RNA fingerprinting of specific plant cell types: Adaptation to plants and optimization of RNA arbitrarily primed PCR (RAP-PCR)

Differential gene expression contributes to cell differentiation and underlies plant responses to hormonal and environmental factors. Most methods available to identify differentially expressed genes in plants are biased towards moderately or strongly expressed genes. RNA arbitrarily primed polymerase chain reaction (RAP-PCR) produces populations of amplicons from reverse transcribed RNA in a process similar to differential display, but with a higher degree of reproducibility and sensitivity, thus enabling the identification of low abundance mRNA. A detailed RAP-PCR protocol allowing the rapid identification of differentially expressed genes in scarce plant cells, such as stomatal guard cells, is presented here. In addition, a fast and reliable method for the semi-quantitative confirmation of gene expression patterns is described.     

Differential display of mRNA

Differential display of mRNA (DD) is a technique in which mRNA species expressed by a cell population are reverse transcribed and then amplified by many separate polymerase chain reactions (PCR). PCR primers and conditions are chosen so that any given reaction yields a limited number of amplified cDNA fragments, permitting their visualization as discrete bands following gel electrophoresis. This robust and relatively simple procedure allows identification of genes that are differentially expressed in different cell populations. Here we review DD including some recent modifications, and compare it with other techniques for analyzing differential mRNA expression.     

Isolation of differentially expressed genes in human heart tissues

We applied RNA arbitrarily primed-PCR (RAP-PCR) to screen the genes differentially expressed between common congenital heart defects (CHD) [atrial septal defect, ventricular septal defect, Tetrology of Fallot (TOF)] and normal human heart samples. Three of these differentially amplified fragments matched cDNA sequences coding for proteins of unknown function in humans: hCALO (human homologue of calossin), NP79 (coding for a nuclear protein of 79KD) and SUN2 (Sad-1 unc-84 domain protein 2). The other four fragments were from known human genes: apolipoprotein J, titin, dystrophin and protein kinase C-delta. Northern blot analysis confirmed that all of these genes are expressed in the human heart. The results of RAP-PCR were reconfirmed by quantitative RT-PCR in TOF and control heart samples. Both techniques showed the levels of expression of hCALO, NP79 and SUN2 to be comparable in TOF and control samples and the level of expression of dystrophin and titin, both coding for cytoskeletal proteins, to be significantly upregulated in TOF samples. In summary, we have shown that the RAP-PCR technique is useful in the identification of differentially expressed gene from biopsy samples of human CHD tissues. In this manner, we have identified three novel genes implicated in the normal function of the human heart and two known genes upregulated in TOF samples.     

Visualization of Differential Gene Expression – Using Fluorescence‐Based cDNA‐AFLP

cDNA‐AFLP is one of the techniques developed to study differentially expressed genes. This recent technique is advantageous because it does not need prior sequence knowledge and is reliable due to highly stringent PCR conditions. The traditional cDNA‐AFLP method uses radioactively labelled products and is characterised by high sensitivity and resolution. Here, the use of Cy5‐labelled primers to detect products on polyacrylamide gels is reported. This non‐radioactive method, based on fluorescence, is shown to be faster and the recovery of interesting bands is easier. The study of the differential gene expression of the interaction between potato and Phytophthora infestans was used for the valuation of this method. Different gene expression profiles – such as up‐regulation, down‐regulation or point expression – were obtained. Moreover, this technique was shown to be highly reproducible.     

Identification of aerobically and anaerobically induced genes in Enterococcus faecalis by random arbitrarily primed PCR

Enterococci have emerged among the leading causes of nosocomial infection. With the goal of analyzing enterococcal genes differentially expressed in environments related to commensal or environmental colonization and infection sites, we adapted and optimized a method more commonly used in the study of eukaryotic gene expression, random arbitrarily primed PCR (RAP-PCR). The RAP-PCR method was systematically optimized, allowing the technique to be used in a highly reproducible manner with gram-positive bacterial RNA. In the present study, aerobiosis was chosen as a variable for the induction of changes in gene expression by Enterococcus faecalis. Aerobically and anaerobically induced genes were detected and identified to the sequence level, and differential gene expression was confirmed by quantitative, specifically primed RT-PCR. Differentially expressed genes included several sharing identity with those of other organisms related to oxygen metabolism, as well as hypothetical genes lacking identity to known genes.     

Evidence for chimeric sequences formed during random arbitrarily primed PCR

Chimeric sequences were observed to occur abundantly (48% of clones) during random arbitrarily primed polymerase chain reaction (RAP-PCR) experiments designed to examine differential expression of genes involved in metal resistance in sulfate-reducing bacteria (SRB). Some of the chimeric sequences were composed of sequence from a gene differentially expressed under the imposed conditions and a sequence of the 16S or 23S rRNA gene. The remainder were composed of two rRNA sequences. Experiments using PCR and genomic sequence analysis showed that the chimeric sequences were not due to a genetic mutation (e.g., recombination, transposition). As RAP-PCR has been widely used to identify differentially expressed genes, this observation may aid in our interpretation of RAP-PCR data.     

Identification of Aerobically and Anaerobically Induced Genes in Enterococcus faecalis by Random Arbitrarily Primed PCR

Enterococci have emerged among the leading causes of nosocomial infection. With the goal of analyzing enterococcal genes differentially expressed in environments related to commensal or environmental colonization and infection sites, we adapted and optimized a method more commonly used in the study of eukaryotic gene expression, random arbitrarily primed PCR (RAP-PCR). The RAP-PCR method was systematically optimized, allowing the technique to be used in a highly reproducible manner with gram-positive bacterial RNA. In the present study, aerobiosis was chosen as a variable for the induction of changes in gene expression by Enterococcus faecalis. Aerobically and anaerobically induced genes were detected and identified to the sequence level, and differential gene expression was confirmed by quantitative, specifically primed RT-PCR. Differentially expressed genes included several sharing identity with those of other organisms related to oxygen metabolism, as well as hypothetical genes lacking identity to known genes.     

Identification of Differentially Expressed Genes Associated with Osteochondrosis in Standardbred Horses Using RNA Arbitrarily Primed PCR

The aim of this study was to investigate genes for differential expression in cartilage of foals predisposed to osteochondrosis (OC). Tissue was sampled from the cranial part of the distal intermediate ridge of the tibia in the tarso-crural joint. Foals were considered predisposed to OC when parents had OC at the distal intermediate ridge of the tibia. RNA was isolated and subjected to arbitrarily primed PCR (RAP-PCR) followed by fingerprinting to screen for differentially expressed genes. By verification of results from the RAP-PCR fingerprint screening using real-time RT-PCR, we identified two genes not previously correlated with OC as differentially expressed. The two genes, which were identical to TLK2 and an equine EST, are good targets for future research on OC.     

大菱鲆肌肉组织中的基因差异表达与体长性状的相关性研究

为了揭示出一些影响鱼类生长发育速度方面的遗传信息,本文应用mRNA差异显示技术,以同一批受精卵孵化的同池养殖的两组大菱鲆鱼为试验材料,检测了在相同生长发育条件下两组体长相差悬殊的3月龄大菱鲆肌肉组织的基因差异表达。结果：18对引物组合共显示出723条带,其中有527条带能够重现,差异显示条带的重现率为72.89%;在527条稳定的条带中有21条为差异带,其余506条为共有带（96.02%）。21条差异表达条带中有16条（3.04%）为阳性差异表达cDNA片段。这些差异表达cDNA片段的存在,说明体长差异悬殊的两组大菱鲆之间存在基因表达上的差异。试验结果对于进一步分析各种差异表达基因与大菱鲆的生长性状之间的相关关系奠定了基础;为深入研究大菱鲆的生长发育性状的分子遗传机制奠定了基础。     

Screening for ribosomal-based false positives following prokaryotic mRNA differential display

Differential display (DD) and the closely related RNA arbitrarily primed PCR (RAP-PCR) have become the molecular tools of choice for identifying and isolating differentially expressed genes in both eukaryotic and prokaryotic systems. However, one of the current drawbacks of both techniques is the high number of false positives generated. In prokaryotic applications, the many false positive typically generated by DD are subsequently identified as rRNAs because of their greater abundance compared to mRNAs. To circumvent this problem, full-length 16S and 23S rDNA probes, derived from Pseudomonas putida G7 and Pseudomonas aeruginosa FRD1, respectively, were used as a prescreening approach to discriminate between those bands, which appear to be differentially expressed mRNAs, but in fact are rRNAs, following prokaryotic mRNA DD.     

Cataloging altered gene expression in young and senescent cells using enhanced differential display.

Recently, a novel PCR-based technique, differential display (DD), has facilitated the study of differentially expressed genes at the mRNA level. We report here an improved version of DD, which we call Enhanced Differential Display (EDD). We have modified the technique to enhance reproducibility and to facilitate sequencing and cloning. Using EDD, we have generated and verified a catalog of genes that are differentially expressed between young and senescent human diploid fibroblasts (HDF). From 168 genetags that were identified initially, 84 could be sequenced directly from PCR amplified bands. These sequences represent 27 known genes and 37 novel genes. By Northern blot analysis we have confirmed the differential expression of a total of 23 genes (12 known, 11 novel), while 19 (seven known, 12 novel) did not show differential expression. Several of the known genes were previously observed by others to be differentially expressed between young and senescent fibroblasts, thereby validating the technique.     

mRNA差异显示条件的优化

运用优化的mRNA差异显示技术分离受内生真菌诱导的差异基因。优化差异显示条件表现在增如指定引物和随机引物的长度、改变PCR参数和再扩增程序、运用银染显色等。应用这些条件共获得7个阳性差异片段。用未优化的PCR程序1筛选35条差异带,得到3个两端均为随机引物的差示片段。而用优化的PCR程序2,52条差异带中得到9条只能用锚定引物和随机引物才能扩增出的片段。地高辛标记的反向-Northern鉴定为阳性后进行克隆和测序。PCR方法1所得的3个差示片段均无开放的阅读框。PCR程序2得到7个差异表达的基因中,2个为已知基因,5个为未知基因。因此可运用优化的差显技术分离差异表达的基因。     

Differentially expressed genes in response to amoxicillin in Helicobacter pylori analyzed by RNA arbitrarily primed PCR

Because the molecular mechanism of amoxicillin resistance in Helicobacter pylori seems to be partially explained by several mutational changes in the pbp1A gene, the aim of the present study was to evaluate the gene expression pattern in response to amoxicillin in the Amx(R) Hardenberg strain using RNA arbitrarily primed PCR (RAP-PCR). In the experiments, c. 100 differentially expressed RAP-PCR products were identified using five arbitrary primers. The cDNAs that presented the highest levels of induction or repression were cloned and sequenced, and the sequences were compared with those present in databases using the blast search algorithm. The differential expression of the isolated cDNAs was confirmed by real-time PCR. The preliminary results showed that amoxicillin alters the expression of five cDNAs involved in biosynthesis, two involved with pathogenesis, four related to cell envelope formation, two involved in cellular processes, three related with transport and binding proteins, one involved with protein degradation, one involved with energy metabolism and seven hypothetical proteins. Further analysis of these cDNAs will allow a better comprehension of both the molecular mechanism(s) of amoxicillin resistance and the adaptative mechanism(s) used by H. pylori in the presence of this antibiotic.     

嗜盐菌Halobacterium species NRC-1不同盐浓度下基因表达差异分析

用RNA随机起始PCR（RAP—PCR）技术分析了盐杆菌NRC-1（Halobacterium NRC-1）不同NaCl盐度下基因表达的差异。81条引物用于比较17％、30％两种盐度下基因表达的差异,每条引物平均可以产生10条以上扩增条带,共得到15条在2种盐度下差异表达的条带,这些差异扩增条带的获得将有助从分子水平上了解Halobacterium NRC-1在高盐环境下的适应机制。     

用差异显示PCR法筛选与血管外膜细胞表型转化相关的基因

为筛选血管外膜成纤维细胞（adventitial fibroblast,AF）与肌成纤维细胞（myofibroblast,MF）间表型转化有关的基因,实验建立了大鼠胸主动脉AF和MF两种细胞模型,用差异显示聚合酶链反应（DD－PCR）技术获得表达差异片段,对差异片段进行克隆和测序分析,并用定量PCR和Northern blot对差别显示结果进行验证。用反义核酸转染技术观察骨桥蛋白（osteopontin,OPN）对AF迁移的影响。结果表明,两种表型细胞存在明显的基因表达差异,其中一个在MF下调的差异片段与GenBank中NADH脱氢酶亚单位5（NADH dehydrogenase subunit 5,Nd5）基因高度同源。另一个在MF上调的差异片段与OPN基因同源。上述差异表达结果被定量PCR及Northern blot证实。此外还有4个表达序列标志（expressed sequence-tag,EST）在GenBank中未查到同源序列。反义OPN寡脱氧核甘酸可抑制AF的迁移活动。结果提示,AF转化为MF可能与ND5基因下调、OPN上调及其它未知基因的表达改变有关。应用反义技术适度抑制OPN表达在防治血管重塑中具有重要作用。     

Modified differential display technique that eliminates radioactivity and decreases screening time

Several techniques are available that detect variations in gene expression between cellular populations. These include subtractive hybridization (SH), differential colony hybridization (DCH) and mRNA differential display, all based on the analysis of mRNA. The first two techniques, however, are limited because they require large amounts of mRNA for SH or several rounds of screening for DCH. Differential display overcomes both of these limitations. However, the conventional differential display technique is plagued by false positives and is labor intensive. The identification of genes that are truly differentially expressed, therefore, becomes a formidable task. We describe a modified differential display technique that overcomes the limitations of the conventional technique. This new technique eliminates a source of false positives, decreases the time required to screen a set of primers and reduces the use of radioactivity.