed and that the Foxa2 inhibition of the Lcn5 promoter is consistent with the lack of expression of Lcn5 in the corpus and cauda. Our approach provides a basic strategy for further analysis of the epididymal lipocalin gene regulation and flexible control of epididymal function. （Asian J Androl 2007 July; 9： 515-521）
基金Supported by Postgraduate Research and Practice Innovation Program of Jiangsu Province,No.KYCX18_0174
文摘BACKGROUND Statistics indicate that the incidence of Crohn’s disease(CD)is rising in many countries.The poor understanding on the pathological mechanism has limited the development of effective therapy against this disease.Previous studies showed that long noncoding RNAs(lncRNAs)could be involved in autoimmune diseases including CD,but the detailed molecular mechanisms remain unclear.AIM To identify the differentially expressed lncRNAs in the intestinal mucosa associated with CD,and to characterize their pathogenic role(s)and related mechanisms.METHODS The differential expression of lncRNAs was screened by high-throughput RNA sequencing,and the top candidate genes were validated in an expanded cohort by real-time PCR.The regulatory network was predicted by bioinformatic software and competitive endogenous RNA analysis,and was characterized in Caco-2 and HT-29 cell culture using methods of cell transfection,real-time PCR,Western blotting analysis,flow cytometry,and cell migration and invasion assays.Finally,these findings were confirmed in vivo using a CD animal model.RESULTS The 3'end of lncRNACNN3-206 and the 3’UTR of Caspase10 contain highaffinity miR212 binding sites.lncRNACNN3-206 expression was found to be significantly increased in intestinal lesions of CD patients.Activation of the lncRNACNN3-206-miR-212-Caspase10 regulatory network led to increased apoptosis,migration and invasion in intestinal epithelial cells.Knockdown of lncRNACNN3-206 expression alleviated intestinal mucosal inflammation and tissue damage in the CD mouse model.CONCLUSION lncRNACNN3-206 may play a key role in CD pathogenesis.lncRNACNN3-206 could be a therapeutic target for CD treatment.
文摘Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern geneediting platforms. In particular, clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.
文摘The common approach to find co-regulated genes is to cluster genes based on gene expression. However, due to the limited information present in any dataset, genes in the same cluster might be co-expressed but not necessarily co-regulated. In this paper, we propose to integrate known transcription factor binding site information and gene expression data into a single clustering scheme. This scheme will find clusters of co-regulated genes that are not only expressed similarly under the measured conditions, but also share a regulatory structure that may explain their common regulation. We demonstrate the utility of this approach on a microarray dataset of yeast grown under different nutrient and oxygen limitations. Our integrated clustering method not only unravels many regulatory modules that are consistent with current biological knowledge, but also provides a more profound understanding of the underlying process. The added value of our approach, compared with the clustering solely based on gene expression, is its ability to uncover clusters of genes that are involved in more specific biological processes and are evidently regulated by a set of transcription factors.
文摘禾谷镰刀菌复合种(Fusarium graminearum species complex,FGSC)引起的赤霉病是小麦生产上危害最为严重的病害之一。赤霉病除了造成减产外,感病籽粒中含有多种镰刀菌毒素,如单端孢霉烯族的呕吐毒素,可引起人畜中毒和重大疾病,给食品安全构成严重威胁。过去20年,随着禾谷镰刀菌全基因组序列的公布和遗传转化体系的成熟,禾谷镰刀菌Fusarium graminearum的功能基因组学的研究取得了较大进展,单端孢霉烯族毒素的产生、调控机制及网络研究成为热点。本文综述国内外单端孢霉烯族毒素的生物合成和分子调控机制,包括合成基因簇及决定不同产毒化学型的基因、产毒调控元件、环境因子调控产毒的分子机制,可为小麦抗赤霉病的育种提供新思路,为新型药剂的研发提供分子靶标,为赤霉病的持续防控和毒素污染的有效治理提供理论依据。
