Comparative sequence analysis of the INS-IGF2-H19 gene cluster in pigs

Abstract

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/intron 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.

Altered Gene Expression Profiles in the Brain, Kidney, and Lung of One-Month-Old Cloned Pigs

“…This may be due to the higher proportions of 5 m C and GC content, as well as more CpG islands in the pig than the other species (Amarger et al, 2002). Cloned pigs at 1 month of age had a higher concentration of 5 m C in their lung DNA than that of age-matched controls.…”

Detection of a novel single nucleotide polymorphism and imprinted status analysis of the Ras protein-specific guanine nucleotide-releasing factor 1 gene in domestic pigs

“…However, this is the first investigation of the imprinting status of the Rasgrf1 gene in swine. By first obtaining the partial exon 14 sequence, we found that, typical of imprinted genes (Amarger et al, 2002;Zhang et al, 2004), exon 14 of the porcine Rasgrf1 gene was highly GC-rich. Furthermore, a de novo polymorphism located in exon 14 of the porcine Rasgrf1 gene was discovered and was presented for the first time here (http://www.ncbi.nlm.nih.gov/ SNP/snp_ref.cgi?locusId=100157221).…”

Methylation and expression changes in imprinted genesH19andIgf2during serial somatic cell nuclear transfer using piglet fibroblasts

“…Igf2 is a complex transcription unit that consists of seven non-coding exons and three coding exons for pre-pro Igf2. Exons 1, 4, 5, and 6 are preceded by distinct promoters P1, P2, P3, and P4 (Mineo et al 2000;Amarger et al 2002) which give rise to a family of mRNA transcripts having different leader exons with the same coding exons at the 3′ ends in human (Holthuizen et al 1990). Our results show that the expression of Igf2 differed by promoters.…”

“…H19 and insulin-like growth factor 2 (Igf2) are the most widely studied imprinted genes Amarger et al 2002;Shen et al 2012). Igf2 is expressed exclusively from the paternal allele, whereas the H19 gene is expressed from the maternal allele, and their imprinted gene expression is controlled by methylation of the H19 DMRs (Tremblay et al 1995).…”