mRNA Differential Display Research Articles

Characterization of gene expression of QM from Caragana jubata, a plant species that grows under extreme cold

Caragana [Caragana jubata (Pall.) Poir] is a temperate plant that thrives well under extremes of cold in high altitude of Himalaya and hence the plant is expected to be a source of genes that might play an important role in tolerance to low temperature (LT). In order to identify LT inducible gene(s), differential display of mRNA (DD) was performed using the apical buds growing under snow as well as growing in the near vicinity without snow, and a LT inducible QM gene (CjQM) homologue was identified. Realizing the importance of QM gene (which encodes human Wilms' tumor suppressor QM protein) in aggregation of 40 and 60S ribosomal subunit and that not much has been reported on this gene in plant systems in relation to its relationship with LT, full length cDNA of CjQM was cloned through rapid amplification of cDNA ends. The gene (977 bp), encoded by small gene family, had an open reading frame of 651 bp and was found to be intronless. The gene exhibited up-regulation within 20 min of exposure to LT and abscisic acid (ABA), but no significant change in gene expression was observed in response to drought stress (DS), salicylic acid (SA) and methyl jasmonate (MJ) application. Up-regulation of CjQM was obtained in the tissues growing in situ under snow. Non-responsiveness of CjQM towards DS, SA and MJ, but up-regulation in response to LT and ABA suggested a specific regulation of the gene in Caragana under varied cues.

Differential display reveals a novel pig gene, PRPF3, which is differentially expressed in Large White versus Wujin skeletal muscle tissues

The mRNA differential display technique was performed to investigate gene expression differences in the longissimus dorsi muscle from Wujin and Large White pigs. A fragment of one differentially expressed gene was isolated and sequenced. A complete cDNA sequence of the gene was obtained using the rapid amplification of cDNA ends method. The open reading frame of this gene encodes a protein of 683 amino acids, which is homologous with the PRP3 pre-mRNA processing factor 3 (PRPF3) of five species: bovine (99%), human (99%), sumatran orangutan (99%), mouse (99%) and chicken (94%). This newly identified gene was respectively defined as the swine PRPF3 gene. This gene is structured in 15 exons and 14 introns as revealed by computer-assisted analysis. The phylogenetic tree analysis revealed that the swine PRPF3 gene has a closer genetic relationship with the PRPF3 gene of sumatran orangutan.

A novel sheep gene,MMP7, differentially expressed in muscles from black-boned sheep and local common sheep

Differences in gene expression in muscles from Chinese black-boned sheep and local common sheep were investigated using mRNA differential display. One differentially expressed novel gene was identified through semi-quantitative RT-PCR, and the full-length cDNA sequence was then obtained using the rapid amplification of cDNA ends (RACE). The nucleotide sequence of this gene is not homologous to any of the known sheep genes, but it contains an open reading frame encoding a protein of 416 amino acids, which has high homology with matrix metallopeptidase 7 (matrilysin, uterine) (MMP7) of 10 species: bovine (93%), rhesus monkey (75%), human (74%), pig (73%), chimpanzee (73%), dog (73%), horse (72%), mouse (66%), rat (65%), and chicken (53%). Thus the novel gene can be defined as the sheep MMP7 gene. It was finally assigned to GeneID:100192317. The phylogenetic tree analysis revealed that the sheep MMP7 gene is closely related to the bovine MMP7. Our experiment is the first one to establish the primary foundation for further research on the sheep MMP7 gene.

Differential gene expression profiles in embryos of the lizard Podarcis sicula under in ovo exposure to cadmium

Screening for differentially expressed genes is a straightforward approach to study the molecular basis of contaminant toxicity. In this paper, the mRNA differential display technique was applied to analyze transcriptional regulation in response to cadmium exposure in the lizard embryos. Lizard eggs may be particularly susceptible to soil contamination and in ovo exposure may interfere or disrupt normal physiological function in the developing embryo, including regulation of gene expression. Fertilized eggs of the lizard Podarcis sicula were incubated in cadmium-contaminated soil at 25 °C for 20 days. Gene expression profiling showed 5 down- and 9 up-regulated genes. Four cDNAs had no homology to known gene sequences, thus suggesting that may either encode not yet identified proteins, or correspond to untranslated regions of mRNA molecules. Four fragments exhibited significant sequence similarity with genes encoding novel proteins or ESTs derived from other vertebrates. The remaining genes are mainly involved in molecular pathways associated with processes such as membrane trafficking, signal transduction, cytoskeletal organization, cell proliferation and differentiation. Cadmium also affected the expression of factors actively involved in the regulation of the transcription machinery. Down-regulated genes are mainly associated with cellular metabolism and cell-cycle regulation and apoptosis. All of these differentially expressed genes may represent candidates that function in cadmium responses. The present study leads to an increased understanding of genes and/or the biochemical pathways involved in perturbation of embryo development following cadmium exposure.

MTOR/S6 Kinase Pathway Contributes to Astrocyte Survival during Ischemia

Neurons are highly dependent on astrocyte survival during brain damage. To identify genes involved in astrocyte function during ischemia, we performed mRNA differential display in astrocytes after oxygen and glucose deprivation (OGD). We detected a robust down-regulation of S6 kinase 1 (S6K1) mRNA that was accompanied by a sharp decrease in protein levels and activity. OGD-induced apoptosis was increased by the combined deletion of S6K1 and S6K2 genes, as well as by treatment with rapamycin that inhibits S6K1 activity by acting on the upstream regulator mTOR (mammalian target of rapamycin). Astrocytes lacking S6K1 and S6K2 (S6K1;S6K2-/-) displayed a defect in BAD phosphorylation and in the expression of the anti-apoptotic factors Bcl-2 and Bcl-xL. Furthermore reactive oxygen species were increased while translation recovery was impaired in S6K-deficient astrocytes following OGD. Rescue of either S6K1 or S6K2 expression by adenoviral infection revealed that protective functions were specifically mediated by S6K1, because this isoform selectively promoted resistance to OGD and reduction of ROS levels. Finally, "in vivo" effects of S6K suppression were analyzed in the permanent middle cerebral artery occlusion model of ischemia, in which absence of S6K expression increased mortality and infarct volume. In summary, this article uncovers a protective role for astrocyte S6K1 against brain ischemia, indicating a functional pathway that senses nutrient and oxygen levels and may be beneficial for neuronal survival.

SOCS6, down-regulated in gastric cancer, inhibits cell proliferation and colony formation

Members of the suppressor of cytokine-induced signaling (SOCS) family are negative regulators of cytokine signaling pathways. By mRNA differential display, we showed that SOCS6 was frequently down-regulated in gastric cancer (GC). Our data showed that allelic loss and promoter hypermethylation may account for the major mechanisms leading to SOCS6 inactivation. Ectopic expression of SOCS6 suppressed cell growth and colony formation, in part through eliciting intrinsic apoptotic pathway, accompanied with decreased mitochondrial membrane potential. Taken together, this study provides molecular and functional data supporting the importance of loss-of-function of SOCS6 as a frequent event in gastric tumorigenesis.

Identification and characterization of a novel CXC chemokine in xenograft tumor induced by mas‐overexpressing cells

Overexpressions of G protein-coupled receptor (GPCR) with elevated downstream signaling events have been reported in various tumors. However, the cellular mechanism that GPCR overexpression leads to tumor formation is largely unknown. The orphan GPCR mas was originally isolated from a human epidermoid carcinoma. In vivo studies of mas-overexpressing cells suggested that xenograft tumor formation was positively correlated with the levels of mas expression. Histochemical analysis indicated that xenograft tumor consisted of mas-transfected and stromal cells. Biochemical analyses revealed that cells overexpressing mas exhibited significantly increased anchorage-independent growth, whereas there was no significant difference in cell proliferation in comparison with empty vector-transfected control cells. Expression profiling using mRNA differential display and Northern analysis indicated an elevated expression of GRO and a novel CXC chemokines, tumor-induced factor (TIF), in mas-transfected cells and xenograft tumor. Bacterially expressed recombinant TIF was found to act as a neutrophil chemoattractant in a chemotactic assay. These results suggest that mas overexpression enables anchorage-independent growth of transformed cells, and interplays of secreted chemokines with stromal cells modulate xenograft tumor formation. Importantly, a novel CXC chemokine, TIF, was identified in the xenograft tumor tissues.

Components of variance in transcriptomics based on electrophoretic separation of cDNA fragments (cDNA‐AFLP)

The sources of variance and errors in transcriptomics based on the electrophoretic separation of amplified cDNA fragments were investigated using cDNA-amplified fragment length polymorphism (AFLP). Transcriptome profiles of the plant-pathogenic fungus Verticillium longisporum were generated by a standard cDNA-AFLP protocol followed by electrophoretic separation of amplified DNA fragments in flatbed polyacrylamide gels with fluorescence detection as well as by capillary electrophoresis (DNA sequencer). The total variance was partitioned into contributions of cDNA synthesis, adapter ligation, preamplification, amplification, and electrophoresis. Parameters of computer-aided peak recognition and matching were investigated and strategies improving matching success based on double passage with different signal intensity thresholds were developed. The overall quality of data was similar for cDNA-AFLP and microarray hybridization. Variance of cDNA-AFLP was independent of signal intensity, whereas microarray data showed higher variance for low-intensity signals. Capillary electrophoresis significantly reduced the number of wrongly matched and unmatched signals as compared with flatbed gels. These results are also likely to apply to related electrophoresis-based transcriptome analysis techniques such as mRNA differential display.

Differential display mediated cloning of anthocyanidin reductase gene from tea (Camellia sinensis) and its relationship with the concentration of epicatechins

Tea [Camellia sinensis (L.) O. Kuntze] leaves are a major source of epicatechin (EC) and its gallolyl derivatives epicatechin gallate, epigallocatechin and epigallocatechin gallate, collectively known as epicatechins (ECs). Epicatechins are important factors determining tea quality, and they also possess many medicinal properties. To gain further information about the regulation of the biosynthesis of ECs, we cloned the gene encoding anthocyanidin reductase from tea (CsANR) by first quantifying changes in the concentrations of ECs in response to drought, gibberellic acid (GA(3)), abscisic acid (ABA) and wounding treatments, followed by differential display of mRNAs and analysis of those bands exhibiting a change in expression paralleling the treatment-induced changes observed in the EC data. Analysis of 133 bands yielded a partial cDNA of CsANR that was later cloned to the full length by rapid amplification of the cDNA ends. The full-length CsANR (Accession No. AY641729) comprised 1233 bp with an ORF of 1014 bp (from 79 to 1092 bp) encoding a polypeptide of 337 amino acids. Expression of CsANR in an Escherichia coli expression vector yielded a functional protein that catalyzed the conversion of cyanidin to EC in the presence of NADPH. Analysis of ECs and gene expression in leaves at different developmental stages and across five tea clones exhibiting variable concentrations of ECs revealed a positive correlation between concentration of ECs and CsANR expression. Expression of CsANR was down-regulated in response to drought, ABA and GA(3) treatments and up-regulated in response to wounding.

A new tip homolog, ShTIP, from Salicornia shows a different involvement in salt stress compared to that of TIP from Arabidopsis

To obtain an insight into the comprehensive molecular characteristics of the salt tolerance mechanism, we performed a screening for salt inducible genes in a halophytic plant, Salicornia herbacea, using mRNA differential display. A comparative analysis of gene expression in Salicornia grown in control and salt-stressed conditions led to the detection of a gene that was induced by salt. Both sequence analysis and a subsequent database search revealed that this gene was highly homologous to tonoplast intrinsic proteins (TIPs) from a variety of plant species. This gene, designated as ShTIP, is 1014 bp in size and contains a coding region of 762 nucleotides, which encodes a protein of 254 amino acids. Northern blot analysis revealed that ShTIP was predominantly expressed in shoots under normal conditions. However, salt stress induced high expression of ShTIP in both the shoots and roots. The expression of ShTIP in a salt-sensitive calcineurin-deficient yeast mutant (cnbΔ) resulted in a resistance to the high salt conditions. In addition, we compared the expression of a TIP gene in Arabidopsis with that of ShTIP under different conditions and found that the Salicornia TIP has a different regulatory mechanism for adapting to salt stress conditions compared with the glycophyte Arabidopsis TIP. These results indicate that ShTIP plays an important role in salt tolerance.

Porcine skeletal muscle differentially expressed gene CMYA1: isolation, characterization, mapping, expression and association analysis with carcass traits

To investigate the differences in gene expression between some obese and lean pig breeds, differential display of mRNA was employed in our previous research. One differentially expressed EST (BI596262) was further identified as the porcine cardiomyopathy associated 1 (CMYA1) gene because of its homology to the human CMYA1 gene. The full-length DNA of the porcine CMYA1 gene encompasses 9379 bp, including a complete open reading frame encoding 1839 amino acid residues, a 158-bp 5'-untranslated region and a 630-bp 3'-untranslated region. The porcine CMYA1 gene was assigned to chromosome 13 by the radiation hybrid panel (IMpRH). The porcine CMYA1 gene was expressed only in the striated muscle. Single nucleotide polymorphism (SNP) scanning in the coding region identified one synonymous mutation (c.1053C>T) and three missense mutations, c.1394A>G (p.His465Arg), c.1751A>G (p.Asp582Gly) and c.3290C>A (p.Thr1097Asp). The allele frequencies were tested among about 200 unrelated pigs from several pig breeds. Linkage mapping was further conducted with the SNP c.1751A>G (p.Asp582Gly) in a Berkshire x Yorkshire resource family and this confirmed that porcine CMYA1 is closely linked with Sw344 (distance = 2 cM, LOD score is 129.47), an interesting region harbouring a QTL for back fat thickness. Association analysis in our experimental pig population showed that different genotypes of CMYA1 gene were associated with different back fat thicknesses (P < 0.05). Our results suggest that the porcine CMYA1 gene has effects on porcine back fat deposition and further investigation will be necessary to illustrate the underlying mechanisms.

T351 protein, a novel tumor associated antigen and potential target for immunotherapy

Tumor immunotherapy has attracted many attentions in recent years because of its high specificity. However, the use of immunotherapy is hampered by the lack of defined target tumor antigens. T351 gene, a novel tumor associated gene identified by mRNA differential display, encodes a transmembrane protein. We found that T351 is overexpressed in tumor tissues and tumor cell lines at both mRNA and protein levels by quantitative reverse transcription-PCR, immunohistochemistry and flow cytometry analyses, respectively. We also show that the extracellular portion of T351 protein termed T351pro.philic specifically activate CTLs to lyse tumor cell targets. In addition, a monoclonal antibody raised against T351pro.philic (McAb C1-1) induced murine macrophages to kill tumor cells effectively both in vitro and in vivo. These results suggest that T351 protein is a novel tumor associated antigen.

The novel epididymis-specific beta-galactosidase-like gene Glb1l4 is essential in epididymal development and sperm maturation in rats.

We describe a novel epididymis-specific cDNA named Glb1l4, which was isolated from rat epididymis by differential display of mRNAs. Glb1l4 cDNA contains 2607 nucleotides and encodes a 637-amino acid protein with 50% similarity to mouse beta-galactosidase. The gene is located on chromosome 8q13, spanning 21 exons. Northern blot analysis reveals that Glb1l4 is specifically expressed in the caput region of epididymis and upregulated by androgen. A specific polyclonal antiserum against the N-terminal peptide of GLB1L4 has been produced. Western blot analysis and immunohistochemistry assay reveal that GLB1L4 is specifically expressed in the principal cells of the caput epididymis. Interestingly, its expression peaks at Postnatal Day 45 in mRNA level and at Postnatal Day 60 in protein level while the epididymis column cells undergo differentiation. Moreover, within this very period this secretory protein is confined inside the cell with a change of subcellular distribution pattern, which implies its important roles in the cell differentiation process. Only after the epididymal epithelium differentiation is completed and the spermatozoa enter the epididymal lumen is the GLB1L4 secreted into the luminal fluid and bound on the sperm head. Our results suggest that GLB1L4 may play various roles in principal cell differentiation and sperm maturation.

Genomic expression analysis by single-cell mRNA differential display of quiescent CD8 T cells from tumour-infiltrating lymphocytes obtained from in vivo liver tumours.

We performed a genomic study combining single-cell mRNA differential display and RNA subtractive hybridization to elucidate CD8 T-cell quiescence/ignorance. By comparing actively maintained quiescent CD8 T cells from liver tumour tumour-infiltrating lymphocytes (TILs) with quiescent T cells at the single-cell level, we identified differentially expressed candidate genes by high-throughput screening and comparative analysis of expressed sequence tags (ESTs). While genes for the T-cell receptor, tumour necrosis factor (TNF) receptor, TNF-related apoptosis inducing ligand (TRAIL) and perforin were down-regulated, key genes such as Tob, transforming growth factor (TGF)-beta, lung Krüpple-like factor (LKLF), Sno-A, Ski, Myc, Ets-2 repressor factor (ERF) and RE1-silencing transcription factor (REST/NRSF) complex were highly expressed in the quiescent TIL CD8 cells. Real-time polymerase chain reaction (PCR) further confirmed these results. A regulation model is proposed for actively maintained quiescence in CD8 T cells, including three components: up-regulation of the TGF-beta pathway, a shift in the MYC web and inhibition of the cell cycle.

Screening and identification of differentially expressed genes in Beijing fatty and broiler breast muscles

mRNA differential display reverse-transcripton PCR(DDRT-PCR) was applied to identify differentially expressed genes in Arbor Acres broiler(AA) and Beijing fatty chicken breast muscles in order to find the mechanism which induces the differential gene expression at the molecular level. A total of 7 ESTs were found using reverse Northern dot blot, and all of them were compared with the nucleotide sequences in GenBank database using BLAST. S1 was highly similar to HMGN3; S3 was highly similar to ChEST294a8 with unknown functions; S4 and S5 were highly similar to PGM; S6 and S2 had highly similar nucleotide sequences with unknown functions in nucleotide databases; S7 had no significant similarity with existing genes or ESTs and was regarded as a new EST. The new EST was submitted to GenBank(Accession number: EU594549). This lays a foundation for further study on the mechanism of differential gene expression in Beijing fatty and AA breast muscles.

A Novel Role for Embigin to Promote Sprouting of Motor Nerve Terminals at the Neuromuscular Junction

Adult skeletal muscle accepts ectopic innervation by foreign motor axons only after section of its own nerve, suggesting that the formation of new neuromuscular junctions is promoted by muscle denervation. With the aim to identify new proteins involved in neuromuscular junction formation we performed an mRNA differential display on innervated versus denervated adult rat muscles. We identified transcripts encoding embigin, a transmembrane protein of the immunoglobulin superfamily (IgSF) class of cell adhesion molecules to be strongly regulated by the state of innervation. In innervated muscle it is preferentially localized to neuromuscular junctions. Forced overexpression in innervated muscle of a full-length embigin transgene, but not of an embigin fragment lacking the intracellular domain, promotes nerve terminal sprouting and the formation of additional acetylcholine receptor clusters at synaptic sites without affecting terminal Schwann cell number or morphology, and it delays the retraction of terminal sprouts following re-innervation of denervated endplates. Conversely, knockdown of embigin by RNA interference in wild-type muscle accelerates terminal sprout retraction, both by itself and synergistically with deletion of neural cell adhesion molecule. These findings indicate that embigin enhances neural cell adhesion molecule-dependent neuromuscular adhesion and thereby modulates neuromuscular junction formation and plasticity.

Molecular cloning, polymorphism and association analyses of a novel differentially expressed porcine mRNA

The mRNA differential display technique was performed to investigate the differences of gene expression in the longissimus muscle tissues from Meishan and Large White pigs. One novel mRNA that was differentially expressed was identified through semi-quantitative RT-PCR and the full-length cDNA sequence was then obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the mRNA is not homologous to any of the known porcine genes. Sequence prediction analysis revealed that this mRNA is no-coding mRNA. Polymorphism analyses revealed that there was a C-T mutation on the position of 505 bp and PCR-HhaI-RFLP analyses revealed that Chinese indigenous pig breeds and exotic pig breeds displayed obvious genotype and allele frequency differences at this locus. Association analyses revealed that this polymorphic locus was significantly associated with the drip loss rate, water holding capacity, dressing percentage, rib numbers, lean meat percentage, estimated lean meat percentage, loin eye width and loin eye area (P < 0.05).

Up-regulation and clinical relevance of novel helicase homologue DHX32 in colorectal cancer

BackgroundThis study aimed to find novel biomarkers for colorectal cancer.MethodsFluorescent mRNA differential display PCR (DD-PCR) was used to screen the genes differentially expressed in colorectal cancer tissues and their adjacent tissues. The differentially expressed genes were confirmed by real-time PCR and then their clinical relevance (such as association with tumor location and lymph gland metastasis) was further investigated.ResultsWe identified by DD-PCR a novel RNA helicase, DHX32, which showed higher expression in colorectal cancer tissues than their adjacent tissues, and this result was confirmed by real time RT-PCR. In addition, we found that the level of DHX32 gene expression in colorectal cancer was significantly associated with cancer location, lymph gland metastasis, cancer nodal status, differentiation grade, and Dukes, stage.ConclusionDHX32 may play an important role in the development of colorectal cancer and could serve as a novel biomarker for colorectal cancer after additional investigation.

Identification of a differentially expressed gene, ACL, between Meishan × Large White and Large White × Meishan F1 hybrids and their parents

ATP-citrate lyase (ACL), one of the lipogenic enzymes, catalyses the formation of acetyl-coenzyme A (CoA) involved in the synthesis of fatty acid and cholesterol. In pig, very little is known about the ACL gene. In this work, the mRNA differential display technique was used to analyse the differences in gene expression between Meishan and Large White pigs and the F1 hybrids of both direct and reciprocal crosses. Our results show that among the differentially expressed genes ACL is up-regulated in the backfat of the F1 hybrids. After cloning and analysing the fulllength cDNA and the 870 bp 5'-flanking sequence of the porcine ACL gene, a C/T mutation at position -97 bp upstream of the transcription site was detected. Luciferase activity detection showed that this mutation changed the transcriptional activity. In F1 hybrids, the heterozygous genotype CT was more frequent than the homozygous genotypes CC and TT. Real-time PCR analysis showed that in Meishan pigs, ACL mRNA expression was more abundant in individuals with genotype CT than in those with genotype CC or TT or in Large White pigs. These results indicate that the C/T mutation affects ACL mRNA expression, probably via the activator protein 2.

Differential expression of wheat transcriptomes in response to varying cadmium concentrations

This study aims to understand the changes in the transcriptome of durum wheat (Tricitum durum cv. Balcali-85) upon exposure to varying Cd concentrations using mRNA differential display (mRNA DD) technique. Sequence analyses of the two heavily induced genes upon exposure to Cd showed high homology to NADH dehydrogenase subunit 1 (EC907725) and PsaC gene encoding a photosystem 1 (PS 1) 9 kDa subunit protein (EC907731). Additionally, three differentially expressed genes (EC907726, EC907729 and EC907730) were identified. Their sequence analyses revealed no significant homologies to known genes. The expressions of NADH dehydrogenase subunit 1 and PsaC genes were confirmed by Northern blot analysis and quantified by real time PCR. This is the first report for the induction of NADH dehydrogenase subunit 1 gene during Cd stress in wheat.