Evolution of duplicate gene expression in polyploid and hybrid plants

Allopolyploidy is a prominent mode of speciation in flowering plants. On allopolyploidy, genomic changes can take place, including chromosomal rearrangement and changes in gene expression; these processes continue over evolutionary time. Recent studies of gene expression in polyploid and hybrid plants, reviewed here, have examined expression in natural polyploids and synthetic neopolyploids as well as in diploid and F(1) hybrids. Considerable changes in gene expression have been observed in allopolyploids, including up- or downregulation of expression in the polyploids compared with their parents, unequal expression of duplicated genes, and silencing of one copy. Genes in a variety of functional categories show altered expression, and the patterns vary considerably by gene. Some changes seem to be stochastic, whereas others are repeatable. Gene expression changes can be organ specific. Reciprocal silencing of duplicates in different organs has been observed, suggesting subfunctionalization and long-term retention of duplicates. It has become clear that hybridization has a much greater effect than chromosome doubling on gene expression in allopolyploids. Diploid and triploid F(1) hybrids can show alterations of expression levels compared with their parents. Parent-of-origin effects on gene expression have been examined, and loss of gene imprinting has been shown. Some gene expression changes in polyploids and hybrids can be correlated with phenotypic effects. Demonstrated mechanisms of gene expression changes include DNA methylation, histone modifications, and antisense RNA. Several hypotheses have been proposed for why gene expression is altered in allopolyploids and hybrids.     

Selection to minimise noise in living systems and its implications for the evolution of gene expression

Gene expression, like many biological processes, is subject to noise. This noise has been measured on a global scale, but its general importance to the fitness of an organism is unclear. Here, I show that noise in gene expression in yeast has evolved to prevent harmful stochastic variation in the levels of genes that reduce fitness when their expression levels change. Therefore, there has probably been widespread selection to minimise noise in gene expression. Selection to minimise noise, because it results in gene expression that is stable to stochastic variation in cellular components, may also constrain the ability of gene expression to respond to non‐stochastic variation. I present evidence that this has indeed been the case in yeast. I therefore conclude that gene expression noise is an important biological trait, and one that probably limits the evolvability of complex living systems.     

Molecular definition of the germinal centre stage of B-cell differentiation

Genomic-scale gene expression analysis provides views of biological processes as a whole that are difficult to obtain using traditional single-gene experimental approaches. In the case of differentiating systems, gene expression profiting can define a stage of differentiation by the characteristic expression of hundreds of genes. Using specialized DNA microarrays termed 'Lymphochips', gene expression during mature B-cell differentiation has been defined. Germinal centre B cells represent a stage of differentiation that can be defined by a gene expression signature that is not shared by other highly proliferative B-cell populations such as mitogenically activated peripheral blood B cells. The germinal centre gene expression signature is maintained to a significant degree in lymphoma cell lines derived from this stage of differentiation, demonstrating that this gene expression programme does not require ongoing interactions with other germinal centre cell types. Analysis of representative cDNA libraries prepared from resting and activated peripheral blood B cells, germinal centre centroblasts, centrocytes and tonsillar memory B cells has confirmed and extended the results of DNA microarray gene expression analysis.     

基因表达谱聚类/分类技术研究及展望

随着人类及多种模式生物全基因组测序基本完成,人类基因组计划的研究进入后基因组时代.后基因组时代研究的焦点已经从测序转向功能研究。聚类/分类技术作为分析基因表达谱和识别基因功能的重要工具之一,近年来获得很大的发展。对目前基因表达谱聚类/分类技术及它们的发展,进行了综述性的研究,分析了它们的优缺点,结合我们的研究,提出了解决问题的思路和方法,为基因表达谱的进一步研究提供了新的途径。     

Databases of free expression

The rapid development of microarray technologies has led to a similar progression in gene expression analysis methods, gene expression applications, and gene expression databases. Public gene expression databases enable any researcher to examine expression of their favorite genes across a wide variety of samples, download sample data for development of new analysis methods, or answer broad questions about gene expression regulation, among other applications. A wide variety of public gene expression databases exist, and they vary in their content, analysis capabilities, and ease of use. This review highlights the current features and describes examples of two broad categories of mammalian microarray databases: tissue gene expression databases and data warehouses.     

Characteristics of expression of the tetracycline resistance gene from the plasmid pBR322 in Bacillus subtilis cells

The expression of Tc resistance gene derived from plasmid pBR322 has been studied in Bacillus subtilis cells where this alien gene is not usually expressed. Fragments of Bacillus subtilis chromosome were inserted into the Tc resistance gene promoter region of the hybrid plasmid pGG20 and the expression of this gene was registered. Plasmid pGG20 confers a constitutive mode of Tc resistance in Escherichia coli cells. In contrast, the inducibility of Tc resistance gene expression in Bacillus subtilis cells has been reported. Optimal concentration for the highest inducibility of Tc resistance by the antibiotic has been determined.     

Retro-Tet:一种基于逆转录病毒的诱导性基因表达系统

 Retro Tet基因表达系统是一种新型的高效、稳定、无毒、具有严密开 关功能的可诱导性真核细胞基因表达系统 .该系统兼备了逆转录病毒基因表达系统和Tet off Tet on基因表达系统的优点 ,在稳定表达细胞系的筛选、基因的表达与调控及基因功能研究等方面得到了成功的应用 ,同时也为基因治疗提供了一种理想的基因载体系统     

Problems and paradigms: Induction mechanism of a single gene molecule: Stochastic or deterministic?

A new field of gene expression regulation research is emerging that has previously been overlooked. This new area is concerned with distinguishing the expression of a single gene from the averaged expression of many gene copies within the cell population. This paper reviews research focused on individual genes in inducible gene expression systems. The main experimental strategy is to measure the gene expression level of a single cell containing a single reporter gene molecule. In contrast to the commonly held belief, gene induction is found to be stochastic under certain conditions. The possible mechanisms and implications are discussed.     

Chromosome-specific spatial periodicities in gene expression revealed by spectral analysis

Recent years have seen an unprecedented surge of research activity in studies of gene expression. This extensive work, however, has been almost uniformly focused on genome-wide gene expression and has largely ignored the fundamental fact that every gene has a specific chromosome location. We propose a novel method of spectral analysis for detecting hidden periodicities in gene expression signals ordered along the length of each chromosome. Using this method, we have discovered that each chromosome in rodents and humans has a unique periodic pattern of gene expression. The uncovered spatial periodicities in gene expression are tissue-specific in the sense that the largest differences in humans were observed between two normal tissues (brain and mammary gland) as well as between their tumor counterparts (glioma and breast cancer). The smallest differences resulted from the comparison of tumors (glioma and breast cancer) with their normal counterparts. All such effects do not extend to all chromosomes but are limited to only some of them. The estimated periods and amplitudes are identical for the genes located on the positive and negative DNA strands. While precise molecular mechanisms of chromosome-specific periodicities in gene expression have yet to be unraveled, their universal presence in different tissues adds another dimension to the current understanding of the genome organization.     

Dynamic model-based clustering for time-course gene expression data

Microarray technology has produced a huge body of time-course gene expression data. Such gene expression data has proved useful in genomic disease diagnosis and genomic drug design. The challenge is how to uncover useful information in such data. Cluster analysis has played an important role in analyzing gene expression data. Many distance/correlation- and static model-based clustering techniques have been applied to time-course expression data. However, these techniques are unable to account for the dynamics of such data. It is the dynamics that characterize the data and that should be considered in cluster analysis so as to obtain high quality clustering. This paper proposes a dynamic model-based clustering method for time-course gene expression data. The proposed method regards a time-course gene expression dataset as a set of time series, generated by a number of stochastic processes. Each stochastic process defines a cluster and is described by an autoregressive model. A relocation-iteration algorithm is proposed to identity the model parameters and posterior probabilities are employed to assign each gene to an appropriate cluster. A bootstrapping method and an average adjusted Rand index (AARI) are employed to measure the quality of clustering. Computational experiments are performed on a synthetic and three real time-course gene expression datasets to investigate the proposed method. The results show that our method allows the better quality clustering than other clustering methods (e.g. k-means) for time-course gene expression data, and thus it is a useful and powerful tool for analyzing time-course gene expression data.     

三疣梭子蟹aqp2基因克隆及其在蜕皮中的功能

为研究水通道蛋白AQP的生理功能, 克隆了三疣梭子蟹 (Portunus trituberculatus) 水通道蛋白2基因(ptaqp2), 该基因全长4126 bp, 编码522个氨基酸, 具有水通道蛋白基因家族的保守结构域及功能结构域; 进化树聚类分析结果显示, ptaqp2基因属于水通道蛋白基因家族C-AQP类基因; 组织表达结果显示, ptaqp2呈泛组织表达特征, 在眼柄中的表达量最高, 在肠和肌肉中也有较高表达, 在血淋巴中的表达最低; ptaqp2基因在不同蜕皮时期呈显著差异表达(P<0.05), 且在蜕皮前期表达量最高; 在蜕皮激素(Molting Hormone简称MH)刺激下, 该基因在肌肉、肠及胃中均呈不同程度的上调表达趋势; 通过RNAi技术在蜕皮前期敲降ptaqp2的表达, 发现能够显著推迟蜕皮过程。研究初步证明了ptaqp2基因在三疣梭子蟹蜕皮中发挥重要作用。     

A cardiovascular EST repertoire: progress and promise for understanding cardiovascular disease

The application of expressed sequence tag (EST) technology has proven to be an effective tool for gene discovery and the generation of gene expression profiles. The generation of an EST resource for the cardiovascular system has revealed significant insights into the changes in gene expression that guide heart development and disease. Furthermore, an important genetic resource has been developed for cardiovascular biology that is valuable for data mining and disease gene discovery.     

The function of the tet gene in the plasmid pBR322 is not inhibited by expression of an anti-tet gene

The possibility of gene suppression by the expression of anti-sense sequences has been tested for tet gene of pBR322 plasmid. Anti-tet gene has been inserted into lac-promoter regulated site of M13mp 10 single-stranded high copy phage vector. To achieve that, HihdIII-BamHI fragment of pBR322 carrying part of the tet gene was inserted into poly-linker of mp 10. The influence of the anti-tet gene expression on growth parameters of cells with or without tetracycline in the growth media was monitored for JM103 cells. The results indicate that in this system the detectable suppression of the tet gene by anti-tet expression was not manifested.     

The role of the sporulation gene spollIE in the regulation of prespore-specific gene expression in Bacillus subtilis

The spoIIIG gene encodes a sigma factor that determines prespore-specific gene expression during sporulation in Bacillus subtilis. Correct spatial and temporal expression of the spoIIIG gene depends on a number of other sporulation (spo) genes, but only one of these genes, spoIIIE, has a specific effect on spoIIIG expression and not on gene expression in the other differentiating cell, the mother cell. However, the spoIIIE gene is expressed predominantly before differentiation begins. Thus, its product must play an important role in sensing or determining the spatial localization of prespore-specific gene expression in this system.     

基因拷贝数与染色体位置对酵母表达乙肝病毒融合表面抗原SA-28基因的影响

应用ＦＬＰ重组酶介导的染色体定点整合技术,将带有不同拷贝数的乙肝病毒融合表面抗原ＳＡ－２８基因表达单元的质粒整合在酵母不同的染色体位点,并测定了ＳＡ－２８基因的表达情况,初步研究了基因拷贝数与染色体位置对酵母表达外源基因的影响。结果表明ＳＡ－２８基因在ＨＩＳ３位点整 合时的表达水平随基因拷贝数的增加而提高,遵循基因剂量效应;在某些染色体位点整２合时,插入方向对其表达有不同程度的影响,呈现出明显的染     

Tet system的调控原理及其在转基因小鼠模型上的应用

基因表达的调控是分子生物学研究的一个重要问题,也是基因治疗和基因功能研究的重要手段。诱导性基因表达系统可以从时间上调控基因的表达,是基因治疗和基因功能研究的重要工具之一。其中,四环素诱导基因表达系统(tetracycline inducible expression system,Tet system)是应用最广泛的一种,它可以在时间和空间上对基因进行严谨和高效地诱导表达。基于该系统获得了不同用途的转基因动物,这些模型动物的建立为研究特定基因的功能及其在疾病发生中的作用打下了实验基础。现就四环素诱导表达系统的原理和在小鼠模型上的研究应用做一综述。