进化上保守的小鼠FLANa基因的计算机克隆

EST(expressed sequence tag,表达序列标签)是对cDNA克隆进行测序时得到的序列,一般位于该克隆的一端,序列为单次测序所得到的。现在EST已成为一个非常大的数据库,并被广泛运用于基因家族新成员的寻找,也可作为人染色体上的标志来寻找多态性位点,还可以用来比较某基因在不同组织和病理状态中的表达模式。在EST数据库中,     

Cloning and characterization of F-LANa, upregulated in human liver cancer

Differentially expressed genes between normal liver and hepatocellular carcinomas were investigated using differential display. Consequently, we identified a fragment cDNA upregulated in tumor tissues. We screened the liver library and cloned the full-length cDNA, named F-LANa. Increased expression of F-LANa was confirmed by Northern blot analysis in 10 of 14 (71%) cases of hepatocellular carcinomas. Human F-LANa gene maps to chromosome 17p at D17S1828-D17S786, spans at least 11.8 kb, and contains 7 exons. This gene encodes a 239 aa protein exhibiting 97.9% similarity to the mouse ortholog gene, identified later by in silico cloning. Homology analysis was carried out in various species and showed that F-LANa was evolutionarily conserved from yeast to human. In addition, F-LANa antisense oligonucleotide suppressed F-LANa expression in human hepatocellular carcinoma BEL-7404 cells and significantly inhibited cell growth. Together, our data demonstrate that overexpression of evolutionarily conserved F-LANa occurs frequently and may play an important role in proliferation.     

A novel zebrafish kelchlike gene klhl and its human ortholog KLHL display conserved expression patterns in skeletal and cardiac muscles

In this study, a novel gene, kelchlike (klhl) was identified in zebrafish by whole-mount in situ hybridization screen for important genes involved in embryogenesis. A full-length klhl cDNA was cloned and characterized. We found that klhl was a member of the kelch-repeat superfamily, containing two evolutionary conserved domains--broad-complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domain, and kelch motif. Database mining revealed the presence of putative orthologs of klhl in human, mouse, rat, and pufferfish. klhl was determined to map to zebrafish linkage group (LG) 13 and was found to be syntenic with the proposed orthologs of klhl in human, mouse, and rat. In an effort to elucidate the function of klhl, klhl expression was investigated by Northern blot analysis and in situ hybridization. klhl is specifically expressed in the fast skeletal and cardiac muscle. Northern blot analyses show that the human ortholog, KLHL, is also specifically expressed in the skeletal muscles and heart. In silico analyses of rat expressed sequence tag (EST) clones corresponding to rat Klhl ortholog also indicate that its expression is also restricted to rat muscle tissues, suggesting a conserved role of klhl in vertebrates. The expression pattern of klhl, as well as the presence of the kelch repeats indicates a possible role for Klhl in the organization of striated muscle cytoarchitecture.     

Intratesticular localization of the organic solute carrier protein, OSCP1, in spermatogenic cells in mice

Organic solute carrier protein 1 (OSCP1) is a recently described human gene that facilitates the transport of various organic solutes into the cell, when expressed in frog eggs. In this study, we cloned a mouse ortholog of OSCP1 encoding 379 amino acid protein, with 94% homology to the human counterpart. The mouse OSCP1 mRNA was predominantly expressed in the testis, in which it was attributed to the spermatogenic cells, except the spermatogonia. Immunohistochemistry confirmed that OSCP1 protein is continuously expressed during spermatogenesis in a stage- and cell type-specific manner, in the leptotene spermatocytes at stage IX through step 15 spermatids. Subcellular fractionation of mouse testis homogenates indicated that OSCP1 is a 45-kDa cytosolic protein. Moreover, when green fluorescent protein-OSCP1 fusion constructs were transfected into cultured cells, the fluorescence localized evenly in the cytoplasm. These results suggest that mouse testis OSCP1 may indirectly mediate substrate uptake into meiotic and spermiogenic germ cells, within the cytosol.     

Cloning and expression analysis of a novel gene, RP42, mapping to an autism susceptibility locus on 6q16

We isolated a novel mouse gene, RP42, in a systematic search for genes expressed in proliferating neuroblasts whose human orthologs map to susceptibility loci for autism. This gene is intronless and encodes a putative 259-amino-acid protein that exhibits 30-36% overall sequence identity to a fission yeast and a nematode protein (GenPept Accession Nos. CAA17006 and CAB54261). Nevertheless, no homology to any known gene was found. RP42 has developmentally regulated expression, particularly in proliferating neuroblasts from which neocortical neurons originate. Its human ortholog is located in a cluster of embryonic neuronally expressed genes on the 6q16 chromosome, making it a positional candidate susceptibility gene for autism.     

Genome-wide detection of allelic gene expression in hepatocellular carcinoma cells using a human exome SNP chip

Allelic variations in gene expression influence many biological responses and cause phenotypic variations in humans. In this study, Illumina Human Exome BeadChips containing more than 240,000 single nucleotide polymorphisms (SNPs) were used to identify changes in allelic gene expression in hepatocellular carcinoma cells following lipopolysaccharide (LPS) stimulation. We found 17 monoallelically expressed genes, 58 allelic imbalanced genes, and 7 genes showing allele substitution. In addition, we also detected 33 differentially expressed genes following LPS treatment in vitro using these human exome SNP chips. However, alterations in allelic gene expression following LPS treatment were detected in only three genes (MLXIPL, TNC, and MX2), which were observed in one cell line sample only, indicating that changes in allelic gene expression following LPS stimulation of liver cells are rare events. Among a total of 75 genes showing allelic expression in hepatocellular carcinoma cells, either monoallelic or imbalanced, 43 genes (57.33%) had expression quantitative trait loci (eQTL) data, indicating that high-density exome SNP chips are useful and reliable for studying allelic gene expression. Furthermore, most genes showing allelic expression were regulated by cis-acting mechanisms and were also significantly associated with several human diseases. Overall, our study provides a better understanding of allele-specific gene expression in hepatocellular carcinoma cells with and without LPS stimulation and potential clues for the cause of human disease due to alterations in allelic gene expression.     

斑马鱼Gfi-1 基因结构和功能分析

目的:研究斑马鱼Gfi-1基因在物种间进化的保守性和功能分析。方法:运用生物信息学方法分析斑马鱼Gfi-1基因结构特征和保守性等。结果:斑马鱼Gfi-1基因在蛋白水平与小鼠、人高度保守;分析斑马鱼和人的Gfi-1基因外显子、内含子和ATG起始、终止密码子也具有高度相似性;从进化树分析斑马鱼Gfi-1基因与人、小鼠、犬、猴等在进化上高度保守;分析斑马鱼、人、小鼠Gfi-1基因在染色体上的位置和相邻基因,显示出惊人的相似性。结论:斑马鱼Gfi-1基因在进化上高度保守,为脊椎动物保守基因,为其后续在造血系统和造血微环境方面的研究提供了理论支持和铺垫。     

Cloning and characterization of a novel mouse Siglec, mSiglec-F: differential evolution of the mouse and human (CD33) Siglec-3-related gene clusters

A novel mouse Siglec (mSiglec-F) belonging to the subfamily of Siglec-3-related Siglecs has been cloned and characterized. Unlike most human Siglec-3 (hSiglec-3)-related Siglecs with promiscuous linkage specificity, mSiglec-F shows a strong preference for alpha2-3-linked sialic acids. It is predominantly expressed in immature cells of the myelomonocytic lineage and in a subset of CD11b (Mac-1)-positive cells in some tissues. As with previously cloned Siglec-3-related mSiglecs, the lack of strong sequence similarity to a singular hSiglec made identification of the human ortholog difficult. We therefore conducted a comprehensive comparison of Siglecs between the human and mouse genomes. The mouse genome contains eight Siglec genes, whereas the human genome contains 11 Siglec genes and a Siglec-like gene. Although a one-to-one orthologous correspondence between human and mouse Siglecs 1, 2, and 4 is confirmed, the Siglec-3-related Siglecs showed marked differences between human and mouse. We found only four Siglec genes and two pseudogenes in the mouse chromosome 7 region syntenic to the Siglec-3-related gene cluster on human chromosome 19, which, in contrast, contains seven Siglec genes, a Siglec-like gene, and thirteen pseudogenes. Although analysis of gene maps and exon structures allows tentative assignments of mouse-human Siglec ortholog pairs, the possibility of unequal genetic recombination makes the assignments inconclusive. We therefore support a temporary lettered nomenclature for additional mouse Siglecs. Current information suggests that mSiglec-F is likely a hSiglec-5 ortholog. The previously reported mSiglec-3/CD33 and mSiglec-E/MIS are likely orthologs of hSiglec-3 and hSiglec-9, respectively. The other Siglec-3-like gene in the cluster (mSiglec-G) is probably a hSiglec-10 ortholog. Another mouse gene (mSiglec-H), without an apparent human ortholog, lies outside of the cluster. Thus, although some duplications of Siglec-3-related genes predated separation of the primate and rodent lineages (about 80-100 million years ago), this gene cluster underwent extensive duplications in the primate lineage thereafter.     

New facets of keratin K77: interspecies variations of expression and different intracellular location in embryonic and adult skin of humans and mice

The differential expression of keratins is central to the formation of various epithelia and their appendages. Structurally, the type II keratin K77 is closely related to K1, the prototypical type II keratin of the suprabasal epidermis. Here, we perform a developmental study on K77 expression in human and murine skin. In both species, K77 is expressed in the suprabasal fetal epidermis. While K77 appears after K1 in the human epidermis, the opposite is true for the murine tissue. This species-specific pattern of expression is also found in conventional and organotypic cultures of human and murine keratinocytes. Ultrastructure investigation shows that, in contrast to K77 intermediate filaments of mice, those of the human ortholog are not attached to desmosomes. After birth, K77 disappears without deleterious consequences from human epidermis while it is maintained in the adult mouse epidermis, where its presence has so far gone unnoticed. After targeted Krt1 gene deletion in mice, K77 is normally expressed but fails to functionally replace K1. Besides the epidermis, both human and mouse K77 are present in luminal duct cells of eccrine sweat glands. The demonstration of a K77 ortholog in platypus but not in non-mammalian vertebrates identifies K77 as an evolutionarily ancient component of the mammalian integument that has evolved different patterns of intracellular distribution and adult tissue expression in primates.     

Genomic structure and expression analyses of the PYGM gene in the thoroughbred horse

Muscle glycogen Phosphorylase (PYGM) has been shown to catalyze the degradation of glycogen to glucose-1-phosphate. The PYGM gene can contribute to providing energy to the body by disassembling the glycogen in muscle. Here, we analyzed the genomic structure and expression of the PYGM gene in the thoroughbred horse. The PYGM gene, containing several transposable elements (MIRs, LINEs, and MERs), was highly conserved in mammalian genomes. In order to understand the expression of the horse PYGM gene, we performed quantitative RT-PCR using 11 thoroughbred horse tissue samples. The horse PYGM gene was broadly expressed in all tissues tested. In particular, the highest expression of the horse PYGM gene was observed in skeletal muscle tissue relative to the other tissues. Interestingly, the horse PYGM gene contains fewer mobile elements than its human ortholog, resulting in an increase in the structural stability of the PYGM gene sequence. This study provides insights into the genomic structure of the horse PYGM gene that may be useful in future studies of its association with exercise capability.     

Cloning and tissue expression of the mouse ortholog of AIM1, a βγ-crystallin superfamily member

We report the isolation of the murine ortholog of AIM1, a human gene whose expression is associated with the reversal of tumorigenicity in an experimental model of melanoma. Mouse and human AIM1 are more than 90% identical in amino acid sequence in the βγ-crystallin repeats and the C-terminal domain, and more than 75% identical in the extended N-terminal domain. Consistent with the isolated cDNA representing the authentic AIM1 ortholog, linkage analysis localized mouse Aim1 to proximal mouse Chromosome (Chr) 10 in a conserved linkage group with genes localized to human Chr band 6q21. Searches of EST databases identified a second AIM1-like gene in both mouse and human, suggesting the existence of a gene family. Northern analysis demonstrates Aim1 is expressed most abundantly in adult skin, lung, heart, liver, and kidney and is temporally regulated during embryogenesis. Aim1 is expressed highly in the shaft region of the hair follicles and the presumptive ectoderm, but not at detectable levels in melanocytes or melanocyte precursor cells. Received: 18 February 1998 / Accepted: 8 May 1998     

家蚕羧酸酯酶基因Bmae35的克隆、 序列分析及表达

昆虫羧酸酯酶是一类能对外源化合物解毒和气味分子降解的重要酶系。本研究选取在家蚕Bombyx mori幼虫嗅觉感器中有表达, 并与蛀茎夜蛾Sesamia nonagrioides触角酯酶基因Snon-EST可能为直系同源基因的Bmae35进行克隆和外源表达研究。结果表明： 该基因编码区长1 581 bp, 共编码526个氨基酸。与其他昆虫触角酯酶的多序列比对分析发现, Bmae35编码的蛋白具有酯酶活性必须的催化残基Ser191, Glu313和His429, 也保持着α-酯酶家族特征基序Gly-x-Ser-x-Gly。RT-PCR分析显示, Bmae35在家蚕5龄第3天各组织中均有表达, 其中在头、 脂肪体、 马氏管、 体壁和丝腺中的表达量较高。Bmae35在雌蛾性信息腺中表达, 并与性信息素合成呈正相关, 暗示其在信息素合成中起重要作用。构建Bmae35与pET28(a) 重组载体, 经异丙基-β-D-硫代半乳糖苷诱导,电泳检测发现该基因以包涵体形式表达, 以镍亲和层析柱纯化, Western blotting鉴定证实Bmae35在大肠杆菌Escherichia coli中正确表达并得以纯化。本实验通过对家蚕Bmae35基因的克隆、 原核表达与纯化, 为进一步深入研究其表达定位和气味降解等功能奠定基础。