Gene expression screening for specific genes associated with mouse mammary tumor development

Identification of okadaic-acid-induced genes by mRNA differential display in glioma cells

To identify novel genes associated with apoptosis in glioma cells, we treated T98G glioma cells with okadaic acid (OA). Differential display using 15 random primers was performed on RNA extracted from these cells. Upregulated bands were excised from polyacrylamide gels and cloned. Northern blots were used to confirm RNA expression in T98G cells. 18 RNA fragments corresponding to the untranslated region of genes were identified and sequenced. Three unknown gene fragments were used to screen a fetal brain cDNA library resulting in three complete cDNA sequences. The three sequences corresponded to a human gene homologous to the yeast translation initiation factor Sui-1, a cAMP-regulated phosphoprotein, ARPP-16/19, and a novel gene designated O48. Transcription of Sui-1 increased in response to all stress factors tested, whereas ARPP only responded to OA. 2-kb and 4-kb O48 RNA species were identified. OA and stress factors increased 2-kb expression while K252a (protein kinase inhibitor) increased 4-kb expression. Differential display is effective for identifying genes associated with apoptosis. Novel genes may be identified by further analysis of the gene fragments identified in this study. The function of O48 is unknown.

Hepatic expression of acute-phase protein genes during carcinogenesis induced by peroxisome proliferators

Concern exists regarding peroxisome proliferator (PP) xenobiotic exposure because many PPs are potent hepatocarcinogens in rodents. The mechanism of carcinogenicity induced by PPs is atypical compared with those of other hepatocarcinogens in that the former appears to involve alterations in expression of PP-activated receptor (PPAR) target genes rather than direct mutagenicity. To begin to identify some of these genes, we used differential display to compare mRNA expression between hepatic adenomas and adjacent non-tumor liver from rats fed the potent PP Wy-14643 (WY) for 78 wk. Here, we report increased expression of the acute-phase protein (APP) gene alpha-1 antitrypsin (AT) and decreased expression of alpha2-urinary globulin in the tumors. Similar changes were seen in hepatic adenomas induced by a diethylnitrosamine and phenobarbital protocol, indicating a lack of specificity for PP-induced tumors. Additional APP genes, including ceruloplasmin, haptoglobin, beta-fibrinogen, and alpha1-acid glycoprotein were also upregulated in WY-induced tumors but were downregulated in the livers of rats administered a different PP for 13 wk. Mice treated with either WY or di(2-ethylhexyl) phthalate for 3 wk had decreased hepatic AT expression but increased expression of ceruloplasmin and haptoglobin. PPARalpha-null mice showed no hepatic APP gene alteration after PP treatment but had higher basal expression than did wild-type controls. We conclude that PPARalpha activation by several different PPs leads to dysregulation of hepatic APP gene expression in rats and mice. This dysregulation may indicate alterations in cytokine signaling networks regulating both APP gene expression and hepatocellular proliferation.

Insecticide resistance resulting from an absence of target-site gene product

Genetic changes in insects that lead to insecticide resistance include point mutations and up-regulation/amplification of detoxification genes. Here, we report a third mechanism, resistance caused by an absence of gene product. Mutations of the Methoprene-tolerant (Met) gene of Drosophila melanogaster result in resistance to both methoprene, a juvenile hormone (JH) agonist insecticide, and JH. Previous results have demonstrated a mechanism of resistance involving an intracellular JH binding protein that has reduced ligand affinity in Met flies. We show that a gamma-ray induced allele, Met27, completely lacks Met transcript during the insecticide-sensitive period in development. Although Met27 homozygotes have reduced oogenesis, they are viable, demonstrating that Met is not a vital gene. Most target-site resistance genes encode vital proteins and thus have few mutational changes that permit both resistance and viability. In contrast, resistance genes such as Met that encode nonvital insecticide target proteins can have a variety of mutational changes that result in an absence of functional gene product and thus should show higher rates of resistance evolution.

Differentially expressed genes in head and neck cancer

Carcinogenesis is considered a multistep process. To further elucidate involved genetic changes, the differential display method was applied to compare gene expression of head and neck carcinoma cells and normal keratinocytes from the upper aerodigestive tract. Total RNA was extracted from cultured squamous carcinoma cells and keratinocytes. mRNA was reverse transcribed into cDNA, amplified by PCR, and separated on a gel. Currently three DNA transcripts were identified with a length of 191 to 336 base pairs (bp) that were either expressed only by the keratinocytes or by the malignant cells. Differentially expressed DNA fragments of the carcinoma cells and the keratinocytes were cloned and sequenced. A gene bank database search identified one fragment expressed by the carcinoma cells as an unknown gene, another one found in the keratinocytes as probably a part of the human cell attachment domain, and the third one with homology to the mRNA of the human epidermal growth factor receptor (EGFR). Northern blot analysis confirmed the differential expression in the malignant cells or the keratinocytes. Differential display seems to confirm the well-known overexpression and up-regulation of the EGFR, the differential expression of the cell attachment domain may play a role as a cofactor in carcinogenesis of head and neck cancer, and the third unknown fragment is still under investigation to elucidate the role in carcinogenesis.

Differential display analysis of gene expression indicates that age-related changes are restricted to a small cohort of genes

It is clear that there is a genetic component associated with the ageing process. Although evolutionary theory has suggested that the activity of certain genes may facilitate ageing by favouring resource utilisation by the germ cells at the expense of somatic cells, there is reason to believe that the senescent phenotype, which is the endpoint of the ageing process, may be due to alterations in the levels of expression of other genes. To investigate this situation we have used the differential display technique to survey gene expression during ageing of the rat brain, heart and liver. By optimising this technique it is possible to identify up to 10000-14000 PCR products, which represent genes expressed in the tissue under study. Interestingly, only a relatively small cohort (approximately 2%) of these genes appear to show significant changes in their levels of expression during ageing. Characterisation of the latter has so far revealed certain genes, such as glial fibrillary acidic protein, which are associated with the senescent phenotype. It has also revealed that the level of fos, a component of the AP-1 transcription factor, decreases with age, which has implications for AP-1 regulated genes. The differential display technique has also revealed an increase in mitochondrial RNA during ageing of the heart, which may be due to a gene dosage effect caused by the presence of increased numbers of mitochondrial genomes in myocytes in old age. The differential display technique therefore appears to offer a powerful tool for identifying genes which contribute to the emergence of a senescent phenotype.

Differential display identified changes in mRNA levels in regenerating livers from chloroform-treated mice

The nongenotoxic-cytotoxic carcinogen chloroform induces liver necrosis, regenerative cell proliferation, and, eventually, liver tumors in female B6C3F1 mice when administered by gavage at doses of 238 or 477 mg/kg/d. Administration of 1800 ppm of chloroform in the drinking water results in similar daily doses but does not produce liver toxicity or cancer. The differential-display technique was used to compare the expression of a subset of mRNAs in normal (control) and regenerating liver after chloroform-induced toxicity to define the proportion of genes whose expression changes under hepatotoxic conditions and to identify the genes that might play a role in regeneration and perhaps cancer. RNA was purified from the livers of female B6C3F1 mice after 4 d or 3 wk of gavage treatment with 3, 238, or 477 mg/kg/d of chloroform or treatment with 1800 ppm chloroform in drinking water. There was a remarkably high degree of consistency of gene expression among the animals and across dose and treatment groups as visualized by the differential-display technique. Of the 387 bands observed, only four (about 1%) changed expression in regenerating liver. The genes were assigned locus names by GenBank after sequence submission. The genes with increased mRNA levels as confirmed by northern blot analysis were MUSTIS21, a mouse primary response gene induced by growth factors and tumor promoters; MUSMRNAH, a gene highly homologous to a human gene isolated from a prostate carcinoma cell line; and MUSFRA, a novel gene. The novel gene MUSFRB exhibited decreased mRNA levels. No change in expression was seen among control mice given the nontoxic regimens of 3 mg/kg/d chloroform or 1800 ppm chloroform in drinking water, indicating that changes in expression were associated with toxicity and regeneration rather than chloroform per se. These genes and others that may be identified by expanding this approach may play a role in regeneration and perhaps in the process of chloroform-induced carcinogenesis in rodent liver.

Differential expression of a cDNA clone in human liver versus hepatic cancer--highly homologous to aryl-dialkyl-phosphatase

We applied the technique of mRNA differential display to normal liver tissue and hepatoma cell line Hep3B. One of the isolated cDNA clones was expressed in human normal liver tissue but not in the human hepatocarcinoma cell line. Northern Blot analysis confirmed that high level of mRNA was expressed in human normal liver tissue but the level was decreased in non-cancerous liver tissue from hepatoma patients. Low level or no expression was observed in human hepatoma tissue. One of these transcripts was about 1.8 kb in length. Southern Blot analysis showed that it was a single copy gene. We obtained a full length cDNA clone of 2,395 bp by screening human liver 5'-stretch plus cDNA library. Nucleotide sequence indicated that this clone was highly homologous to aryl-dialkyl-phosphatase and possessed two polymorphic sites. Aryl-dialkyl-phosphatase which has a prominent role in the metabolism of several toxic, synthetic compounds, may be potentially related to human hepatocarcinoma susceptibility. The biological significance of its differential expression in normal versus malignant tissue is discussed.

Identification of seven differentially displayed transcripts in human primary and matched metastatic head and neck squamous cell carcinoma cell lines: implications in metastasis and/or radiation response

The patterns of differential gene expression were examined in two primary (A's) and two matched-metastatic (B's) head and neck squamous cell carcinoma (HNSCC) cell lines by differential display of mRNAs and northern blot hybridisation. Three cell lines used (PCI-04A, PCI-04B and PCI-06A) were established independently prior to therapy, whereas one cell line (PCI-06B) was established from a recurrent tumor after radiation therapy. A total of seven differentially displayed mRNA clones were identified, of which six clones were obtained by comparison of PCI-06A cells with PCI-06B cells (SCC-S1a/b, SCC-1c, and SCC-S2, PCI-06B; SCC-S3 to SCC-S5, PCI-06A), and one clone was obtained from the PCI-04A and PCI-04B match (SCC-Sa, PCI-04B). Based on the DNA database search for homology to the known sequences, six of the seven partial cDNA clones (SCC-S1a/b, SCC-1c, SCC-S2 to SCC-S4, and SCC-Sa may represent novel genes, whereas one cDNA clone (SCC-S5) shows significant homology to the HLA class II antigen gene (DPW2 beta chain). Each of the seven clones revealed preferential expression by northern blotting in the cell line of origin as compared to the matched counterpart. The transcripts ranged in size from approximately 7.0 Kb to 0.5 Kb. Interestingly, the SCC-Sa clone was preferentially expressed in both metastatic cell lines compared to the primary tumour-derived cell lines. We conclude that the SCC-Sa gene may be more commonly involved in tumour metastasis, whereas expression of the other genes (SCC-S1a/b, SCC-S1c, SCC-S2-SCC-S5) may be associated with metastasis and/or response of HNSCC to ionising radiation.

mRNA differential display of colonic mucosa cells in ulcerative colitis

Involvement of mucosal cells in inflammatory bowel disease (IBD) may be a sequenced process and the molecular difference between involved and uninvolved cells might implicate a possible mechanism in the disease process. The aim of this study was to compare gene expression between involved and uninvolved colonic mucosa cells in an individual with ulcerative colitis (UC) and to clone, sequence, and identify those differentially expressed genes, mRNA differential display was used to identify the gene expression in the mucosa of the UC patient. Anchored oligo(dT) primers and random 5' oligonucleotide 10-mer were used to carry out polymerase chain reaction on reverse-transcribed RNA (RT-PCR). The amplified cDNAs were displayed on a standard sequencing gel and comparisons were drawn between each two lanes representing either involved or uninvolved cells from a specific combination of two primers. Wherever differences were noted between lanes, the bands were reamplified using PCR, cloned into specialized vectors for positive selection, and then confirmed by dot blot. The cloned genes were then sequenced and compared with the GenBank database. About 1200 mRNA species were displayed in the sequencing gel. Among them, 106 fragments were differentially expressed between the two groups. Twenty-five of those differentially displayed gene fragments have been isolated, reamplified, and cloned for sequencing and dot blot analysis. Seventeen of the fragments were differentially expressed using the dot blot technique. Among those 25 gene fragments, 14 have homology to known genes and 11 have no match to any reported genes. Those matched known genes included genes for parathyroid tumor, T cell receptor-beta, alpha-nascent polypeptide-associated complex, ovarian cancer, and myeloblast. This is the first study using mRNA differential display to observe differential gene expression between involved and uninvolved mucosa cells in UC and it shows that differential display is a rapid method for characterizing gene changes in vivo in ulcerative colitis. The results from this study may provide useful information and facilitate further gene studies in this disease.

Inhibition of spermidine synthase gene expression by transforming growth factor-beta 1 in hepatoma cells

We screened genes responsive to transforming growth factor-beta (TGF-beta 1) protein in a human hepatoma cell line (Hep3B) using a PCR-mediated differential display technique, in order to investigate the mechanisms involved in TGF-beta-induced growth suppression. We found a gene that was down-regulated by TGF-beta 1 to be completely identical in an approx. 620 bp segment to the gene for the enzyme spermidine synthase, which mediates the conversion of putrescine into spermidine. Both spermidine synthase mRNA expression and its enzyme activity were decreased after TGF-beta 1 treatment of Hep3B cells. The inhibition of spermidine synthase gene expression by TGF-beta 1 protein was also observed in other hepatoma cell lines. The expression of genes for other biosynthetic enzymes in polyamine metabolism (ornithine decarboxylase and S-adenosylmethionine decarboxylase) was also inhibited to the same extent as for spermidine synthase, while the gene expression of spermidine/spermine N1-acetyltransferase, a catabolic enzyme, was relatively resistant to TGF-beta 1. Spermine levels in Hep3B cells were decreased by TGF-beta 1 treatment, although the levels of spermidine and putrescine were unchanged, probably due to compensation by remaining spermidine/spermine N1-acetyltransferase activity. Exogenously added spermidine or spermine, but not putrescine, partially antagonized the growth-inhibitor effects of TGF-beta 1 on Hep3B cells. Our data suggest that down-regulation of gene expression of the enzymes involved in polyamine metabolism, including spermidine synthase, may be associated with the mechanism of TGF-beta-induced growth suppression.

Isolation of differentially expressed cDNAs during ferret tracheal development: application of differential display PCR

The technique of differential display polymerase chain reaction (DD-PCR) was used to identify cDNA sequences, which are temporally expressed during ferret tracheal airway development. Such differentially expressed cDNAs may ultimately prove to be useful markers in elucidating mechanisms of epithelial differentiation and submucosal gland development in the airway. Using two sets of oligonucleotide primers 15 differentially amplified cDNAs were isolated by comparative reverse transcriptase (RT) PCR of 6-h and 3-day postnatal tracheal poly-A mRNA. In situ hybridization was used to assess the reliability of this method and confirm the differential mRNA expression patterns of cloned cDNAs. Results of in situ hybridization analysis demonstrated that 10 of the 15 cDNA sequences gave a temporally regulated pattern of expression, which was concordant with that of the differential display. Furthermore, sequence analysis of the 15 isolated cDNAs revealed that the majority of clones were amplified from two inverted decamer primers. These findings demonstrate the lack of poly-T priming in the differential display reaction, which suggests that this method may yield substantially more information regarding the coding sequence of cloned genes. In support of this observation, 6 of the 15 cDNA sequences contained one complete open reading frame. Although the majority of cDNAs demonstrated no homology to sequence data bases at the DNA or amino acid level, clone FT-4, which demonstrated a differential expression pattern limited to 3-day tracheal time points, was composed of a 10-amino acid repeat domain that was structurally similar to neuropeptide anthoRFamide and barley D hordein seed protein. A second interesting clone, FT-3, demonstrated an infrequent pattern of expression within a subset of epithelial cells limited to early developmental time points (6 h) and was dramatically reduced by 3 days postnatally. Several additional clones with no homologies to previously cloned genes demonstrated expression patterns that were also temporally regulated throughout tracheal development. Although the function of these temporally regulated genes has not been determined, these genes may ultimately prove to be useful markers of cellular differentiation during tracheal development.

PCR-mediated differential display and cloning of a melanocyte gene decreased in malignant melanoma and up-regulated with sensitization to DNA damage

Characterization of genes expressed in normal cells and decreased in their malignant counterparts is important for detecting candidate tumor suppressor genes. We have now used comparative differential display of MRNAs from B16 melanoma and matched syngeneic normal melanocytes to detect a G0A gene expressed preferentially in resting G0 melanocytes compared to proliferating cells. Cloning and sequencing revealed no homology of G0A in the GenBank Database, suggesting that this is a new gene. Northern blot analysis with the cloned probe, confirmed about a five-fold higher expression in normal melanocytes compared to melanoma. Up-regulation of this gene was not detected by L-tyrosine induction of B16 melanoma terminal differentiation, but was seen in these cells, when exposed to the radiation sensitizer bromodeoxyuridine and subsequent UV radiation. Our differential expression data suggest that the G0A gene is important for melanocytic growth control and for the response of melanoma cells to radiation sensitizers.

Identifying changes in gene expression in the nervous system: mRNA differential display

The majority of cellular and developmental processes are characterized by changes in gene expression. Recently, several polymerase chain reaction-based methods have been introduced for detecting genes whose expressions differ between cells or tissues. It is now possible to investigate whether novel gene expression occurs within many systems as a response to extracellular signals, and to identify systematically those genes. The characterization of cell-, tissue- or stage-specific gene expression will broaden our understanding of many complex biological processes.

Characterization of the cDNA and pattern of expression of a new gene over-expressed in human hepatomas and colonic tumors

A cDNA clone of 6.449 kb ch-TOG (for colonic and hepatic tumor over-expressed gene) initially selected from various human libraries and completed by 5' rapid amplification of cDNA ends (RACE) PCR is described. The original cDNA clone was extracted from an expression library constructed from a human tumoral brain. This library was screened with an antibody raised against the cytochrome P450tu that was shown to be over-expressed in chemically induced mouse hepatic tumors. Using this cDNA as a probe, a full-length cDNA was characterized. Its nucleotide sequence shows no significant similarity with any of the gene sequences collected in the various DNA data bases. The translation of the larger open reading frame leads to a putative protein of 1972 amino acids (molecular mass = 218453 Da). Hybridization analyses on Southern blot and on metaphase chromosomes indicate that this gene is present as a single copy in the genome and is localized on the short arm of chromosome 11. ch-TOG transcripts are present in several human tissues. Over-expression of ch-TOG in neoplastic liver and colon compared with the corresponding normal corresponding tissues is demonstrated. The level of the expression of ch-TOG transcripts was also studied in the various differentiation stages of the human colonic adenocarcinoma cell line Caco-2.

Nucleic acid fingerprinting by PCR-based methods: applications to problems in aging and mutagenesis

There are many methods of inference in common use in biology that are based on population sampling, including such diverse areas as sampling organisms to determine the population structure of an ecosystem, sampling a set of DNA sequences to infer evolutionary history, sampling genetic loci to build a genetic map, sampling differentially expressed genes to find phenotypic markers, and many others. Recently developed PCR-based methods for nucleic acid fingerprinting can be used as sampling tools with general applicability in molecular biology, evolution and genetics. These methods include arbitrarily primed PCR (AP-PCR; Welsh and McClelland, 1990) and random amplified polymorphic DNA (RAPD; Williams et al., 1990) for the fingerprinting of DNA, and RNA arbitrarily primed PCR (RAP-PCR; Welsh et al., 1992a) and differential display (DD; Liang and Pardee, 1992) for the fingerprinting of RNA. Novel ways of looking at genetic control are facilitated by the high data-acquisition capabilities of the fingerprinting methods. In this article, we review some of the applications of DNA fingerprinting to the study of mutagenesis, and of RNA fingerprinting to the study of normal and abnormal signal transduction. We propose that these fingerprinting approaches may also have applications in the study of senescence and aging.

Modulation of the signal recognition particle 54-kDa subunit (SRP54) in rat preosteoblasts by the extracellular matrix

Rat preosteoblastic cells, UMR201, develop a more mature phenotype when subcultured onto a type I collagen gel when compared with their growth on plastic. Basal osteopontin mRNA expression is up-regulated, whereas retinoic acid-induced alkaline phosphatase expression is reduced in cells on collagen when compared with cells plated onto plastic. We have used differential display polymerase chain reaction (PCR) of mRNA to identify other mRNA species that are regulated by collagen and/or retinoic acid in UMR201 cells. A number of differentially expressed PCR products were isolated, whose sequences did not correspond to known sequences in the data bank. However, one species which was up-regulated by growth on collagen showed 95 and 94% homology to the murine and canine 54-kDa subunit of the signal recognition particle (SRP54), respectively. In time course experiments, using reverse transcription PCR, it was found that SRP54 mRNA was up-regulated in UMR201 cells as early as 1 h after subculture onto collagen, when compared with cells subcultured onto plastic, and levels remained elevated after 48 h. The increased expression of SRP54 paralleled the increased expression of a known secreted protein, osteopontin. SRP54 recognizes signal sequences of proteins destined for secretion and retards them for further elongation in the endoplasmic reticulum. The increased expression may correlate with the synthesis of specific extracellular matrix molecules in differentiating osteoblasts.

Differential display of messenger ribonucleic acid: a useful technique for analyzing differential gene expression in human brain tumors

In this study, a differential display method for messenger ribonucleic acid was successfully used to identify genes differentially expressed between normal human brain and malignant glioma tissues. A total of 60 differentially expressed sequences were initially identified, of which 21 were cloned and sequenced. Twenty of the cloned sequences represented novel genes, and one sequence represented a kinesin heavy chain (KHC) gene isoform. The KHC isoform was selected for further characterization. Northern blots of total ribonucleic acid isolated from normal brain and a glioblastoma were probed with our KHC probe and confirmed the differential expression of this gene. Expression analysis of a variety of normal human tissues demonstrated that this KHC isoform is expressed only in brain tissues, with no detectable expression in placenta, spleen, kidney, lung, liver, or skeletal muscle. Our results confirm the rapid and sensitive nature of the differential display technique in identifying differential gene expression. This method offers a means to identify new genes of biological interest in human brain tumors such as oncogenes, tumor suppressor genes, and tumor-specific markers.

Identification of a human hepatocellular carcinoma-associated tumor suppressor gene by differential display polymerase chain reaction

Differential gene expression between the normal human liver and a cell line derived from human hepatocellular carcinoma (HCC) was studied using the differential display polymerase chain reaction technique. One gene (mitochondria proteolipid like gene, MPL), whose expression was found to be repressed in the HCC cell line compared to normal liver, was cloned and sequenced. Amino acid sequence translated from the nucleotide sequence had a 73% homology with the carboxyl terminus of a mitochondria proteolipid (MPLP) isolated from beef heart. Northern blot analysis showed that the expression of the 3 kb MPL transcript was undetectable in 20 of 45 (44%) of human hepatocellular carcinomas, whereas only 1 of 14 (17%) of cirrhotic livers without HCC had undetectable expression when compared to normal livers. Hence MPL may be a candidate tumor suppressor gene for human HCC. This decrease in MPL expression was not due to gross alteration of its genomic DNA.

Characterization of cDNA clones for differentially expressed genes in embryos of dormant and nondormant Avena fatua L. caryopses

The molecular regulation of seed dormancy was investigated using differential display to visualize and isolate cDNAs representing differentially expressed genes during early imbibition of dormant and nondormant Avena fatua L. embryos. Of about 3000 cDNA bands examined, 5 cDNAs hybridized with mRNAs exhibiting dormancy-associated expression patterns during the first 48 h of inhibition, while many more nondormancy-associated cDNAs were observed. Dormancy-associated clone AFD1 hybridized with a 1.5 kb mRNA barely detectable in dry dormant and nondormant embryos that became more abundant in dormant embryos after 24 h of imbibition. Clone AFD2 hybridized with two mRNAs, a 1.3 kb message constitutively expressed in dormant and nondormant embryos and a 0.9 kb message present at higher levels in dormant embryos after 3 h of imbibition. Nondormancy-associated clones AFN1, AFN2 and AFN3 hybridized with 1.5 kb, 1.7 kb and 1.1 kb mRNAs, respectively, that were more abundant in nondormant embryos during imbibition. Expression patterns of some mRNAs in dormant embryos induced to germinate by GA3 treatment were different than water controls, but were not identical to those observed in nondormant embryos. DNA sequence analysis revealed 76% sequence identity between clone AFN3 and a Citrus sinensis glutathione peroxidase-like cDNA, while significant sequence similarities with known genes were not found for other clones. Southern hybridization analyses showed that all clones represent low (1 to 4) copy number genes.

Recent advances in differential display

Differential display and RNA arbitrary primed polmerase chain reaction are methods recently designed to identify and isolate differentially expressed genes. Methodological modifications have since been introduced to streamline the techniques. The major effort has centered on how to eliminate false positives as approached from a variety of angles, ranging from RNA sample preparation, northern blot confirmation, primer length variation, to better experimental design.