References of "Mammalian Genome"
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See detailCurrent transcriptomics in pig immunity research
Schroyen, Martine ULg; Tuggle, C. K.

in Mammalian Genome (2015), 26(1-2),

Swine performance in the face of disease challenge is becoming progressively more important. To improve the pig’s robustness and resilience against pathogens through selection, a better understanding of ... [more ▼]

Swine performance in the face of disease challenge is becoming progressively more important. To improve the pig’s robustness and resilience against pathogens through selection, a better understanding of the genetic and epigenetic factors in the immune response is required. This review highlights results from the most recent transcriptome research, and the meta-analyses performed, in the context of pig immunity. A technological overview is given including wholegenome microarrays, immune-specific arrays, small-scale high-throughput expression methods, high-density tiling arrays, and next generation sequencing (NGS). Although whole genome microarray techniques will remain complementary to NGS for some time in domestic species, research will transition to sequencing-based methods due to cost-effectiveness and the extra information that such methods provide. Furthermore, upcoming high-throughput epigenomic studies, which will add greatly to our knowledge concerning the impact of epigenetic modifications on pig immune response, are listed in this review. With emphasis on the insights obtained from transcriptomic analyses for porcine immunity, we also discuss the experimental design in pig immunity research and the value of the newly published porcine genome assembly in using the pig as a model for human immune response. We conclude by discussing the importance of establishing community standards to maximize the possibility of integrative computational analyses, such as was clearly beneficial for the human ENCODE project. © 2014, Springer Science+Business Media New York. [less ▲]

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See detailComparative sequence analysis of the INS-IGF2-H19 gene cluster in pigs
Amarger, V.; Nguyen, Minh Ngoc ULg; Van Laere, Anne-Sophie ULg et al

in Mammalian Genome (2002), 13(7), 388-398

IGF2 is the major candidate gene for a paternally expressed Quantitative Trait Locus (QTL) in the pig primarily affecting muscle development. Here we report two sequence contigs together comprising almost ... [more ▼]

IGF2 is the major candidate gene for a paternally expressed Quantitative Trait Locus (QTL) in the pig primarily affecting muscle development. Here we report two sequence contigs together comprising almost 90 kb containing the INS-IGF2 and H19 genes. A comparative sequence analysis of the pig, human, and mouse genomic sequences was conducted to identify the exon/intros organization, all promoters, and other evolutionarily conserved elements. RT-PCR analysis showed that IGF2 transcripts originated from four different promoters and included various combinations of seven untranslated exons together with three coding exons, in agreement with previous findings in other mammals. The observed sequence similarity in intronic and intragenic regions among the three species is remarkable and is most likely explained by the complicated regulation of imprinting and expression of these genes. The general trend was, as expected, a higher sequence similarity between human and pig than between these species and the mouse, but a few exceptions to this rule were noted. This genomic region exhibits several striking features, including a very high GC content, many CpG islands, and a low amount of interspersed repeats. The high GC and CpG content were more pronounced in the pig than in the two other species. The results will facilitate the further characterization of this important QTL in the pig. [less ▲]

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