Quantitative analysis of leptin mRNA using competitive reverse transcription polymerase chain reaction and capillary electrophoresis with laser-induced fluorescence detection

Mapping of leptin and its syntenic genes to chicken chromosome 1p

Background

Misidentification of the chicken leptin gene has hampered research of leptin signaling in this species for almost two decades. Recently, the genuine leptin gene with a GC-rich (~70%) repetitive-sequence content was identified in the chicken genome but without indicating its genomic position. This suggests that such GC-rich sequences are difficult to sequence and therefore substantial regions are missing from the current chicken genome assembly.

Results

A radiation hybrid panel of chicken-hamster Wg3hCl2 cells was used to map the genome location of the chicken leptin gene. Contrary to our expectations, based on comparative genome mapping and sequence characteristics, the chicken leptin was not located on a microchromosome, which are known to contain GC-rich and repetitive regions, but at the distal tip of the largest chromosome (1p). Following conserved synteny with other vertebrates, we also mapped five additional genes to this genomic region (ARF5, SND1, LRRC4, RBM28, and FLNC), bridging the genomic gap in the current Galgal5 build for this chromosome region. All of the short scaffolds containing these genes were found to consist of GC-rich (54 to 65%) sequences comparing to the average GC-content of 40% on chromosome 1. In this syntenic group, the RNA-binding protein 28 (RBM28) was in closest proximity to leptin. We deduced the full-length of the RBM28 cDNA sequence and profiled its expression patterns detecting a negative correlation (R = − 0.7) between the expression of leptin and of RBM28 across tissues that expressed at least one of the genes above the average level. This observation suggested a local regulatory interaction between these genes. In adipose tissues, we observed a significant increase in RBM28 mRNA expression in breeds with lean phenotypes.

Conclusion

Mapping chicken leptin together with a cluster of five syntenic genes provided the final proof for its identification as the true chicken ortholog. The high GC-content observed for the chicken leptin syntenic group suggests that other similar clusters of genes in GC-rich genomic regions are missing from the current genome assembly (Galgal5), which should be resolved in future assemblies of the chicken genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-017-0543-1) contains supplementary material, which is available to authorized users.

Quantitation of mRNA levels of steroid 5alpha-reductase isozymes: a novel method that combines quantitative RT-PCR and capillary electrophoresis

A novel, accurate, rapid and modestly labor-intensive method has been developed to quantitate specific mRNA species by reverse transcription-polymerase chain reaction (RT-PCR). This strategy combines the high degree of specificity of competitive PCR with the sensitivity of laser-induced fluorescence capillary electrophoresis (LIF-CE). The specific target mRNA and a mimic DNA fragment, used as an internal standard (IS), were co-amplified in a single reaction in which the same primers are used. The amount of mRNA was then quantitated by extrapolation from the standard curve generated with the internal standard. PCR primers were designed to amplify both a 185 bp fragment of the target cDNA for steroid 5alpha-reductase 1 (5alpha-R1) and a 192 bp fragment of the target cDNA for steroid 5alpha-reductase type 2 (5alpha-R2). The 5' forward primers were end-labeled with 6-carboxy-fluorescein (6-FAM). Two synthetic internal standard DNAs of 300 bp were synthesized from the sequence of plasmid pEGFP-C1. The ratio of fluorescence intensity between amplified products of the target cDNA (185 or 192 bp fragments) and the competitive DNA (300 bp fragment) was determined quantitatively after separation by capillary electrophoresis and fluorescence analysis. The accurate quantitation of low-abundance mRNAs by the present method allows low-level gene expression to be characterized.

Quantitation of mRNA levels of steroid 5alpha-reductase isozymes in the rat brain by "one-step" RT-PCR and capillary electrophoresis

The enzyme 5alpha-reductase (5alpha-R) is present in many mammalian tissues, including the brain. The physiological importance of 5alpha-R in the brain derives from its capability to convert testosterone (T) to a more potent androgen, dihydrotestosterone (DHT), and to convert progesterone to its 5alpha-reduced derivative, precursors of allopregnanolone, potent allosteric modulator of the gamma-aminobutyric acid receptor (GABA(A)-R). 5alpha-R occurs as two isoforms, 5alpha-R type 1 (5alpha-R1) and 5alpha-R type 2 (5alpha-R2). We present an accurate, rapid, and modestly labor-intensive method to precisely quantitate 5alpha-R mRNA species in the cerebral cortex of the rat. This approach combines the high specificity of "one-step" reverse transcription-polymerase chain reaction (RT-PCR) with the sensitivity of laser-induced fluorescence capillary electrophoresis (LIF-CE). Both cDNA synthesis and PCR amplification are performed with the same enzyme and site-specific primers, improving the efficiency of cDNA synthesis. The specific target mRNA and a mimic DNA fragment, used as a competitive internal standard, were co-amplified in a single reaction in which the same primers are used. The method presented in this paper enables a more efficient quantitative determination of 5alpha-R mRNA isozymes, and may lead to a better understanding of the role of 5alpha-R isozymes in the physiology of the central nervous system.

Quantitation of mRNA levels of steroid 5α-reductase isozymes in the rat brain by “one-step” RT-PCR and capillary electrophoresis

The enzyme 5alpha-reductase (5alpha-R) is present in many mammalian tissues, including the brain. The physiological importance of 5alpha-R in the brain derives from its capability to convert testosterone (T) to a more potent androgen, dihydrotestosterone (DHT), and to convert progesterone to its 5alpha-reduced derivative, precursors of allopregnanolone, potent allosteric modulator of the gamma-aminobutyric acid receptor (GABA(A)-R). 5alpha-R occurs as two isoforms, 5alpha-R type 1 (5alpha-R1) and 5alpha-R type 2 (5alpha-R2). We present an accurate, rapid, and modestly labor-intensive method to precisely quantitate 5alpha-R mRNA species in the cerebral cortex of the rat. This approach combines the high specificity of "one-step" reverse transcription-polymerase chain reaction (RT-PCR) with the sensitivity of laser-induced fluorescence capillary electrophoresis (LIF-CE). Both cDNA synthesis and PCR amplification are performed with the same enzyme and site-specific primers, improving the efficiency of cDNA synthesis. The specific target mRNA and a mimic DNA fragment, used as a competitive internal standard, were co-amplified in a single reaction in which the same primers are used. The method presented in this paper enables a more efficient quantitative determination of 5alpha-R mRNA isozymes, and may lead to a better understanding of the role of 5alpha-R isozymes in the physiology of the central nervous system.

Quantification of gene expression in methanotrophs by competitive reverse transcription-polymerase chain reaction

To improve the monitoring of methanotrophic activity, a competitive reverse transcription-polymerase chain reaction (RT-PCR) methodology was developed. Homologous internal RNA standards were created for mmoX and pmoA, genes encoding polypeptides of sMMO and pMMO, respectively. Using specific primer sets, expression of sMMO and pMMO could be quantified by means of competitive RT-PCR and capillary electrophoresis with uncoated bare-fused silica columns and UV detection. Using this technique, it was discovered that the amount of mRNA transcript for both mmoX and pmoA correlated well with whole-cell sMMO and pMMO activity respectively. A method for soil RNA extraction was also developed to utilize this RNA quantification technique for the monitoring of methanotrophic activity in situ. In a model soil slurry system with a background concentration of 2.9 micro M copper, it was found that only pmoA was transcribed by cells capable of expressing both forms of MMO. As pMMO and sMMO have very different substrate ranges and kinetics, this methodology may prove useful for optimizing in situ bioremediation by methanotrophs. Provided sufficient sequence information is available to create specific primer sets, these techniques can be applied for monitoring and measuring the activity of other microbial communities in situ.

DNA diagnosis by capillary electrophoresis and microfabricated electrophoretic devices

DNA diagnosis is experiencing an impressive progression towards the development of novel technology to identify various clinically relevant categories of genetic changes and to meet the exponential growth of genomics. The introduction of capillary electrophoresis has dramatically accelerated the completion of the first draft of the human DNA sequence in the Human Genome Project, and thus, has become the method of choice for analysis of various genetic variants. The recent development of microfabricated electrophoretic devices has led to the possibility of integrating multiple sample handling with the actual measurement steps required for automation of molecular diagnostics. This review highlights the most recent progress in capillary electrophoresis and electrophoretic microdevices for DNA-based diagnostics, including the important areas of genotyping for point mutation, single nucleotide polymorphisms, short tandem repeats and organism identification. The application of these techniques for infectious and genetic disease diagnosis, as well as forensic identification purpose, are covered. The promising development and the challenges for techinical problems are also discussed.

Expression of an uncoupling protein gene homolog in chickens

An avian uncoupling protein (UCP) gene homolog was recently sequenced from skeletal muscle and was proposed to have a role in thermogenesis in chickens, ducks and hummingbirds. Since mammalian UCP 2 and UCP 3 also appear to have functions associated with energy and substrate partitioning and body weight regulation, the purpose of this study was to further characterize chicken UCP under conditions of nutritional stress and/or leptin administration. Male 3-week-old chickens were starved for 24 or 48 h and then half of each group was refed for an additional 24 h. In a follow-up experiment, chickens were fed or starved for 48 h with or without leptin administration. Feed deprivation increased UCP mRNA expression in skeletal muscle by up to 260% (P<0.001), and in a time-dependent manner in pectoralis muscle. Refeeding for 24 h normalized muscle UCP mRNA levels. Leptin administration had no effect on muscle UCP. Chicken muscle UCP mRNA levels were highly correlated with plasma triglyceride and non-esterified fatty acid (NEFA) concentrations, and with circulating levels of insulin, insulin-like growth factor (IGF)-I and IGF-II. These results suggest that, as in mammals, avian UCP is up-regulated during feed deprivation and is highly correlated with increased fatty acid oxidation and flux into skeletal muscle.

The ontogeny of leptin mRNA expression in growing broilers and its relationship to metabolic body weight

The polypeptide hormone leptin is produced by both adipose tissue and the liver and has been shown to induce satiety in chickens. In this study we have investigated the developmental regulation of leptin mRNA expression in growing broiler chickens. Leptin expression generally increases in all tissues from 1-12 weeks of age. In the subcutaneous fat depot there is an apparent pattern of increased leptin mRNA expression occurring at 2, 6, and 10 weeks post-hatch. This pattern was not evident in the other tissues surveyed and may relate to the cycle of loading and unloading of adipocytes with lipid. No consistent gender differences in leptin expression patterns were detected in the tissues surveyed, as is often observed in mammals. Positive correlations between metabolic body weight and adipose leptin expression levels were observed. Leptin expression by the liver was highly correlated with metabolic body weight from 1-6 weeks of age, and uncorrelated from 6-12 weeks of age. This pattern of increasing liver leptin expression with increasing body weight during the early rapid growth phase of the bird may be due to limited fat storage during this period, which is followed by rapid body fat accumulation from 6-12 weeks. The characterization and tissue specific distribution of leptin mRNA expression in the growing broiler indicate similar patterns of leptin production to that of growing mammals. Leptin may be involved in lipid flux through the adipocyte as well as the shift in lipid metabolism to increased storage during pre-puberty.

Identification of nine alternatively spliced alpha2,3-sialyltransferase, ST3Gal IV, transcripts and analysis of their expression by RT-PCR and laser-induced fluorescent capillary electrophoresis (LIF-CE) in twenty-one human tissues

In order to characterise the candidate alpha2,3-sialyltransferases necessary for biosynthesis of the selectin ligand SLe(x) and related antigens we have cloned and sequenced, from peripheral blood leukocytes of single individuals, various transcripts from the human ST3Gal III, IV and VI genes. Our clones have revealed a considerable heterogeneity in transcript isoforms. Among our ST3Gal IV clones we isolated nine alternatively spliced transcripts covering the coding region of the human ST3Gal IV gene (A1, A1 - 12, A1 + 18, A2, A2 - 12, A2 + 18, B, B - 12 and B + 18). Five of these isotranscripts A1 - 12, A1 + 18, A2 - 12, A2 + 18 and B + 18 have not been described before. In order to investigate if the alternatively spliced isotranscripts were specific for human PBL, we analysed the expression by RT-PCR and laser-induced fluorescent capillary electrophoresis (LIF-CE) in twenty other human tissues. We found a tissue specific expression of ST3Gal IV A1, A1 - 12, A1 + 18, A2, A2 - 12, A2 + 18 and B + 18 as well as a general expression of ST3Gal IV B and B - 12 isotranscripts in all tissues examined.