Table 3

Predicted positions of chromosome position according to various parameters compared to actual distribution
Chromosome Actual porcine chromosome territory position Analogous human chromosome territory position1 Human epigenetic markers2 Porcine epigenetic markers3 Predictedin silicoporcine gene density4 Size5
1 P P I P I P
2 I I I/Int Int Int P
3 I I I I I I
4 I I I P I I
5 I P Int P I I
6 I Int Int Int I P
7 I Eq Int Int I I
8 P P P P P I
11 Int P P P P Int
13 P P P Int P P
15 P P P P I P
16 Eq I P P I Int
17 Int Eq Int Int I Int
18 Int P Int P I Int
X P P I I

This table displays comparisons between the chromosome territory positioning of actual porcine chromosomes from 2D FISH in SOB cells relative to predictions from synteny with human chromosomes, epigenetic markers, in silico gene data and chromosome size. This allows a comparison to show how the positioning of whole porcine chromosomes within the nucleus fit with the size and gene density theories of organisation. 1 Synteny between the human and porcine genome (https://wwwlgc.toulouse.inra.fr/pig/compare/SSC.htm webcite, see also http://piggenome.org/docs/index.php webcite) was used to predict the analogous porcine chromosome territory position from human chromosome territory data [6]. 2 The assignment of human epigenetic markers (e.g. CpG island-rich chromatin, early replicating DNA, late replicating DNA) [42,53] can be used through synteny studies as markers to predict the gene density of chromosomes. A projection of chromosome territory positioning can be made according to the gene-density theory of organisation, since more gene-rich chromosomes would be expected to occupy internal nuclear positions, and gene-poor chromosomes having more peripheral localities. 3 Porcine epigenetic markers (e.g. CpG island-rich chromatin and H3-isochore rich chromatin) were used to predict potential chromosome positioning according to the gene density theory of organisation. The last two columns show the chromosomes and their categorised nuclear locations in order of gene density and size. Key, P – peripheral; I – intermediate; Int – interior; Eq – equally distributed.

Foster et al.

Foster et al. BMC Cell Biology 2012 13:30   doi:10.1186/1471-2121-13-30

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