Comparative sequence analysis of the INS-IGF2-H19 gene cluster in pigs.
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.
Amarger
Valérie
V
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 597, SE-751 24 Uppsala, Sweden.
Nguyen
Minh
M
Van Laere
Anne-Sophie
AS
Braunschweig
Martin
M
Nezer
Carine
C
Georges
Michel
M
Andersson
Leif
L
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D018899:CpG Islands / Q000235:genetics; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D006801:Humans; D007328:Insulin / Q000235:genetics*; D007335:Insulin-Like Growth Factor II / Q000235:genetics*; D007438:Introns / Q000235:genetics; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D062085:RNA, Long Noncoding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics*; D020218:Response Elements / Q000235:genetics; D015183:Restriction Mapping; D016415:Sequence Alignment; D013552:Swine / Q000235:genetics*
C094335:H19 long non-coding RNA; D007328:Insulin; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D022661:RNA, Untranslated; D007335:Insulin-Like Growth Factor II