The Human Genome Heterogeneity Revealed by the Human/Mouse/Rat Synteny
|
Properties |
Human chr |
Mouse/rat synteny |
|---|---|---|
| Chromosomal associationsa | H3/H21, H4q/H8p, H12/H22, H21/H22, H13/H14b H1/H10, H7/H22, and H19p/H16q | Fragments from the two human chromosomes are adjacent to each other syntenic to the same mouse/rat chromosomal region |
| Intra-chromosomal Rearrangementsc | H1q, H2, H3, H4, H7, H8p, H9, H10, H11, H12, H13, H15, H16, H17, H18, and H20 | Obtained with dog as the outgroup, where dog is continuously syntenic to mouse/rat without interruption, but human breaks into two syntenic blocks |
| Two arms with unrelated synteny | H16, H8, H10, and H19d | P-arm and q-arm are syntenic to fragments from completely different mouse/rat chromosomes |
| Synteny uninterrupted by the centromere | H4, H5, H6, H11, and H12 | A single mouse/rat syntenic block continues from p-arm to q-arm without any rearrangements detected around the centromeric region |
| Synteny broken at the centromere | H7, H2, H8, H9, H10, H16, H18, H19, HX, and H20 | Different syntenic blocks were found on the two sides of the centromere |
| Intermediate rearrangements at the centromere
|
H1, H3
|
Except two inversions at the first 780 kb of H1q, H1's centromere is within a single syntenic block. H3 splits at its centromere
for rat, but not for mouse (see Table 4).
|
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↵a Some of the associations are not exactly the same in the two rodents. For instance, further reorganization has occurred to H3/H21 in rat (see Table 4 and Supplemental material). In addition, we found several associations different from reported (Richard et al. 2000; Murphy et al. 2001; Stanyon et al. 2003). For instance, instead of H7partial/H16p and H16q/H19q identified in a number of placental mammals (Richard et al. 2000), we observed H19p(partial)/H16q and did not find any associations between H7 and H16.
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↵b The tip of H14 is adjacent to the tip of H13 corresponding to the same rodent chromosomes, whereas H15 is syntenic to rodent chromosomes that have no homology to either H13 or H14 (see Supplementary material).
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↵c These rearrangements account for about 58 of the 255 mouse/rat shared breakpoints shown in Table 2.
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↵d Evidence has indicated that the two arms of these chromosomes were unlinked in a primate ancestor (Haig 1999; Richard et al. 2000, 2003; Murphy et al. 2001; Carbone et al. 2002; Misceo et al. 2003).
