小鼠新基因Ayu17-449的克隆及表达分析

在利用PU8捕获载体从小鼠ES细胞中寻找有关对发育起重要作用基因时,一阳性ES克隆编号为Ayu17-449被捕获,经过Southern blotting法证实捕获载体单一整合在Ayu17-449号ES细胞的基因组中。通过用5＇RACE法得到所捕获基因的一小段cDNA,在EST数据库中比对,得到一5523bp cDNA序列,在Celera数据库中它包含于两个相邻基因,根据这两个基因的mRNA设立了一系列的引物进行RT-PCR和测序,用这两个基因的不同片段分别作探针进行Northern blotting分析,确定这是一个RNA约9kb并编码1920个氨基酸的新基因（定名为Ayu17-449基因,其cDNA序列和编码蛋白序列发表在NCBI数据库,编号为DQ079067）。Northern blotting揭示Ayu17-449基因高度表达在小鼠的脑、肾脏、心脏、肺、肌肉和胃等组织。PU8捕获载体具有X-gal报告基因,能从蛋白表达水平揭示它所捕获的基因的表达模式。X-gal染色结果显示,Ayu17-449蛋白高度表达在小鼠的脑、肾脏、心脏等组织,与Northern blotting法的结果高度一致。X-gal染色切片结果进一步证明Ayu17-449蛋白主要表达在脑的神经细胞和肾脏近曲小管细胞中。Ayu17-449基因的编码蛋白在数据库（Scansite,http：//scansite．mit．edu/）做功能基团分析后,揭示其编码蛋白的N末端含有Granin基团,大量文献证实Granin基团具有参与激素的分泌的功能,显示Ayu17-449基因可能与激素的分泌有关。     

用基因诱捕法制作Ayu17-449基因敲除小鼠模型

为了探明Ayu17-449基因在小鼠生长发育过程中的功能, 用特殊的诱捕载体（Gene trapping vector）导入小鼠ES细胞中,5′RACE、Southern blot方法鉴定成功地单一捕获Ayu17-449基因后,由这种ES制作了Ayu17-449 敲除小鼠并用Northern blot方法该基因在突变小鼠体内的表达。结果在Ayu17-449 敲除小鼠体内,诱捕载体位于Ayu17-449基因的翻译起始密码上游,Ayu17-449基因的转录被抑制。表明Ayu17-449敲除小鼠为分析Ayu17-449基因的功能提供了可靠的实验材料。      

Database for exchangeable gene trap clones: Pathway and gene ontology analysis of exchangeable gene trap clone mouse lines

Gene trapping in embryonic stem (ES) cells is a proven method for large‐scale random insertional mutagenesis in the mouse genome. We have established an exchangeable gene trap system, in which a reporter gene can be exchanged for any other DNA of interest through Cre/mutant lox‐mediated recombination. We isolated trap clones, analyzed trapped genes, and constructed the database for Exchangeable Gene Trap Clones (EGTC) [ http://egtc.jp ]. The number of registered ES cell lines was 1162 on 31 August 2013. We also established 454 mouse lines from trap ES clones and deposited them in the mouse embryo bank at the Center for Animal Resources and Development, Kumamoto University, Japan. The EGTC database is the most extensive academic resource for gene‐trap mouse lines. Because we used a promoter‐trap strategy, all trapped genes were expressed in ES cells. To understand the general characteristics of the trapped genes in the EGTC library, we used Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathway analysis and found that the EGTC ES clones covered a broad range of pathways. We also used Gene Ontology (GO) classification data provided by Mouse Genome Informatics (MGI) to compare the functional distribution of genes in each GO term between trapped genes in the EGTC mouse lines and total genes annotated in MGI. We found the functional distributions for the trapped genes in the EGTC mouse lines and for the RefSeq genes for the whole mouse genome were similar, indicating that the EGTC mouse lines had trapped a wide range of mouse genes.     

新基因水稻 OsLSD1 的克隆及拟南芥和水稻类 LSD1 基因家族的生物信息学分析

类 LSD1 (LSD1-like) 基因家族是一类特殊的 C2C2 型锌指蛋白基因,编码植物特有的转录因子 . 目前已经研究的 2 个成员拟南芥 LSD1 (lesions stimulating disease resistance 1) 和 LOL1 (LSD-One-Like 1) 基因均参与植物细胞程序化死亡 (programmed cell death, PCD) 的调控 . 从水稻 cDNA 文库中克隆到 1 个类 LSD1 基因,命名为 OsLSD1. 该基因长 988 bp ,包含一个 432 bp 的开放阅读框,推导的氨基酸序列 (143 个氨基酸 ) 含有 3 个内部保守的锌指结构域 . DNA 印迹结果表明 OsLSD1 基因在水稻基因组中为单拷贝,且在根、茎和叶中表达 . 借助于生物信息学分析技术,从拟南芥和水稻数据库中各识别出 5 个和 7 个 ( 包括 OsLSD1) 类 LSD1 基因 . 分析了这些类 LSD1 基因的结构,蛋白质结构域组成 . 系统进化分析表明,无论基于编码区的核苷酸或氨基酸序列都可以将这些类 LSD1 基因分为 2 类 . 虽然不存在拟南芥或水稻特有的类 LSD1 蛋白,但有些结构域是水稻所特有的,也有些基因是来源于复制事件 .     

表达序列标签数据库搜索鉴定小鼠UBAP1基因及其数字化表达分析

UBAP1(ubiquitin associated protein 1)基因是最近克隆的一个定位于人类染色体9p21-22鼻咽癌杂合性丢失高频区的泛肽相关蛋白家族新成员.为了深入研究UBAP1基因的功能,利用计算机对表达序列标签(expressed sequence tag, EST)、UniGene等数据库进行综合搜索分析,结合cDNA克隆测序的方法, 成功地获得了UBAP1基因在小鼠中的同源基因.小鼠UBAP1基因cDNA全长为2 676 bp,编码一个由441个氨基酸组成的蛋白质,在其蛋白质C端只有一个泛肽相关功能域（UBA domain）.与人UBAP1基因相比,两者编码的氨基酸序列有89%相同.基于EST的数字化表达分析显示UBAP1基因在小鼠正常组织中广泛高表达.     

Characterization of Ayu17-449 gene expression and resultant kidney pathology in a knockout mouse model

The gene trap technique is a powerful approach for characterizing and mutating genes in the mouse. We used this method to identify a mouse gene of unknown function and to establish a mutant mouse line. We subsequently identified one gene, denoted Ayu17-449, on mouse chromosome 3 that comprised 14 exons encoding 1920 amino acids with a granin motif in its N-terminal sequence. In adult mice, this gene was highly expressed in the brain, heart, lung, muscle, stomach, and kidney. The insertion of a trap vector into the second intron of this gene resulted in the null mutation. Homozygous mice for these mutation died by 1 day after birth. Mutant mice showed a loss of acidic granules in the proximal convoluted tubules of the kidney. Our data demonstrates that Ayu17-449 is important for mouse survival.     

蜻蜓凤梨花发育相关B类MADS-box基因克隆及表达分析

为探索MADS-box基因在凤梨花发育过程中的调控机制,通过设计简并引物,利用RACE技术,从蜻蜓凤梨花蕾中分离得到2个花发育相关B类MADS-box基因,分别命名为AfAP3和AfPI;AfAP3cDNA全长957bp,编码区编码226个氨基酸;AfPI cDNA全长808bp,编码区编码198个氨基酸,二者均具有典型的植物MADS-box蛋白结构.RT-PCR分析结果表明,AfAP3和AfPI基因主要在花器官中表达,在根系中也有微量表达;乙烯诱导后7d,AfPI基因在茎尖处开始有表达,表明此时蜻蜓凤梨花芽分化可能已经完成,AfAP3基因表达晚于AfPI.     

小鼠植入前胚胎紧密化相关基因Crg1的克隆

从已获得的运用抑制消减杂交技术(Suppression Subtractive Hybridization,SSH)分离、克隆和筛选代表8-细胞早期胚胎和紧密化8-细胞胚胎差别表达基因的ESTs片段(GenBank登录号：BQ740263、BQ740251)入手,经比较二者的同源性发现这两个EST末端反向互补,拼接成一个cDNA片段,经分析此序列包含一个完整的阅读框,提交给GenBank,登录号为AY134859。根据此序列设计引物从小鼠8-细胞紧密化胚胎cDNA中经PCR扩增出目的片段,克隆入pUCm—T载体后测序而获得全长cDNA,为小鼠植入前胚胎紧密化相关基因Crg1,分析比较证明Crg1基因与AY134859基本吻合。Crg1基因的cDNA全长为810bp,只有一个外显子,编码由150个氨基酸组成,分子量理论值为17．67kD的蛋白质。与最新的小鼠基因组工作草图进行电子杂交,该基因被定位在小鼠的14号染色体上。RT—PCR实验证明在小鼠植入前各个时期的胚胎、小鼠胚胎干细胞中均有表达,在小鼠胚胎成纤维细胞中没有表达。半定量RT—PCR实验证明Crg1基因在紧密化胚胎中表达较8—细胞胚胎高。采用Northern—blot手段分析Crg1基因在成年小鼠的8种组织中的表达情况,结果表明该基因只在小鼠卵巢中有微弱的表达,转录本大小为1．2kh,而在成年小鼠的脑、心脏、肾、睾丸、肝脏、肺、脾等中没有表达。研究表明,Crg1基因可能与小鼠胚胎紧密化及保持细胞的全能性相关。     

睾丸生精细胞凋亡相关基因TSARG1与Mtsarg1的分子克隆及Mtsarg1基因的表达谱分析

从已获得的在隐睾和正常睾丸对照中表达量有明显差异的EST片段（GenBank登录号：BE644538）出发,利用生物信息学和实验技术,克隆了小鼠睾丸生精细胞凋亡相关新基因Mtsarg1及相应的人类新基因TSARG1,Gen-Bank登录号分别为AF399971和AY032925。小鼠Mtsargl与人类TSARGl基因在氨基酸水平有55％的一致性和61％相似性,与其他已知蛋白质无明显同源性。小鼠10种组织的RT-PCR分析结果表明,Mtsargl基因在睾丸中高表达,在附睾中呈微弱表达,在其他组织不表达,提示Mtsargl和TSARGl基因在生精细胞凋亡或精子发生中具有潜在的重要作用。     

A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins II: public release of inaugural version of InGaP database containing gene/protein expression profiles for 127 mouse KIAA genes/proteins.

The inaugural version of the InGaP database (Integrative Gene and Protein expression database; http://www.kazusa.or.jp/ingap/index.html) is a comprehensive database of gene/protein expression profiles of 127 mKIAA genes/proteins related to hypothetical ones obtained in our ongoing cDNA project. Information about each gene/protein consists of cDNA microarray analysis, subcellular localization of the ectopically expressed gene, and experimental data using anti-mKIAA antibody such as Western blotting and immunohistochemical analyses. KIAA cDNAs and their mouse counterparts, mKIAA cDNAs, were mainly isolated from cDNA libraries derived from brain tissues, thus we expect our database to contribute to the field of neuroscience. In fact, cDNA microarray analysis revealed that nearly half of our gene collection is predominantly expressed in brain tissues. Immunohistochemical analysis of the mouse brain provides functional insight into the specific area and/or cell type of the brain. This database will be a resource for the neuroscience community by seamlessly integrating the genomic and proteomic information about the mouse KIAA genes/proteins.