Prediction of the Coding Sequences of Unidentified Human Genes. IV. The Coding Sequences of 40 New Genes (KIAA0121-KIAA0160) Deduced by Analysis of cDNA Clones from Human Cell Line KG-1

In this series of projects regarding the accumulation of sequenceinformation of unidentified human genes, we newly deduced thesequences of 40 full-length cDNA clones of human cell line KG-1,and predicted the coding sequences of the corresponding genes,named KIAA0121 to 0160. The results of a computer search ofpublic databases indicated that the sequences of 13 genes wereunrelated to any reported genes, while the remaining 27 genescarried sequences which showed some similarities to known genes.Obvious unique sequences noted were as follows. A stretch oftriplet repeats was contained in each of three genes: Thesewere GAG(Glu) in KIAA0122 and KIAA0147, and TCC(Ser) in KIAA0150.A stretch of 10 amino acidresidues was repeated 21 times inKIAA0139, and a homologous sequence of 76–78 nucleotideswas found repeated 6 times in the untranslated region of KIAA0125.northern hybridization analysis demonstrated that 13 genes wereexpressed in a cell- or tissue-specific manner. Although a vastnumber of expressed sequence tags (ESTs) have been registeredfor comprehensive analysis of cDNA clones, our sequence dataindicated that their distribution is very unbalanced: e.g. whileno EST hit 7 genes, 85 ESTs fell in a single gene.     

Prediction of the Coding Sequences of Unidentified Human Genes. III. The Coding Sequences of 40 New Genes (KIAA0081-KIAA0120) Deduced by Analysis of cDNA Clones from Human Cell Line KG-1

We isolated full-length cDNA clones from size-fractionated cDNAlibraries of human immature myeloid cell line KG-1, and thecoding sequences of 40 genes were newly predicted. A computersearch of the GenBank/EMBL databases indicated that the sequencesof 14 genes were unrelated to any reported genes, while theremaining 26 genes carried some sequences with similaritiesto known genes. Significant transmembrane domains were identifiedin 17 genes, and protein motifs that matched those in the PROSITEmotif database were identified in 11 genes. Northern hybridizationanalysis with 18 different cells and tissues demonstrated that10 genes were apparently expressed in a cell-specific or tissue-specificmanner. Among the genes predicted, half were isolated from themedium-sized cDNA library and the other half from the small-sizedcDNA library, and their average sizes were 4 kb and 1.4 kb,respectively. As judged by Northern hybridization profiles,small-sized cDNAs appeared to be expressed more ubiquitouslyand abundantly in various tissues, compared with that of medium-sizedcDNAs.     

鳜鱼胰蛋白酶和淀粉酶与胃蛋白酶原基因的克隆与序列分析

采用RT-PCR及RACE法,克隆得到鳜鱼(Siniperca chuatsi)肝胰脏胰蛋白酶(trypsin, Try)、淀粉酶(amylase, Amy)基因 cDNA全序列.结果表明,鳜鱼Try基因cDNA全长为896 bp,其中开放阅读框 (open reading frame,ORF)为744 bp,编码247个氨基酸. 序列同源性分析发现,鳜鱼Try与 斑马鱼(Danio rerio)、非洲爪蟾(Xenopus laevis)、 小鼠Try和人TRY氨基酸序列同源性分别为81.4%、75.3%、74.5%和71.4%.鳜鱼Amy 基因cDNA全长为1 647 bp,其中ORF为1 539 bp,编码512个氨基酸.鳜鱼Amy与斑马鱼 、非洲爪蟾、小鼠Amy和人AMY氨基酸序列同源性分别为79.7%、75.4%、71.9%和70.9%. 同时对鳜鱼基因组进行PCR,获得鳜鱼Try、Amy与胃蛋白酶原(pepsinogen, Pep)全基因组DNA序列.序列分析表明,鳜鱼Try基因由4个内含子和5个外显子组成,全长1 362 bp;鳜鱼Amy基因由8个内含子和9个外显子组成,全长4 267 bp;鳜鱼Pep基因由8个内含子和9个外显子组成,全长 4 032 bp,与其它脊椎动物基因结构相似.应用Genome walker方法在鳜鱼克隆得到长度分别为1 189 bp、413 bp和527 bp的Try、Amy和Pep基因的5′侧翼区序列以及1段长为704 bp的Pep 基因3′侧翼区序列,并利用相关软件预测其中具有多个可调节其表达的调控元件.鳜鱼Try、Am y和Pep基因组全序列的克隆及其序列、结构分析和分子系统进化等的研究,为鱼类消化代谢相关基因的生理功能及表达调控机理进一步研究提供依据.     

Sequences and Evolution of Human and Squirrel Monkey Blue Opsin Genes

The sequences of the entire blue opsin gene in the squirrel monkey (Saimiri boliviensis) and the five introns of the human blue opsin gene were obtained. Intron 3 of these genes contains an Alu sequence and intron 4 contains a partial mer13 sequence. A comparison of the squirrel monkey opsin sequence with published mammalian opsin sequences shows that features believed to be functionally critical are all conserved. However, the blue opsin has evolved twice as fast as rhodopsin and is only as conservative as the β globin, which has evolved at the average rate of mammalian proteins. Interestingly, the interhelical loops are, on average, actually more conservative than the transmembrane α helical regions. The introns of the blue opsin gene have evolved at the average rate of introns in primate genes. Received: 5 August 1996 / Accepted: 2 October 1996     

Isolation of Expressed Sequences Encoded by the Human Xq Terminal Portion Using Microclone Probes Generated by Laser Microdissection

The genes that cause a variety of neurologic and neuromuscular disorders have been mapped to the distal region of Xq. In an effort to isolate genes from this area, a regional genomic library of the distal 30% of Xq was constructed from a single metaphase spread by means of laser microdissection and single unique primer-polymerase chain reaction. Using pooled probes of 1000 clones from the genomic library, human brain cDNA libraries were screened for expressed sequences encoded by this region. From the 250,000 cDNA clones screened so far, 10 nonoverlapping sequences that mapped back to the target portion were isolated. The complete nucleotide sequences of these cDNA clones have been determined. Analysis of the sequences indicates that none has significant similarity to previously characterized primate genes. One sequence mapping to Xq27.3-qter contained an open reading frame of 281 amino acids and was expressed in every tissue tested. This gene, as well as others isolated in this manner, may prove to be a candidate gene for heritable disorders mapping to this region.     

Clustered Genes Require Extragenic Territorial DNA Sequences

This paper is concerned with the basic question as to whether there exists a complex interaction between DNA sequences which have little specific function and functional genes regarding the spatial arrangement of the gene. Since gene clusters are a characteristic and basic feature of gene structure in higher eukaryotes, the size of extragenic DNA sequences surrounding the individual genes of various clustered gene families were compared. The size of the intergenic region, which is composed of the extragenic DNA sequences flanking the 3'-end of one gene and those flanking the 5'-end of the other gene, of the paired genes increases as the genes becomes larger. However, such a gene size-dependent increase is not seen if the total gene size of the paired genes is less than 0.3 kb or greater than 4 kb. The results suggests that a higher eukaryote gene requires extragenic territorial DNA sequences surrounding it, which presumably are necessary to maintain the gene's active functions.     

Expressed sequence tags of Chinese cabbage flower bud cDNA.

We randomly selected and partially sequenced cDNA clones from a library of Chinese cabbage (Brassica campestris L. ssp. pekinensis) flower bud cDNAs. Out of 1216 expressed sequence tags (ESTs), 904 cDNA clones were unique or nonredundant. Five hundred eighty-eight clones (48.4%) had sequence homology to functionally defined genes at the peptide level. Only 5 clones encoded known flower-specific proteins. Among the cDNAs with no similarity to known protein sequences (628), 184 clones had significant similarity to nucleotide sequences registered in the databases. Among these 184 clones, 142 exhibited similarities at the nucleotide level only with plant ESTs. Also, sequence similarities were evident between these 142 ESTs and their matching ESTs when compared using the deduced amino acid sequences. Therefore, it is possible that the anonymous ESTs encode plant-specific ubiquitous proteins. Our extensive EST analysis of genes expressed in floral organs not only contributes to the understanding of the dynamics of genome expression patterns in floral organs but also adds data to the repertoire of all genomic genes.     

cDNA表达文库转染NIH3T3-从高转移人肺腺癌细胞系Anip973中克隆新肿瘤转移相关基因

培养人高转移肺腺癌细胞系Anip973,构建其cDNA表达文库并转染小鼠成纤维细胞NIH3T3,将经药物筛选后的转染细胞克隆消化为单细胞,接种到软琼脂中培养2周,根据细胞明显的形态学变化挑选出有意义的细胞克隆,扩增再培养,提取DNA,PCR扩增插入片段并进行测序分析。结果表明:软琼脂中挑选出克隆100多个,PCR测序后,得到3个已知基因包括人类核糖体蛋白L23、人类假定蛋白FLJ22104和人类丝氨酸蛋白酶抑制因子6亚型以及一些氨基末端截短的核酸序列。进一步的研究表明转染人类核糖体蛋白L23的细胞与转染空载体细胞相比具有较高的侵袭能力(P<0.02)。利用cDNA文库在NIH3T3细胞中的表达,随后筛查鉴定在软琼脂中发生形态学变化的细胞,是一种寻找恶性转化和癌转移相关基因的有效方法。人类核糖体蛋白L23基因在细胞的运动和转移中发挥重要作用。     

四甲基氯化铵在PCR扩增小麦基因中的关键作用

利用高简并性引物,用PCR法从小麦DNA或cDNA中合成小麦几丁质酶基因、葡 聚糖酶基因和苯丙氨酸解氨酶基因片段。在PCR反应中添加四甲基氯化铵(TMACl)是合成这些特异基因片段的关键。合成的PCR片段都经末端补齐和磷酸化后用于克隆。核酸序列分析证实,这些PCR产物分别与用于设计PCR引物的基因具有高度的同源性。 Abstract:In the presence of tetramethy1 ammonium chloride(TMAC1),a chitinase gene sequence,a phenylalanine ammonia-lyase gene sequence and a glucanase cDNA sequence of wheat were amplified with highly degenerate primers by PCR.The inclusion of TMAC1 in the PCR reactions was essential for successful amplification of the desired sequences from genomic DNA or cDNA in wheat.The ends of the PCR fragments were made flush and phosphorylated prior to cloning.Sequence analyses of the above PCR fragments confirmed their identities,showing high sequence similarities to the genes used for the design of PCR primers.