Application of mRNA Differential Display to the Identification of Genes Related to Embryonic Development

mRNA differential display was established by Liang and Pardee in 1992 for the purpose of displaying the mRNA differences between two tissues. The early embryonic development in animals is primarily controlled by the maternal RNAs stored in egg. These mRNAs are being degraded as the development proceeds. In some animals, such as fish and amphibian, new transcripts do not appear until the midblastula stage (midblastula transition, MBT). In other animals, for example in mouse, the zygotic genes are expressed during very early stages of development. The mRNA programmed synthesis and degradation during embryonic development controls the cell differentiation, germlayer formation and pattern formation. All these mRNA changes could be displayed side by side as cDNA band differences by mRNA differential display and the genes corresponding to these differential mRNAs could thus be obtained.

Progress in mRNA Differential Display

The mRNA Differential Display is a new molecular biological strategy for detecting and characterizing altered gene expression in eukaryotic cells which wad developed in 1992.Because of its simplicity,sensitivity and reproducibility,this method should find wide-ranging underpaid application developmental and molecular biology.Therecent successful applications of this method to gene hunting and the technological improvement promise great potential of mRNA Differential Display.

Identification of Differentially Expressed Genes Induced by Ammonium Nitrogen in Rice Using mRNA Differential Display

RNAs isolated from ammonium- and nitrate-treated rice leaves were used to screen differentially expressed genes through mRNA differential display. A total of 72 bands appeared significant differences and some of them were further confirmed by reverse Northern and Northern blot. The results showed that two genes, A-02 （Oryza sativa drought stress related mRNA） and A-03 （Zea mays partial mRNA for TFIIB-related protein） were highly up-regulated in the ammonium-fed rice leaves. The enzyme assays showed that the activities of the two anti-oxidative enzymes, catalase and peroxidase, and the content of a non-enzymic antioxidant, glutathione, were significantly higher in the ammonium-fed rice leaves than those in the nitrate-fed ones, indicating that the ammonium nutrition might be beneficial for rice plants to improve the stress resistance during growth and development.

Isolation, Cloning, and Identification of Expressed Sequence Tags from the Backfat Tissue in Duroc and Tongcheng Pigs by mRNA Differential Display

mRNA differential display technique was performed to discuss the differential expression of genes in fat tissue between introduced European and Chinese indigenous pigs. Four anchor primers in combination with five arbitrary primers （20 sets in total） were used and nearly 300 bands were observed in polyacrylamide gel, among which 29 differential display bands were obtained. Twelve of 29 cDNA fragments were identified using reverse Northern dot blot, and subsequently cloned and sequenced. Eight of 12 cDNAs had no matches in GenBank and were submitted to GenBank, and the other 4 showed similarity to identified genes from GenBank. Three among 8 novel ESTs were selected to be further identified by semiquantitative RT-PCR. In our experiment, silver staining DDRT-PCR and DIG primer DNA labeling reverse Northern dot blot were used to avoid radioactive pollution. The result showed that the expressions of 5 among 8 novel ESTs were stronger in the backfat of Tongcheng pigs and the others were weaker than that in Duroc pigs. These novel ESTs were prepared for selecting genes related to adipose cells.

mRNA differential display on gene expression in settlement metamorphosis process of Ruditapes philippinarum larvae

The mRNA differential display (DDRT-PCR) technique was adopted to find out the genes related tosettlement metamorphosis development process of Ruditapes philippinarum larvae.In this study,we haveobtained three hundred and forty-six amplification bands in total from pediveliger larvae,veliger larvae,eye spot larvae and post-larvae.Sixty-five out of three hundred and forty-six bands are distinctly differen-tial display from band pattern,which can be put into four groups,standing for different expression char-acters.Sixteen differential display bands were cloned,sequenced and analyzed and nine different se-quences are obtained in the study.Three sequences have higher similarity to the cDNAs deposited indatabase and three are very similar to the rDNA of other species,considered as the rDNA of Ruditapesphilippinarum.The rest three sequences are found to be novel sequences after analyzed.Their accessionnumbers are AY916799,AY916798,and AY916797 respectively.We thought the novel sequences arepossibly relevant to the early embryo development of Ruditapes philippinarum larvae and can provide somefundamental understandings that are helpful for the improvement of scallop seed raising industry.

Screening for glutamate-induced and dexamethasone-downregulated epilepsy-related genes in rats by mRNA differential display

Background It is known that excessive release of glutamate can induce excitotoxicity in neurons and lead to seizure. Dexamethasone has anti-seizure function. The aim of this study was to investigate glutamatedexamethasone interaction in the pathogenesis of epilepsy, identify differentially expressed genes in the hippocampus of glutamate-induced epileptic rats by mRNA differential display, and observe the effects of dexamethasone on these genes expression. Methods Seizure models were established by injecting 5μl （250 μg/μl） monosodium glutamate （MSG） into the lateral cerebral ventricle in rats. Dexamethasone （5 mg/kg） was injected intraperitoneally at 30 minutes after MSG inducing convulsion. The rats＇ behavior and electroencephalogram （EEG） were then recorded for 1 hour. The effects of dexamethasone on gene expression were observed in MSG-induced epileptic rats at 1 hour and 6 hours after the onset of seizure by mRNA differential display. The differentially expressed genes were confirmed by Dot blot. Results EEG and behaviors showed that MSG did induce seizure, and dexamethasone could clearly alleviate the symptom, mRNA differential display showed that MSG increased the expression of some genes in epileptic rats and dexamethasone could downregulate their expression. From more than 10 differentially expressed eDNA fragments, we identified a 226 bp eDNA fragment that was expressed higher in the hippocampus of epileptic rats than that in the control group. Its expression was reduced after the administration of dexamethasone. Sequence analysis and protein alignment showed that the predicted amino acid sequence of this cDNA fragment kept 43% identity to agmatinase, a member of the ureohydrolase superfamily. Conclusions The results of the current study suggest that the product of the 226 bp eDNA has a function similar to agmatinase. Dexamethasone might relax alleviate seizure by inhibiting expression of the gene.

Stage-specific expression genes of the Spirometra erinaceieuropaei plerocercoid screened by mRNA differential display technique

Background The stage-specific expression of genes is o ne of the most characteristics of parasites. It has been found that a lot of gen es of Spriometra erinaceieuropaei are specifically expressed in pleroceroid in large amount, but not expressed when the plerocercoid development into adult worm. The study is to screen other stage-specific ecpression genes of plerocerc oid of Spirtmetra erinceieuropaei.Methods RNA was separately extracted by acid guanidinium thiocyanate-phenol-chloroform from plerocercoids and adult worms of Spirometra erinaceieuropaei, DN A contaminated in the RNA was digested by RNase-free DNase. After the RNA was reverse transcripted to cDNA using T 12 MA, T 12 MC, T 12 MG and T 12 MT anchor-primers, PCR was done using the same T 12 MN and one random primer with α 35 S-dATP in the system. The PCR products were fractionated on an 8% denatured polyacrylamide gel. Differential bands of the plerocercoid found in the gel were cut out, amplified by PCR and sequenced. Northern hybridization was used to identify the stage-specific expression genes.Results Eleven differential bands were selected from the gel and classified into 3 kinds of gene fragments by hybridization, after they were amplified by PCR. Fragments 1 (238 bp) and 2 (383 bp), were confirmed by Northern hybridization, as being expressed in the plerocercoid. However, fragment 3 (433 bp), was expressed in both the plerocercoid and the adult worm. Data from the 3 gene fragments underwent homological analysis in GenBank. The sequence which was homologous with fragments 1 and 2 was not found, but fragment 3 had high homology with many kinds of 28S rRNA. Conclusions The gene expressions of plerocercoids are different from adult worms because they live in different hosts. Two types of different gene fragments from the plerocercoid were found by mRNA differential display technique.

ESTABLISHMENT OF DIFFERENTIAL DISPLAY mRNA AND ITS APPLICATION IN THE STUDY ON THE MECHANISM OF LUNG CANCER INDUCED BY RADIATION

Objective: A method for separating mRNAs by means of the polymerase chain reaction (differential display mRNA), and identifying the genes related to radiation-induced lung cancer was introduced. Methods: The RNAs were isolated from two pairs of samples, SV40-immortalized human fetal tracheal fibroblast cell (SHTF) versus αSHTF cell (transformed SHTF cell induced by α particles) and lung cancer tissue versus normal lung tissue obtained from one miner, and amplified by RTPCR. The differential expressed gene fragments were displayed by autoradiograph or silver nitrate stain. Results: The differential display mRNA method was established using both cell and tissue samples. The bands stained by silver nitrate were clearer than those on X-ray film. The rate of reamplification of differentially expressed gene fragments stained by silver nitrate is 80%, higher than that by autoradiograph, 50%. Conclusion: Differential display mRNA method was established successfully on both cell and tissue samples. The modified method for staining band increased the rate of reamplification and established the basis for confirming relative genes.

Genes Differentially Expressed in Human Lung Fibroblast Cells Transformed by Glycidyl Methacrylate

Objective To define the differences in gene expression patterns between glycidyl methacrylate (GMA)-transformed human lung fibroblast cells (2BS cells) and controls. Methods The mRNA differential display polymerase chain reaction (DD-PCR) technique was used. cDNAs were synthesized by reverse transcription and amplified by PCR using 30 primer combinations. After being screened by dot blot analysis, differentially expressed cDNAs were cloned, sequenced and confirmed by Northern blot analysis. Results Eighteen differentially expressed cDNAs were cloned and sequenced, of which 17 were highly homologous to known genes (homology = 89%-100%) and one was an unknown gene. Northern blot analysis confirmed that eight genes encoding human zinc finger protein 217 (ZNF217), mixed-lineage kinase 3 (MLK-3), ribosomal protein (RP) L15, RPL41, RPS16, TBX3, stanniocalcin 2 (STC2) and mouse ubiquitin conjugating enzyme (UBC), respectively, were up-regulated, and three genes including human transforming growth factor b inducible gene (Betaig-h3), a-1,2-mannosidase 1A2 (MAN 1A2) gene and an unknown gene were down-regulated in the GMA-transformed cells. Conclusion Analysis of the potential function of these genes suggest that they may be possibly linked to a variety of cellular processes such as transcription, signal transduction, protein synthesis and growth, and that their differential expression could contribute to the GMA-induced neoplastic transformation.

Isolation, Identification and Tissue Expression Profile Analysis of One Novel Differentially Expressed Sequence Tag in the Longissimus dorsi Muscle from Meishan, Meishan × Large White Hybrid and Large White Pigs

In order to detect the molecular mechanism of heterosis in pigs, the mRNA differential display technique was performed to investigate the differences of gene expression in the Longissimus dorsi tissue from Meishan, Meishan × Large White hybrid and Large White pigs with nine 3'-end anchored primers in combination with ten 5'-end arbitrary primers and nearly 3000 reproducible bands were examined. One novel expressed sequence tag (EST4, GenBank accession number: AY553914) that was differentially expressed in Meishan, Meishan× Large White hybrid and Large White pigs was isolated from the Longissimus dorsi muscle tissue and identified through semi-quantitative RT-PCR. BLAST analysis revealed that the 350 bp long EST (EST4) was not homologous to any of the known porcine genes. Tissue expression profile analyses showed that the EST4 was expressed in most of tissues.LIU Yong-gang, Ph D candidate

Differential Gene and Protein Expression in Soybean at Early Stages of Incompatible Interaction with Phytophthora sojae

Soybean root and stem rot caused by Phytophthora sojae is a destructive disease worldwide. Using genetic resistance is an important and major component in the integrated pest management of this disease. To understand molecular mechanisms of root and stem rot resistance in soybeans, the gene and protein expression in hypocotyls and stems of variety Suinong 10 carrying resistance genes Rps1a and Rps2 was investigated by using mRNA differential display reverse transcription PCR and two-dimensional electrophoresis at 0, 0.5, 1, 2, and 4 h after inoculation with P. sojae race 1. The results of the comparison of gene and protein expression showed that at least eight differential fragments at the transcriptional level were related to metabolic pathway, phytoalexin, and signal transduction in defense responses. Sequence analyses indicated that these fragments represented cinnamic acid 4-hydroxylase gene, ATP b gene coding ATP synthase b subunit and ubiquitin-conjugating enzyme gene which upregulated at 0.5 h post inoculation, blue copper protein gene and UDP-N-acetyl-a-D-galactosamine gene which upregulated at 2 h post inoculation, TGA-type basic leucine zipper protein TGA1.1 gene, cyclophilin gene, and 14-3-3 protein gene which upregulated at 4 h post inoculation. Three resistance-related proteins, a-subunit and b-subunit of ATP synthase, and cytochrome P450-like protein, were upregulated at 2 h post inoculation. The results suggested that resistance-related multiple proteins and genes were expressed in the recognition between soybean and P. sojae during zoospore germination, penetration and mycelium growth of P. sojae in soybean.

Isolation, Identification of Differentially Expressed Sequence Tags in the Backfat Tissue from Meishan, Large White and MeishanLarge White Cross Pigs

In order to detect the molecular mechanism of heterosis in pigs, the mRNA differential display technique was performedto investigate the differences of gene expression in the backfat tissue from Meishan, Large White and MeishanLargeWhite cross pigs. Nine 3'-end anchored primers in combination with ten 5'-end arbitrary primers were used to perform thedifferential display PCR and nearly 3 000 reproducible bands were examined. Fifteen expressed sequence tags that weredifferentially expressed were isolated and then identified through semi-quantitative RT-PCR. BLAST analysis revealedthat the fifteen expressed sequence tags (ESTs) were not homologous to any of the known porcine genes or ESTs. Thesenovel ESTs were then submitted to GenBank.

Identification of a Lectin Gene Induced in Rice in Response to Magnaporthe grisea Infection

By mRNA differential display, eight induced cDNAs were obtained from rice leaves infected with an incompatible race 131 of Magnaporthe grisea, and one of these cDNAs was highly similar to salt-induced mannose-binding lectin gene. Using this fragment as a probe, a full length cDNA was isolated from a nice cDNA library, which was constructed using mRNA from the incompatible race-infected leaves. Sequence analysis indicates that the cDNA encodes a protein of 15 kD with 145 amino, acids and shares 96% identity at nucleotide level with MRL and salT, but is identical to MRL at amino acid level. Genomic Southern blotting shows that there are two mannose-binding lectin genes in rice genome. Northern blotting analysis indicates that the gene was strongly and specifically induced in rice leaves infected with the incompatible race, suggesting that the lectin induction be involved in the defense of rice to M. grisea.

Identification of a Herbicide Safener AD-67 Inducible cDNA in Rice

A herbicide safener AD-67 inducible cDNA was identified in an indica rice variety 9311 by mRNA differential display. The transcript was increased 6 h after sprayed with the safener solution, and 4 days later, the expression still could be detected. The fragment was recycled from the polygel and sequenced, and homologous analysis revealed the cDNA was 100% identical to some ESTs and cDNAs in rice database, and the amino acid sequence was 60-84% homologous to those of the Yippee genes in several eukaryotes. The fragment was extended to the whole long cDNA, and thus a primer pair was designed. RT-PCR analysis for the designed primer supported the induction result.

Construction of Hybrid Enzyme from HEC-SOD and Cu,Zn-SOD

Human extracellular superoxide dismutase(hEC-SOD) is a secreted tetrameric protein involved in the protection of a human body from oxygen free radicals. Its three-dimensional structure has not been confirmed. hEC-SOD couldn′t be expressed in E.coli. We constructed a hybrid enzyme, which comprises the N-terminal and C-terminal domains from hEC-SOD, fused it to human Cu,Zn-SOD. The hybrid enzyme is expressed successfully in E.coli. Further, we analyzed the expression of hEC-SOD in E.coli by mRNA differential displaying.

SCREENING OF DRUG RESISTANCE-RELATED GENES FROM HUMAN OVARIAN CANCER CELL LINE OC3/ADR BY DD-PCR

Objective: To screen novel genes related to adriamycin (Adr) resistance from human ovarian cancer resistance cell line OC3/Adr. Methods: Multidrug resistant ovarian cancer cell line OC3/Adr was induced by intermittent treatment of the human parent cell line OC3 with high concentration Adr. The difference of gene expression was screened by using different display analysis to the acquired Adr-resistance subline OC3/Adr and its parent cell line OC3. Results: OC3/Adr cell line was obtained which was more resistance to Adr than the parent cell line OC3 with the resistance index (RI) of 15.4. The OC3/Adr cell line also showed cross-resistance to other anti-cancer drugs (VP16, CDDP,5FU). It grew slowly and exhibited changes of cell cycle. A number of differentially expressed ESTs (Expressed Sequence Tags, ESTs) were identified at mRNA level between the OC3/Adr and OC3. Four of 18 different ESTs were sequenced. The 431/432 base pair S1 was homologous to human sperm zona pellucida binding protein, while the other two ESTs, S3 and S4, were new gene segments, which were registered to GenBank with the number of AF 117656 and AF 126507 respectively. Particularly, the expression of S2 sequence increased in all the drug-resistance cell lines and S3 sequence overexpressed in human ovarian cancer tissues as compared with benign ovarian tumors. Conclusion: Drug resistance induced by Adr in ovarian cancer OC3/Adr is involved with changes of multiple gene expressions.

IDENTIFICATION OF DRUG RESISTANT RELATED cDNA IN LUNG ADENOCARCINOMA CELL LINES

Objective: To clone multidrug resistance (MDR) related genes in lung adenocarcinoma cell lines. Methods: The differentially expressed cDNA fragments between A549 and A549 DDP cells were analyzed by mRNA differential display PCR(DD RT-PCR). The fragments thus obtained were further analyzed by DNA sequencing and Northern blotting. Results: Three differentially expressed cDNA fragments were obtained and confirmed by Northern blot. Sequence analysis revealed that two of them were novel and one was 100% identical with ICE gene. Conclusion: Analyzing differentially expressed fragment between A549 and A549 DDP cells may be helpful for finding new MDR related genes. The drug resistance of A549 DDP cells may be related to the inhibition or down-regulation of ICE gene.

Screening of Novel Epilepsy-Related Genes and Isolation and Identification of cDNAs

Summary: Twenty cDNA differential fragments were isolated from the hippocampus of rats in epileptic state. using mRNA differential display technique. Four fragments were sequenced and compared with the known sequences in the Genebank, which showed that ERGS, ERG12, ERG12 had no significant identity to any known sequences; ERG14 had 64 %-69 % identity to micro- tubulin-associated protein of the rat. Because the differential expression of these genes was caused by epilepsy inducer coriaria lactone (CL) and anti-epilepsy drug MK-801 and ERGS might be a novel candidate epilepsy gene; ERG11 and ERG12 might be novel candidate anti-epilepsy genes. Since the microtubulin-associated protein is closely associated with the collateral sprouting of mossy.fibers in the hippocampus of seizured rat, the high expression of ERG14 in the early stage of epilepsy might predict the growth of axon and formation of synapse.

Active Methyl Cycle and Transfer Related Gene Expression in Response to Drought Stress in Rice Leaves

Three rice varieties, Zhonghan 3, Shanyou 63 and Aizizhan, were used as materials in detecting differential active methyl cycle and transfer related gene expression in response to drought stress. The experiment was performed by gene chip and mRNA differential display technologies under the conditions of drought simulated with 10% PEG6000 solution. The results indicated that the methyl cycle could be activated in the leaves of Zhonghan 3 and Shanyou 63 but inhibited in the leaves of Aizizhan under drought stress. Furthermore, drought stress could induce the expression of a large number of methyltransferase genes, especially the transcription of Rubisco protein methylation related genes, which are beneficial for prevention of Rubisco protein oxidation and degradation, and drought stress could inhibit the transcription of DNA methyltransferase genes and histone methyltransferase genes. This result confirmed that the active methyl cycle and transfer related genes were involved in rice drought resistance.