目的:在中国人非综合征型唇裂伴或不伴腭裂(non-syndromic cleft lip with or without palate,NSCL/P)核心家系中,利用全外显子组测序探索与NSCL/P发病相关的新生突变位点。方法:对22个中国NSCL/P核心家系进行全外显子组测序,采用基因...目的:在中国人非综合征型唇裂伴或不伴腭裂(non-syndromic cleft lip with or without palate,NSCL/P)核心家系中,利用全外显子组测序探索与NSCL/P发病相关的新生突变位点。方法:对22个中国NSCL/P核心家系进行全外显子组测序,采用基因组分析工具包(Genome Analysis ToolKit,GATK)通过对比亲代与子代同一位点的等位基因识别新生突变位点,采用SnpEff软件对位点进行功能注释。对新生突变位点进行富集分析,检验全外显子区域内存在的新生突变数量是否高于预期值,以及是否存在包含新生突变数量显著高于预期值的基因。通过查阅文献总结既往研究提示与NSCL/P发病存在较强证据支持的基因,根据注释信息筛选能够引起蛋白质改变的新生突变位点,对该类位点所在基因编码的蛋白质与NSCL/P相关基因编码的蛋白质进行交互作用分析。利用R软件的denovolyzeR包进行富集分析(Bonferroni多重检验校正:P=0.05/n,n为基因个数)。利用STRING数据库预测新生突变所在基因与已知NSCL/P致病基因编码的蛋白质间的交互作用。结果:全外显子组测序得到的位点中共有339908个位点通过质量控制,经GATK软件比对共筛选出345个高置信度新生突变,其中错义突变44个,无义突变1个,经典剪接位点2个,同义突变20个,内含子区或基因间区位点278个。富集分析显示,全外显子组中引起蛋白质改变的新生突变数量显著高于预期值(P<0.05),KRTCAP2、HMCN2、ANKRD36C、ADGRL2和DIPK2A 5个基因所含的新生突变位点高于预期(P<0.05/(2×19618))。蛋白质交互作用分析纳入46个包含能够引起蛋白质序列改变的新生突变所在的基因及13个既往研究提示与NSCL/P存在关联的基因,两类基因编码的蛋白质之间存在6组交互作用,其中RGPD4与SUMO1编码的蛋白质的交互作用证据可信度最高,STRING数据库交互作用评分为0.868。结论:研究为NSCL/P的发病提供了新的证据,对携带新生突变的基因进行功能分析有助于揭示复杂疾病的遗传结构。展开更多
Protein-protein interactions （PPIs） are of vital importance for virtually all processes of a living cell. The study of these associations of protein molecules could improve people＇s understanding of diseases and pr...Protein-protein interactions （PPIs） are of vital importance for virtually all processes of a living cell. The study of these associations of protein molecules could improve people＇s understanding of diseases and provide basis for therapeutic approaches. Although efforts have been devoted to the development of methodology for predicting PPIs and protein interaction networks, the application of most existing methods is limited because they need information about protein homology or the interaction marks of the protein partners.展开更多
Interactions are the essence of all biomolecules because they cannot fulfill their roles without interacting with other molecules. Hence, mapping the interactions of biomolecules can be useful for understanding their ...Interactions are the essence of all biomolecules because they cannot fulfill their roles without interacting with other molecules. Hence, mapping the interactions of biomolecules can be useful for understanding their roles and functions. Furthermore, the development of molecular based systems biology requires an understanding of the biomolecular interactions. In recent years, the mapping of protein-protein interactions in different species has been reported, but few reports have focused on the large-scale mapping of protein-protein interactions in human. Here, we review the developments in protein interaction mapping and we discuss issues and strategies for the mapping of the human protein interactome.展开更多
AIM： To identify the proteins interacting with nucleostemin （NS）, thereby gaining an insight into the function of NS. METHODS： Yeast two-hybrid assay was performed to screen a human placenta cDNA library with the ...AIM： To identify the proteins interacting with nucleostemin （NS）, thereby gaining an insight into the function of NS. METHODS： Yeast two-hybrid assay was performed to screen a human placenta cDNA library with the full length of NS as a bait. X-Gal assay and β-galactosidase filter assay were subsequently conducted to check the positive clones and the gene was identified by DNA sequencing. To further confirm the interaction of two proteins, the DNA fragment coding NS and the DNA fragment isolated from the positive clone were inserted into the mammalian expression vector pcDNA3 and pcDNA3-myc, respectively. Then, two plasmids were cotransfected into the COS-7 cells by DEAE-dextron. The total protein from the cotransfected cells was extracted and coimmunoprecipitation and Western blot were performed with suitable antibodies sequentially. RESULTS： Two positive clones that interacted with NS were obtained from human placenta cDNA library. One was an alpha isoform of human protein phosphatase 2 regulatory subunit B （B56） （PPP2RSA） and the other was a novel gene being highly homologous to the gene associated with spondylo paralysis. The co-immunoprecipitation also showed that NS specifically interacted with PPP2R5A. CONCLUSION： NS and PPP2R5A interact in yeast and mammalian cells, respectively, which is helpful for addressing the function of NS in cancer development and progression.展开更多
Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However...Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However, it is difficult to find a study comparing the precision of the extracted pockets from known pockets on the protein. In this paper, we propose an algorithm for extracting pockets from structure data of proteins and analyze the quality of the algorithm by comparing the extracted pockets with some known pockets. These results in this paper can be used to set the parameter values of the pocket extraction algorithm for getting better results.展开更多
Using atom force microscopy (AFM), in vitro transcription, PAGE and other experimental technologies, it is observed that, in active genes of mice (Balb/c) nuclear DNA fragments of non-transcriptional state, only regul...Using atom force microscopy (AFM), in vitro transcription, PAGE and other experimental technologies, it is observed that, in active genes of mice (Balb/c) nuclear DNA fragments of non-transcriptional state, only regulation sequences at both ends are associated with scaffold proteins (indissociable proteins) and some transcriptional factors such as complexes (dissociable proteins) made of gene-coding proteins and specific auxiliary small molecules, while there are no combining proteins in intermediate coding sequences. However, in active genes of transcriptional state, both regulation sequences and intermediate coding sequences are associated with active transcriptional factors by non-covalent bonds.This paper shows the prospective application of AFM observation and in vitro transcription in the research on gene expression and regulation. It also offers some theoretical basis for localization of specific genes in human genomes.展开更多
Leptospira interrogans serovar Lai is a pathogenic bacterium that causes a spirochetal zoonosis in humans and some animals. With its complete genome sequence available, it is possible to analyze protein-protein intera...Leptospira interrogans serovar Lai is a pathogenic bacterium that causes a spirochetal zoonosis in humans and some animals. With its complete genome sequence available, it is possible to analyze protein-protein interactions from a whole- genome standpoint. Here we combine four recently developed computational approaches (gene fusion method, gene neighbor method, phylogenetic profiles method, and operon method) to predict protein-pro- tein interaction networks of Leptospira interrogans strain Lai. Through comprehensive analysis on in- teractions among proteins of motility and chemotaxis system, signal transduction, lipopolysaccaride bio- synthesis and a series of proteins related to adhesion and invasion, we provided information for further studying on its pathogenic mechanism. In addition, we also assigned 203 previously uncharacterized proteins with possible functions based on the known functions of its interacting partners. This work is helpful for further investigating L. interrogans strain Lai.展开更多
Protein-protein interactions(PPIs)play vital roles in biological processes.However,the discovery of transient and biologically relevant PPIs remain a formidable challenge using conventional strategies such as co-immun...Protein-protein interactions(PPIs)play vital roles in biological processes.However,the discovery of transient and biologically relevant PPIs remain a formidable challenge using conventional strategies such as co-immunoprecipitation(CoIP),yeast two hybrids(Y2H)and Forster resonance energy transfer(FRET)[1].Genetically encoded photocrosslinkers have recently emerged as a powerful approach for probing intracellular PPIs with the capability for in situ studies,low perturbation to cells as well as the wide generality.This facile strategy also demonstrated an advantage of high spatiotemporal resolution,which offers a robust capture strategy for the discovery of transient and/or weak PPIs with lowered false-positive backgrounds[2].展开更多
文摘目的:在中国人非综合征型唇裂伴或不伴腭裂(non-syndromic cleft lip with or without palate,NSCL/P)核心家系中,利用全外显子组测序探索与NSCL/P发病相关的新生突变位点。方法:对22个中国NSCL/P核心家系进行全外显子组测序,采用基因组分析工具包(Genome Analysis ToolKit,GATK)通过对比亲代与子代同一位点的等位基因识别新生突变位点,采用SnpEff软件对位点进行功能注释。对新生突变位点进行富集分析,检验全外显子区域内存在的新生突变数量是否高于预期值,以及是否存在包含新生突变数量显著高于预期值的基因。通过查阅文献总结既往研究提示与NSCL/P发病存在较强证据支持的基因,根据注释信息筛选能够引起蛋白质改变的新生突变位点,对该类位点所在基因编码的蛋白质与NSCL/P相关基因编码的蛋白质进行交互作用分析。利用R软件的denovolyzeR包进行富集分析(Bonferroni多重检验校正:P=0.05/n,n为基因个数)。利用STRING数据库预测新生突变所在基因与已知NSCL/P致病基因编码的蛋白质间的交互作用。结果:全外显子组测序得到的位点中共有339908个位点通过质量控制,经GATK软件比对共筛选出345个高置信度新生突变,其中错义突变44个,无义突变1个,经典剪接位点2个,同义突变20个,内含子区或基因间区位点278个。富集分析显示,全外显子组中引起蛋白质改变的新生突变数量显著高于预期值(P<0.05),KRTCAP2、HMCN2、ANKRD36C、ADGRL2和DIPK2A 5个基因所含的新生突变位点高于预期(P<0.05/(2×19618))。蛋白质交互作用分析纳入46个包含能够引起蛋白质序列改变的新生突变所在的基因及13个既往研究提示与NSCL/P存在关联的基因,两类基因编码的蛋白质之间存在6组交互作用,其中RGPD4与SUMO1编码的蛋白质的交互作用证据可信度最高,STRING数据库交互作用评分为0.868。结论:研究为NSCL/P的发病提供了新的证据,对携带新生突变的基因进行功能分析有助于揭示复杂疾病的遗传结构。
文摘Protein-protein interactions （PPIs） are of vital importance for virtually all processes of a living cell. The study of these associations of protein molecules could improve people＇s understanding of diseases and provide basis for therapeutic approaches. Although efforts have been devoted to the development of methodology for predicting PPIs and protein interaction networks, the application of most existing methods is limited because they need information about protein homology or the interaction marks of the protein partners.
文摘Interactions are the essence of all biomolecules because they cannot fulfill their roles without interacting with other molecules. Hence, mapping the interactions of biomolecules can be useful for understanding their roles and functions. Furthermore, the development of molecular based systems biology requires an understanding of the biomolecular interactions. In recent years, the mapping of protein-protein interactions in different species has been reported, but few reports have focused on the large-scale mapping of protein-protein interactions in human. Here, we review the developments in protein interaction mapping and we discuss issues and strategies for the mapping of the human protein interactome.
基金Supported by the National High Technology Research and Development Program of China, No. 200BA711A11A06Beijing Science and Technology Project, No. H020220020310
文摘AIM： To identify the proteins interacting with nucleostemin （NS）, thereby gaining an insight into the function of NS. METHODS： Yeast two-hybrid assay was performed to screen a human placenta cDNA library with the full length of NS as a bait. X-Gal assay and β-galactosidase filter assay were subsequently conducted to check the positive clones and the gene was identified by DNA sequencing. To further confirm the interaction of two proteins, the DNA fragment coding NS and the DNA fragment isolated from the positive clone were inserted into the mammalian expression vector pcDNA3 and pcDNA3-myc, respectively. Then, two plasmids were cotransfected into the COS-7 cells by DEAE-dextron. The total protein from the cotransfected cells was extracted and coimmunoprecipitation and Western blot were performed with suitable antibodies sequentially. RESULTS： Two positive clones that interacted with NS were obtained from human placenta cDNA library. One was an alpha isoform of human protein phosphatase 2 regulatory subunit B （B56） （PPP2RSA） and the other was a novel gene being highly homologous to the gene associated with spondylo paralysis. The co-immunoprecipitation also showed that NS specifically interacted with PPP2R5A. CONCLUSION： NS and PPP2R5A interact in yeast and mammalian cells, respectively, which is helpful for addressing the function of NS in cancer development and progression.
基金Project supported by Creative Research Initiative from the Ministry of Science and Technology (MOST), Korea. BHAK Jonghwa is supported by Biogreen21 Fund and MOST Funds, Korea
文摘Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However, it is difficult to find a study comparing the precision of the extracted pockets from known pockets on the protein. In this paper, we propose an algorithm for extracting pockets from structure data of proteins and analyze the quality of the algorithm by comparing the extracted pockets with some known pockets. These results in this paper can be used to set the parameter values of the pocket extraction algorithm for getting better results.
文摘Using atom force microscopy (AFM), in vitro transcription, PAGE and other experimental technologies, it is observed that, in active genes of mice (Balb/c) nuclear DNA fragments of non-transcriptional state, only regulation sequences at both ends are associated with scaffold proteins (indissociable proteins) and some transcriptional factors such as complexes (dissociable proteins) made of gene-coding proteins and specific auxiliary small molecules, while there are no combining proteins in intermediate coding sequences. However, in active genes of transcriptional state, both regulation sequences and intermediate coding sequences are associated with active transcriptional factors by non-covalent bonds.This paper shows the prospective application of AFM observation and in vitro transcription in the research on gene expression and regulation. It also offers some theoretical basis for localization of specific genes in human genomes.
文摘目的本研究旨在探究差异表达基因(Differentially expressed genes,DEG),然后鉴别出急性心肌梗死(Acute myocardial infarction,AMI)关键基因,由此筛查出可用于这种研究早期诊断的心脏疾病潜在生物标记物。方法 AMI患者(GSE19339)的基因表达数据下载自基因表达汇编数据库。采用affy程序包预处理后,在samar程序包内通过微阵列显著性分析(Significance analysis of mycroarray,SAM)算法筛选DEG。然后使用DAVID(注释可视化和整合发现数据库软件,database for annotation visualization and integrated discovery software)在线工具进行DEG功能和通路富集分析。进而采用GENET-IC_ASSOCIATION_DB_DISEASE分析和blastp比对算法筛选出AMI的相关基因。最后,将这些新基因用于转录因子和蛋白-蛋白相互作用网络分析。结果在AMI患者与正常对照样本间共筛选出633个DEG,包括378个上调DEG和255个下调DEG。在AMI中发现了一种显著差异表达的新基因LCK(淋巴细胞特异性蛋白酪氨酸激酶,lymphocytespecific protein tyrosine kinase)。进一步分析显示LCK参与CXCL12(趋化因子(C-X-C基序)配体12,chemokine(C-X-Cmotif)ligand12)的表达调节,而LCK的表达则由不同的转录因子进行调节。结论这项研究中,我们对AMI的发病机制提出了新见解,并提出LCK是这种严重心脏疾病的一个引人注目的候选标记物。
文摘Leptospira interrogans serovar Lai is a pathogenic bacterium that causes a spirochetal zoonosis in humans and some animals. With its complete genome sequence available, it is possible to analyze protein-protein interactions from a whole- genome standpoint. Here we combine four recently developed computational approaches (gene fusion method, gene neighbor method, phylogenetic profiles method, and operon method) to predict protein-pro- tein interaction networks of Leptospira interrogans strain Lai. Through comprehensive analysis on in- teractions among proteins of motility and chemotaxis system, signal transduction, lipopolysaccaride bio- synthesis and a series of proteins related to adhesion and invasion, we provided information for further studying on its pathogenic mechanism. In addition, we also assigned 203 previously uncharacterized proteins with possible functions based on the known functions of its interacting partners. This work is helpful for further investigating L. interrogans strain Lai.
基金supported by the National Key Research and Development Program(2016YFA0501500)the National Natural Science Foundation of China(21225206,21432002,21521003)
文摘Protein-protein interactions(PPIs)play vital roles in biological processes.However,the discovery of transient and biologically relevant PPIs remain a formidable challenge using conventional strategies such as co-immunoprecipitation(CoIP),yeast two hybrids(Y2H)and Forster resonance energy transfer(FRET)[1].Genetically encoded photocrosslinkers have recently emerged as a powerful approach for probing intracellular PPIs with the capability for in situ studies,low perturbation to cells as well as the wide generality.This facile strategy also demonstrated an advantage of high spatiotemporal resolution,which offers a robust capture strategy for the discovery of transient and/or weak PPIs with lowered false-positive backgrounds[2].
