Evolutionary significance of gene expression divergence

Recent large-scale studies of evolutionary changes in gene expression among mammalian species have led to the proposal that gene expression divergence may be neutral with respect to organismic fitness. Here, we employ a comparative analysis of mammalian gene sequence divergence and gene expression divergence to test the hypothesis that the evolution of gene expression is predominantly neutral. Two models of neutral gene expression evolution are considered: 1-purely neutral evolution (i.e., no selective constraint) of gene expression levels and patterns and 2-neutral evolution accompanied by selective constraint. With respect to purely neutral evolution, levels of change in gene expression between human-mouse orthologs are correlated with levels of gene sequence divergence that are determined largely by purifying selection. In contrast, evolutionary changes of tissue-specific gene expression profiles do not show such a correlation with sequence divergence. However, divergence of both gene expression levels and profiles are significantly lower for orthologous human-mouse gene pairs than for pairs of randomly chosen human and mouse genes. These data clearly point to the action of selective constraint on gene expression divergence and are inconsistent with the purely neutral model; however, there is likely to be a neutral component in evolution of gene expression, particularly, in tissues where the expression of a given gene is low and functionally irrelevant. The model of neutral evolution with selective constraint predicts a regular, clock-like accumulation of gene expression divergence. However, relative rate tests of the divergence among human-mouse-rat orthologous gene sets reveal clock-like evolution for gene sequence divergence, and to a lesser extent for gene expression level divergence, but not for the divergence of tissue-specific gene expression profiles. Taken together, these results indicate that gene expression divergence is subject to the effects of purifying selective constraint and suggest that it might also be substantially influenced by positive Darwinian selection.     

Regulation of specific genes during the cell cycle. Utilization of homologous cDNAs and cloned sequences for studying histone gene expression in human cells

Evidence for differential gene expression during the cell cycle and approaches for studying cell-cycle-stage specific gene expression are summarized. Attention is focused on regulation of histone gene expression during the cell cycle of continuously dividing cells and after stimulation of nondividing cells to proliferate. The level(s) at which control of histone gene expression occurs and the possible involvement of chromosomal proteins in the regulation of histone gene expression are discussed. The preparation of cloned human histone sequences and their use in studying the structural and functional properties of human histone genes are presented. Index Entries: Cell cycle, gene regulation during; gene regulation, during the cell cycle; regulation of specific genes, during the cell cycle; DNAs, homologous, and histone gene expression; cloned DNAs, and histone gene expression; histone gene expression; gene expression, histone; cloned human histone sequences.     

Effect of FAK, DLC-1 gene expression on OVCAR-3 proliferation

The study investigates the effect of FAK, DLC-1 on OVCAR-3 proliferation. FAK gene siRNA vector recombinant plasmid was constructed using RNA interference technique. FAK gene-transfected OVCAR-3 cells, OVCAR-3 cells with DLC-1 gene expression, and OVCAR-3 cells with simultaneous expression of DLC-1 and FAK genes were obtained using gene transfection technology. In addition, siRNA control group and blank control were also given. Effect of FAK, DLC-1 gene expression on OVCAR-3 proliferation was examined by FCM and Cell Counting Kit-8 (CCK-8) methods. Results showed that DLC-1 gene high expression and FAK gene silencing, single silencing FAK gene, and single DLC-1 gene high expression in OVCAR-3 cells may decrease S and G2/M phase proportion of the cell cycle. Moreover, DLC-1 gene high expression and FAK gene silencing in OVCAR-3 cells can display the most significant effect. This confirmed that DLC-1 gene high expression and FAK gene silencing may significantly inhibit the OVCAR-3 cells proliferation. CCK-8 analysis showed that silence FAK gene exprssion or/and increasing DLC-1 gene expression may decrease OVCAR-3 growth rate. Moreover, simultaneous silence the exprssion of FAK gene and high expression of DLC-1 gene can display the most significant effect on OVCAR-3 growth. It can be concluded that downregulation of FAK gene expression or/and upregulation of DLC-1 gene expression can all inhibit the OVCAR-3 growth. Moreover, DLC-1 gene expression and FAK gene silencing can display the most marked inhibitory effect on the OVCAR-3 growth.     

Monoallelic gene expression and its mechanisms

Although the majority of genes are expressed equally from both alleles, some genes are differentially expressed. Monoallelic gene expression, the differential gene expression of the alleles such as genomic imprinting, is reported in several organisms and plays significant roles in proper development and diversity in gene expression and phenotypic variation. Recent studies in flowering plants have greatly increased our understanding of the underlying mechanisms of monoallelic gene expression. They indicate that machineries of gene silencing such as DNA methylation, histone modifications, and noncoding RNAs function in monoallelic gene expression. A combination of genetics and high-throughput technologies expands the scope of study on monoallelic gene expression in flowering plants.     

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.     

Oligonucleotide-based strategies to reduce gene expression

Research on embryonic development and differentiation provides a sensitive, but challenging opportunity to use a variety of techniques designed to modulate gene expression. Changes in the expression of a single gene can alter levels of other genes and provide information on developmentally regulated gene expression pathways. The morphological consequences of altered gene expression can link gene expression to developmental fate. Oligonucleotide-based approaches offer a variety of means to potentially disrupt normal gene expression. The basis for some of these approaches is presented in this review.     

调控通路内基因表达的相关性分析

本研究从基因表达调控通路的角度分析了基因功能与基因表达之间的关系,利用7套酿酒酵母基因芯片表达谱数据和通路数据库（KEGG和CYGD）所提供的信息,应用我们研制的Genehub软件分析研究了同一基因表达调控通路内的基因在mRNA表达水平上的相关性,共涉及16条通路,495个基因。通过Pearson相关系数和Spearman相关系数两种相似性测度的分析,我们发现有94%（15条）的基因表达调控通路内的基因在大于等于4套的表达谱数据中是共表达的,以上结果从基因表达调控通路的角度,证实了基因功能与基因表达之间存在着一定的相关性。     

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.     

Triggering of apoptosis is not sufficient to induce human immunodeficiency virus gene expression

We examined whether there is any causative link between apoptosis and HIV gene expression elicited in response to ultraviolet light (UV) and ionizing radiation (IR). We found that both UV and IR activate HIV gene expression in human T lymphoblastoid 1G5 (HIVluc) cells, but with different kinetics and magnitudes. Treatment with either type of radiation resulted in increased apoptosis, which correlated closely with HIV gene expression. The involvement of caspases in the IR response was demonstrated by using zVAD-FMK and zDEVD-FMK caspase inhibitors; both apoptosis and HIV gene expression were inhibited to similar extent. Surprisingly, treatment of 1G5 cells with FAS antibody triggered apoptosis but did not increase HIV gene expression. A correlation between increased apoptosis and gene expression was also demonstrated in human carcinoma HIVcat/A549 cells with UV whereas IR triggered apoptosis but did not activate HIV gene expression. Most significantly, UV activation of HIV gene expression, and NF-kappa-B and p38 MAP kinase, both important for efficient HIV gene expression, were not affected by treatment with the zVAD-FMK and zDEVD-FMK inhibitors. Treatment of HIVcat/A549 cells with staurosporine or scrape-loading of cells with cytochrome c resulted in apoptosis but no increase in HIV gene expression. Altogether, a direct correlation exists between apoptosis and HIV gene expression in T-cells in response to both UV and IR but this is not the case in carcinoma cells. Triggering of apoptosis per se in either cell type does not necessarily result in increased HIV gene expression. Most importantly, the apoptotic and HIV gene expression responses elicited by UV are different to some extent and can be separated.     

Organ-specific and dosage-dependent expression of a leaf/stem specific gene from potato after tagging and transfer into potato and tobacco plants.

ST-LS1, a single copy gene from potato displaying a leaf/stem specific gene expression, was tagged by an exon modification and introduced into both potato and tobacco cells using Agrobacterium vectors. After regeneration of whole plants, the expression of the tagged gene was analyzed with respect to its organ specificity and compared to the expression of the corresponding resident gene. The expression of the transferred gene in transgenic plants closely followed the expression of the resident gene. No marked influence of the plant species serving as host was observed. The level of expression of the introduced gene varied by a factor of at least 100 in independent transformants when normalized to the expression of the resident gene. Southern analysis performed on the transformed plants indicated a correlation between copy number of the introduced gene and its expression level. The activity of the tagged gene as well as of the resident gene was significantly inhibited by treatment of the transgenic plants with the herbicide norfluorazon, indicating that this gene activity is dependent on the presence of functional chloroplasts in the leaves.     

Wrestling with pleiotropy: genomic and topological analysis of the yeast gene expression network

The vast majority (>95%) of single-gene mutations in yeast affect not only the expression of the mutant gene, but also the expression of many other genes. These data suggest the presence of a previously uncharacterized "gene expression network"--a set of interactions between genes which dictate gene expression in the native cell environment. Here, we quantitatively analyze the gene expression network revealed by microarray expression data from 273 different yeast gene deletion mutants.(1) We find that gene expression interactions form a robust, error-tolerant "scale-free" network, similar to metabolic pathways(2) and artificial networks such as power grids and the internet.(3-5) Because the connectivity between genes in the gene expression network is unevenly distributed, a scale-free organization helps make organisms resistant to the deleterious effects of mutation, and is thus highly adaptive. The existence of a gene expression network poses practical considerations for the study of gene function, since most mutant phenotypes are the result of changes in the expression of many genes. Using principles of scale-free network topology, we propose that fragmenting the gene expression network via "genome-engineering" may be a viable and practical approach to isolating gene function.     

Gene expression analysis for the identification of selection and local adaptation in fishes

In recent years, variation in gene expression has been recognized as an important component of environmental adaptation in multiple model species, including a few fish species. There is, however, still little known about the genetic basis of adaptation in gene expression resulting from variation in the aquatic environment (e.g. temperature, salinity and oxygen) and the physiological effect and costs of such differences in gene expression. This review presents and discusses progress and pitfalls of applying gene expression analyses to fishes and suggests simple frameworks to get started with gene expression analysis. It is emphasized that well-planned gene expression studies can serve as an important tool for the identification of selection in local populations of fishes, even for non-traditional model species where limited genomic information is available. Recent studies focusing on gene expression variation among natural fish populations are reviewed, highlighting the latest applications that combine genetic evidence from neutral markers and gene expression data.     

蛋白核酸合成抑制剂和蛋白磷酸化对基因表达的调节

环己酰亚胺和放线菌素D明显降低小麦幼苗中BADH基因的表达,表明BADH基因表达在转录和转译水平上受到调控。氯霉素则有增加表达的效应。线粒体可能形成阻遏蛋白参与调节。H7和甘露糖降低BADH基因表达,相应地冈田酸(Okadaic acid)明显增加表达,说明蛋白磷酸化积极参与小麦幼苗中BADH基因表达的调节。     

Variation in the large-scale organization of gene expression levels in the hippocampus relates to stable epigenetic variability in behavior

Background

Despite sharing the same genes, identical twins demonstrate substantial variability in behavioral traits and in their risk for disease. Epigenetic factors–DNA and chromatin modifications that affect levels of gene expression without affecting the DNA sequence–are thought to be important in establishing this variability. Epigenetically-mediated differences in the levels of gene expression that are associated with individual variability traditionally are thought to occur only in a gene-specific manner. We challenge this idea by exploring the large-scale organizational patterns of gene expression in an epigenetic model of behavioral variability.

Methodology/Findings

To study the effects of epigenetic influences on behavioral variability, we examine gene expression in genetically identical mice. Using a novel approach to microarray analysis, we show that variability in the large-scale organization of gene expression levels, rather than differences in the expression levels of specific genes, is associated with individual differences in behavior. Specifically, increased activity in the open field is associated with increased variance of log-transformed measures of gene expression in the hippocampus, a brain region involved in open field activity. Early life experience that increases adult activity in the open field also similarly modifies the variance of gene expression levels. The same association of the variance of gene expression levels with behavioral variability is found with levels of gene expression in the hippocampus of genetically heterogeneous outbred populations of mice, suggesting that variation in the large-scale organization of gene expression levels may also be relevant to phenotypic differences in outbred populations such as humans. We find that the increased variance in gene expression levels is attributable to an increasing separation of several large, log-normally distributed families of gene expression levels. We also show that the presence of these multiple log-normal distributions of gene expression levels is a universal characteristic of gene expression in eurkaryotes. We use data from the MicroArray Quality Control Project (MAQC) to demonstrate that our method is robust and that it reliably detects biological differences in the large-scale organization of gene expression levels.

Conclusions

Our results contrast with the traditional belief that epigenetic effects on gene expression occur only at the level of specific genes and suggest instead that the large-scale organization of gene expression levels provides important insights into the relationship of gene expression with behavioral variability. Understanding the epigenetic, genetic, and environmental factors that regulate the large-scale organization of gene expression levels, and how changes in this large-scale organization influences brain development and behavior will be a major future challenge in the field of behavioral genomics.     

急性髓系白血病患者HtrA2基因、Set基因表达与疗效和预后的关系研究

摘要 目的：探讨急性髓系白血病（AML）患者HtrA2基因、Set基因表达与疗效和预后的关系。方法：选择2017年6月~2019年6月来我院进行治疗的90例病历资料完整的初诊为AML患者作为本次研究对象,作为AML组,另选取同时期来我院进行健康体检的90例志愿者作为对照组。检测HtrA2基因、Set基因在两组受试者外周血中的表达;分析HtrA2基因、Set基因的表达与AML患者年龄、性别、白细胞计数、NCCN预后分型和疗效的关系。结果：HtrA2基因在AML组中表达水平低于对照组,Set基因在AML组中表达水平高于对照组（P<0.05）。HtrA2基因的表达和年龄、性别、白细胞计数无关（P>0.05）;Set基因的表达和年龄、性别无关（P>0.05）,与白细胞计数有关（P<0.05）。HtrA2基因在NCCN不同的预后分组中的表达差异无统计学意义（P>0.05）;Set基因在NCCN不同的预后分组中的表达差异有统计学意义（P<0.05）。HtrA2基因和Set基因在不同疗效患者中的表达差异有统计学意义（P<0.05）。结论：AML患者HtrA2基因表达下降,Set基因表达升高,Set基因和HtrA2基因具有评估AML疗效的潜力,Set基因可辅助评估AML患者的预后。     

BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development

Embryonic gene expression patterns are an indispensable part of modern developmental biology. Currently, investigators must visually inspect numerous images containing embryonic expression patterns to identify spatially similar patterns for inferring potential genetic interactions. The lack of a computational approach to identify pattern similarities is an impediment to advancement in developmental biology research because of the rapidly increasing amount of available embryonic gene expression data. Therefore, we have developed computational approaches to automate the comparison of gene expression patterns contained in images of early stage Drosophila melanogaster embryos (prior to the beginning of germ-band elongation); similarities and differences in gene expression patterns in these early stages have extensive developmental effects. Here we describe a basic expression search tool (BEST) to retrieve best matching expression patterns for a given query expression pattern and a computational device for gene interaction inference using gene expression pattern images and information on the associated genotypes and probes. Analysis of a prototype collection of Drosophila gene expression pattern images is presented to demonstrate the utility of these methods in identifying biologically meaningful matches and inferring gene interactions by direct image content analysis. In particular, the use of BEST searches for gene expression patterns is akin to that of BLAST searches for finding similar sequences. These computational developmental biology methodologies are likely to make the great wealth of embryonic gene expression pattern data easily accessible and to accelerate the discovery of developmental networks.     

Mechanoregulation of gene expression in fibroblasts

Mechanical loads placed on connective tissues alter gene expression in fibroblasts through mechanotransduction mechanisms by which cells convert mechanical signals into cellular biological events, such as gene expression of extracellular matrix components (e.g., collagen). This mechanical regulation of ECM gene expression affords maintenance of connective tissue homeostasis. However, mechanical loads can also interfere with homeostatic cellular gene expression and consequently cause the pathogenesis of connective tissue diseases such as tendinopathy and osteoarthritis. Therefore, the regulation of gene expression by mechanical loads is closely related to connective tissue physiology and pathology. This article reviews the effects of various mechanical loading conditions on gene regulation in fibroblasts and discusses several mechanotransduction mechanisms. Future research directions in mechanoregulation of gene expression are also suggested.