差异表达基因的分离策略

生命活动的各个进程伴随着不同基因的选择性开启和关闭。如何有效地分离克隆各种差异表达的基因,成为分子生物学研究的一个努力方向,大量差异基因分离策略因之问世。本文扼要介绍了近年来发展的几种主要分离策略,并详细介绍一种新的差异基因分离方法--抑制差减杂交。     

Expression and evolutionary conservation of nanos-related genes in Hydra

The Drosophila gene nanos encodes two particular zinc finger motifs which are also found in germline-associated factors from nematodes to vertebrates. We cloned two nanos (nos)-related genes, Cnnos1 and Cnnos2 from Hydra magnipapillata. Using whole-mount in situ hybridization, the expression of Cnnos1 and Cnnos2 was examined. Cnnos1 was specifically expressed in multipotent stem cells and germline cells, but not in somatic cells. Cnnos2 was weakly expressed in germline cells and more specifically in the endoderm of the hypostome where it appears to be involved in head morphogenesis. In addition to structural conservation in the zinc finger domain of nanos-related genes, functional conservation of Cnnos1 was also demonstrated by the finding that a Cnnos1 transgene can partially rescue the nos ^RC phenotype that is defective in the egg production of Drosophila. Thus, the function of nanos-related genes in the germline appears to be well conserved from primitive to highly evolved metazoans. Received: 28 April 2000 / Accepted: 1 July 2000     

Involvement of polycomb-group genes in establishing HoxD temporal colinearity

Temporal colinearity in mouse HoxD is dependent on repressive activity of sequences within the 5' end of the complex. We show that a 5-kb DNA fragment from this region represses transgenes when combined in mouse as well as in Drosophila melanogaster. Moreover, repressive activity in Drosophila depends on some members of the Polycomb-group (PcG) genes, for example, extra sex combs. We also showed direct association of these factors with the repressive fragment, both in transgenic flies and in the context of the native mouse HoxD complex. These results suggest that the global repressive region of the HoxD complex functions in two very different species and that some PcG genes are involved in establishing the early repressive state of the HoxD complex, thus contributing to temporal colinearity.     

Subtractive differential display: a modified differential display technique for isolating differentially expressed genes

Differential display (DD) is a novel PCR-based technique, very commonly used to study differentially expressed genes at the mRNA level. In this paper we report a modified version of this technique that we have used to study the differences between the mRNA population from brain tissue of adult and old rats. We have modified the technique to enhance reproducibility and reduce false positives and redundancy. It is fast and does not require any expensive or uncommon reagent. We choose to call it as subtractive differential display as it is a differential display performed over subtracted mRNA population. We have used this protocol successfully to clone a number of age-related differentially expressed sequences from rat brain that need to be sequenced to establish the gene identity.     

转化的大鼠胚胎成纤维细胞系差异表达基因的筛选研究

来源于转化的大鼠胚胎成纤维细胞系的两株细胞,A1－5细胞与B4细胞相比表现出非常强的抗辐射性并伴随不同寻常强的G2延迟效应;用PCR选择性抑制消减杂交方法对这两株细胞进行差减,希望找到对A1－5细胞表现出的不同寻常的表型起关键作用的某一个或某一些基因。结果得到了160个差减转化子,逐个进行序列测定,并进行Dot blot杂交,共得到35个差异表达基因片段（EST）。通过对美国国家生物技术信息中心（NCBI）的非冗余序列库（NT）、鼠EST库及人EST库的BLAST进行同源检索,发现其中21个代表了尚未登录的新基因,另外14个分别与已知基因高度同源。     

Determination of genes involved in the early process of molar root development initiation in rat by modified subtractive hybridization

Rat molars and incisors have different root patterning mechanisms: the former form a multirooted pattern while the latter form a single-rooted analogue. But the genetic signals that control root patterning are poorly understood. In this study, to identify the special molecular signals which may lead to the molar root development, we firstly observed that at embryonic day 19 the molar and the incisor began differentially developing: the molar formed double-layered cells of the root sheath while the incisor formed a cervical loop. By using the subtractive hybridization method, we successfully constructed a subtraction cDNA library of the rat molar and incisor tissues. Differentially expressed gene clones were evaluated by dot-blot and sequencing. Sel1l, Nfic, Edar, GATA6, and some novel genes were found differentially expressed, which were strongly related the tooth root patterning. It is anticipated that further study of genes identified will provide insights into their specific roles in the tooth root patterning.     

Putative in vitro expressed gene fragments unique to Mycobacterium avium subspecies paratuberculosis

By a suppression subtractive hybridization based method, nine novel Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) fragments of between 318 and 596 bp have been identified and characterized. Database search revealed little or no similarity with other mycobacteria. The uniqueness and diagnostic potential of seven of these fragments in relation to M. paratuberculosis closest relative Mycobacterium avium subsp. avium (M. avium) was confirmed by species-specific PCR and Southern blot. Furthermore, RT-PCR indicated that eight of the nine fragments originate from areas of the genome that are expressed in vitro.     

Strategies for isolation of in vivo expressed genes from bacteria

The discovery and characterization of genes specifically induced in vivo upon infection and/or at a specific stage of the infection will be the next phase in studying bacterial virulence at the molecular level. Genes isolated are most likely to encode virulence-associated factors or products essential for survival, bacterial cell division and multiplication in situ. Identification of these genes is expected to provide new means to prevent infection, new targets for, antimicrobial therapy, as well as new insights into the infection process. Analysis of genes and their sequences initially discovered as in vivo induced may now be revealed by functional and comparative genomics. The new field of virulence genomics and their clustering as pathogenicity islands makes feasible their in-depth analysis. Application of new technologies such as in vivo expression technologies, signature-tagged mutagenesis, differential fluorescence induction, differential display using polymerase chain reaction coupled to bacterial genomics is expected to provide a strong basis for studying in vivo induced genes, and a better understanding of bacterial pathogenicity in vivo. This review presents technologies for characterization of genes expressed in vivo.     

Transgenic stem cells in Hydra reveal an early evolutionary origin for key elements controlling self-renewal and differentiation

Little is known about stem cells in organisms at the beginning of evolution. To characterize the regulatory events that control stem cells in the basal metazoan Hydra, we have generated transgenics which express eGFP selectively in the interstitial stem cell lineage. Using them we visualized stem cell and precursor migration in real-time in the context of the native environment. We demonstrate that interstitial cells respond to signals from the cellular environment, and that Wnt and Notch pathways are key players in this process. Furthermore, by analyzing polyps which overexpress the Polycomb protein HyEED in their interstitial cells, we provide in vivo evidence for a role of chromatin modification in terminal differentiation. These findings for the first time uncover insights into signalling pathways involved in stem cell differentiation in the Bilaterian ancestor; they demonstrate that mechanisms controlling stem cell behaviour are based on components which are conserved throughout the animal kingdom.     

Stem cell protein Piwil2 modulates expression of murine spermatogonial stem cell expressed genes

The piwi family genes are highly conserved during evolution and play essential roles in stem cell self-renewal, gametogenesis, and RNA interference in diverse organisms ranging from Arabidopsis to human. Piwil2, known also as Mili gene, is one of three mouse homologues of piwi. Piwil2 was found in germ cells of adult testis, suggesting that this gene functions in spermatogonial stem cell self-renewal. In order to find molecular mechanisms underlying stem cell activity mediated by Piwil2 gene, an in vitro gain of function cell culture model was established. Messenger RNAs isolated from cells expressing Piwil2 and mRNAs isolated from cells without Piwil2 expression were compared using a stem cell array technique. It was shown that Piwil2 modulates expression of stem cell specific genes, including platelet-derived growth factor receptor, beta polypeptide (Pdgfrb), solute carrier family 2 member 1 (Slc2a1), gap junction membrane channel protein alpha 7 (Gja7), and spermatogonial cell surface markers Thy-1 (CD90), integrin alpha 6 (Itga6), CD9, and spermatogonia specific markers heat shock protein 90 alpha (Hsp90a), and stimulated by retinoic acid gene 8 (Stra8). These molecules play essential role in stem cells proliferation (Pdgfrb), energy metabolism (Slc2a1), cell adhesion, cell-cell interaction (Itga6, Gja7, Thy-1, and CD9), and germ cell differentiation (Stra8). The expression of these markers in spermatogonial stem cells and other nongerminal stem cells suggests that these cells share elements of common molecular machinery with stem cells in other tissues which are modulated by stem cell protein Piwil2.     

Identification of differentially expressed genes related to metabolic syndrome induced with high-fat diet in E3 rats

Understanding the genes differentially expressing in aberrant organs of metabolic syndrome (MetS) facilitates the uncovering of molecular mechanisms and the identification of novel therapeutic targets for the disease. This study aimed to identify differentially expressed genes related to MetS in livers of E3 rats with high-fat-diet-induced metabolic syndrome (HFD-MetS). E3 rats were fed with high-fat diet for 24 weeks to induce MetS. Then, suppression subtractive hybridization (SSH) technology was used to identify the genes differentially expressed between HFD-MetS and control E3 rat livers. Twenty positive recombinant clones were chosen randomly from forward subtractive library and sent to sequence. BLAST analysis in GenBank database was used to determine the property of each cDNA fragment. In total, 11 annotated genes, 3 ESTs, and 2 novel gene fragments were identified by SSH technology. The expression of four genes (Alb, Pip4k2a, Scd1, and Tf) known to be associated with MetS and other five genes (Eif1, Rnase4, Rps12, Rup2, and Tmsb4) unknown to be relevant to MetS was significantly up-regulated in the livers of HFD-MetS E3 rats compared with control rats using real-time quantitative PCR (RT-qPCR). By analyzing the correlations between the expression of these nine genes and serum concentrations of TG, Tch, HDL-C, and LDL-C, we found that there were significant positive correlations between TG and the expression of five genes (Alb, Eif1, Pip4k2a, Rps12, and Tmsb4x), Tch and three genes (Rnase4, Scd1, and Tmsb4x), and LDL-C and two genes (Rnase4 and Scd1), as well there were significant negative correlations between HDL-C and the expression of three genes (Rup2, Scd1, and Tf). This study provides important clues for unraveling the molecular mechanisms of MetS.     

Identification of differentially expressed genes in seeds of two near-isogenic Brassica napus lines with different oil content

The regulation of seed oil synthesis in rapeseed is largely unknown. In this study, we compared the gene expression during seed development between two lines of Brassica napus with a 10% difference in oil content. We isolated the immature seeds 15 and 25 days after flowering at periods preceding and including the major accumulation of storage oils and proteins. The differentially expressed gene clones between the two rape lines were isolated by subtractive suppression hybridization (SSH). All SSH clones were arrayed and screened by dot blot hybridization, followed by RT-PCR analysis for selected clones. A total of 217 cDNA clones corresponding to 30 genes were found to have a high expression in seeds with high oil content. Six genes were highly expressed in seeds with low oil content. Northern blot and enzyme activity analysis demonstrated a change in expression pattern of several genes. The results provide information on gene-encoding factors responsible for the regulation of oil synthesis. The possible role of these genes in seeds is discussed. The genes in this study may be suitable as novel targets for genetic improvement of seed oil content and may also provide molecular markers for studies of rape breeding.     

The roles of ncRNAs and histone-modifiers in regulating breast cancer stem cells

Cancer stem cells (CSCs), a subpopulation of cancer cells with ability of initiating tumorigenesis, exist in many kinds of tumors including breast cancer. Cancer stem cells contribute to treatment resistance and relapse. Conventional treatments only kill differentiated cancer cells, but spare CSCs. Combining conventional treatments with therapeutic drugs targeting to CSCs will eradicate cancer cells more efficiently. Studying the molecular mechanisms of CSCs regulation is essential for developing new therapeutic strategies. Growing evidences showed CSCs are regulated by non-coding RNA (ncRNA) including microRNAs and long non-coding RNAs (lncRNAs), and histone-modifiers, such as let-7, miR-93, miR-100, HOTAIR, Bmi-1 and EZH2. Herein we review the roles of microRNAs, lncRNAs and histonemodifiers especially Polycomb family proteins in regulating breast cancer stem cells (BCSCs).     

Identification of genes preferentially expressed in periodontal ligament: specific expression of a novel secreted protein, FDC-SP

Gene expression in human periodontal ligament (PDL) was examined by suppression subtractive hybridization to identify genes that are preferentially expressed in tissue compared to cultured PDL fibroblasts. The most enriched genes in a subtracted cDNA library are primarily genes for extracellular matrix components, types I and III collagen, lumican, periostin, and asporin, among others, whose expression conveys unique mechanical properties to the PDL. Also within this group is the gene for follicular dendritic cell secreted protein (FDC-SP), a small protein like statherin in saliva, not previously found in PDL. FDC-SP's presence in PDL was confirmed by in situ hybridization in mouse which also showed that it was definitely present in the parotid gland, but, surprisingly, not in the other salivary glands: submandibular and sublingual. Since only normal tissue was examined, these findings suggest that FDC-SP plays an important but previously unsuspected role within oral connective tissue.