cDNA AFLP-based techniques for studying transcript profiles in horses

Epigenetic control of exercise adaptations in the equine athlete: Current evidence and future directions

Horses (Equus ferus caballus) have evolved over the past 300 years in response to man-made selection for particular athletic traits. Some of the selected traits were selected based on the size and horses' muscular power (eg Clydesdales), whereas other breeds were bred for peak running performance (eg Thoroughbred and Arabian). Although the physiological changes and some of the cellular adaptations responsible for athletic potential of horses have been identified, the molecular mechanisms are only just beginning to be comprehensively investigated. The purpose of this review was to outline and discuss the current understanding of the molecular mechanisms underpinning the athletic performance and cardiorespiratory fitness in athletic breeds of horses. A brief review of the biology of epigenetics is provided, including discussion on DNA methylation, histone modifications and small RNAs, followed by a summary and critical review of the current work on the exercise-induced epigenetic and transcriptional changes in horses. Important unanswered questions and currently unexplored areas that deserve attention are highlighted. Finally, a rationale for the analysis of epigenetic modifications in the context with exercise-related traits and ailments associated with athletic breeds of horses is outlined in order to help guide future research.

Transcriptome response of the Pacific oyster (Crassostrea gigas) to infection with Vibrio tubiashii using cDNA AFLP differential display

We used qualitative complementary DNA-amplified fragment length polymorphism (cDNA-AFLP) differential display analysis and real-time, quantitative PCR (RT-qPCR) to identify genes in the Pacific oyster Crassostrea gigas, whose transcription either changes in response to exposure to a pathogenic bacterium (Vibrio tubiashii) or varies between families known to differ in sensitivity to heat stress, before and at 12 and 36 h after bacterial exposure at a temperature of 25 degrees C. These conditions simulate those associated with summer mortality syndrome, a poorly understood cause of massive mortalities in cultured Pacific oysters in North America, Asia and Europe. Using 32 AFLP primer pairs, we identified 92 transcript-derived fragments that are qualitatively differentially expressed. We then cloned and sequenced 14 of these fragments, designed fragment-specific primers and quantified their transcription patterns using RT-qPCR. Most of the differences in transcription patterns between stress-tolerant and stress-sensitive families were evident before bacterial exposure, and genes that responded to bacterial exposure did so in parallel between stress-sensitive and stress-tolerant families. Blast searches of sequence databases revealed that these fragments represent genes involved in immune response as well as genes related to metabolic processes. Our data support the hypothesis that family level differences in resistance to stress in Pacific oysters are largely attributable to constitutive differences in gene transcription or 'general vigour' that are detectable before and maintained after infection, rather than being due to induced responses at the transcriptome level.

AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis

Although DNA microarrays are currently the standard tool for genome-wide expression analysis, their application is limited to organisms for which the complete genome sequence or large collections of known transcript sequences are available. Here, we describe a protocol for cDNA-AFLP, an AFLP-based transcript profiling method that allows genome-wide expression analysis in any species without the need for prior sequence knowledge. In essence, the cDNA-AFLP method involves reverse transcription of mRNA into double-stranded cDNA, followed by restriction digestion, ligation of specific adapters and fractionation of this mixture of cDNA fragments into smaller subsets by selective PCR amplification. The resulting cDNA-AFLP fragments are separated on high-resolution gels, and visualization of cDNA-AFLP fingerprints is described using either a conventional autoradiography platform or an automated LI-COR system. Observed differences in band intensities between samples provide a good measure of the relative differences in the gene expression levels. Identification of differentially expressed genes can be accomplished by purifying cDNA-AFLP fragments from sequence gels and subsequent sequencing. This method has found widespread use as an attractive technology for gene discovery on the basis of fragment detection and for temporal quantitative gene expression analysis. The protocol can be completed in 3-4 d.

cDNA-AFLP analysis of differential gene expression in human hepatoma cells (HepG2) upon dengue virus infection

In infectious diseases, the disease pathogenesis is the outcome of the interaction between the genome of the host and the genome of the pathogen. Despite the wide distribution of dengue infections in the world, and the large number of annual infections, few studies have investigated how the dengue genome alters the global transcriptional profile of the host cell. To investigate alterations in the liver cell transcriptome in response to dengue virus infection, liver cells (HepG2) were infected with dengue serotype 2 at MOI 5 and at 3 days post-infection RNA extracted and analyzed by cDNA-AFLP in parallel with mock-infected cells. From 73 primer combinations over 5,000 transcription-derived fragments (TDFs) were observed, of which approximately 10% were regulated differentially in response to infection. Sixty-five TDFs were subsequently cloned and sequenced and 27 unique gene transcripts identified. Semi-quantitative reverse transcription (RT)-PCR was used to validate the expression of 12 of these genes and 10 transcripts (CK2, KIAA509, HSP70, AK3L, NIPA, PHIP, RiboS4, JEM-1, MALT1, and HSI12044) were confirmed to be differentially regulated, with four transcripts (HSP70, NIPA, RiboS4, and JEM-1) showing a greater than twofold regulation. These results suggest that the expression of a large number of genes is altered in response to dengue virus infection of liver cells, and that cDNA-AFLP is a useful tool for obtaining information on both characterized and as yet uncharacterized transcripts whose expression is altered during the infection process.

Analysis of peripheral blood mononuclear cells gene expression in endurance horses by cDNA-AFLP technique

The knowledge of molecular mechanisms of stress response in athlete horses can allow us to plan an appropriate and high-grade training to obtain better performance and to preserve horse welfare. It is well known that excessive muscular exercise can lead to a number of responses which may be associated with modification of the mRNA levels for a number of metabolic genes such as those involved in the immune response. In the present study cDNA-AFLP technique was applied to Arab endurance horses under stressing conditions to visualise variations of transcriptional profiles; 49 transcript derived fragments (TDFs), differentially expressed, were cloned and sequenced. Four of these showed high sequence similarity with genes probably involved in exercise-induced stress response and resulted to be not sequenced in the horse. Their modulation was confirmed by RT-PCR and the full-length transcripts were isolated by RACE-PCR. The mRNAs sequences obtained were included in the GenBank database as Equus caballus interleukin 8 (IL8), E. caballus retinoblastoma binding protein 6 mRNA (RBBP6), E. caballus eukaryotic translation initiation factor 4 gamma 3 (eIF4G3) and E. caballus heat shock protein 90 (Hsp90). The expression pattern of these genes was verified in other endurance horses under stressing conditions, strengthening the hypothesis of their real involvement in exercise stress-induced response.