Molecular cytogenetic dissection of human chromosomes 3 and 21 evolution

Abstract

Chromosome painting in placental mammalians illustrates that genome evolution is marked by chromosomal synteny conservation and that the association of chromosomes 3 and 21 may be the largest widely conserved syntenic block known for mammals. We studied intrachromosomal rearrangements of the syntenic block 3/21 by using probes derived from chromosomal subregions with a resolution of up to 10-15 Mbp. We demonstrate that the rearrangements visualized by chromosome painting, mostly translocations, are only a fraction of the actual chromosomal changes that have occurred during evolution. The ancestral segment order for both primates and carnivores is still found in some species in both orders. From the ancestral primate/carnivore condition an inversion is needed to derive the pig homolog, and a fission of chromosome 21 and a pericentric inversion is needed to derive the Bornean orangutan condition. Two overlapping inversions in the chromosome 3 homolog then would lead to the chromosome form found in humans and African apes. This reconstruction of the origin of human chromosome 3 contrasts with the generally accepted scenario derived from chromosome banding in which it was proposed that only one pericentric inversion was needed. From the ancestral form for Old World primates (now found in the Bornean orangutan) a pericentric inversion and centromere shift leads to the chromosome ancestral for all Old World monkeys. Intrachromosomal rearrangements, as shown here, make up a set of potentially plentiful and informative markers that can be used for phylogenetic reconstruction and a more refined comparative mapping of the genome.

Figure 1

A summary of the mapping positions of DNA probes included in this study given in fractional length from the telomere (FL) on human chromosome 3. (A) Centre d'Etude du Polymorphisme Humain (CEPH) YACs 852b3 (#1), 938 g11 (#2), 936c1 (#3), 961f12 (#4), 870e5 (#5), 965a3 (#6), 808b10 (#7), 929 g8 (#8), 960f11 (#9), 806c12 (#10), 958 g10 (#11), and 866e7 (#12) (34). (B) Human subchromosomal probes derived from human/hamster somatic cell hybrids: Lia 4L, HY3B6, RJ3PT2, HA3, and HY1A2 (33). (C) C. aethiops (CAE) chromosome 15- and 22-specific paints (25). (D) T. belangeri (TBE) chromosome 6-, 7-, 24-, and 28-specific paints (11) and (E) S. oedipus (SOE) chromosome 15-, 17-, and 19-specific paints (unpublished data). TBE 7 and SOE 19 also show homology to human chromosome 21.

Figure 2

Examples for chromosome painting of various primates and nonprimate outgroup mammals. (A) T. belangeri chromosome 6-, 7-, 24-, and 28- specific probes (yellow) on pig (SSC), cat (FCA), lemur (EMA), macaque (MNE), and Bornean orangutan (PPY_bo) and human (HSA); chromosomes are counterstained in red. The order of probes in the lemur is the same as in the ring-tailed cat (not shown) and represents the ancestral condition for both carnivores and primates. The pig shows a derived inversion with breakpoints very close to the borders of tupaia probes 28 and 24. The cat shows a derived translocation of a segment closely identical to the tupaia segment 24 to form cat chromosomes C2 and A2. (B) Hybridization patterns on human and various higher primate homologs observed with a C. aethiops chromosome 22-specific paint (yellow). Human (HSA), chimpanzee (PTR), and Gorilla (GGO) chromosome 3 homologs show the same two hybridization segments, whereas on Bornean orangutan (PPY_bo), macaque (MNE), Douc langur (PNE), and African green monkey (CAE) only one distinct signal was observed, with the exception of PPY_bo interrupted by the centromere (arrow heads). On silvered-leaf monkey (PCR) chromosomes two signals were detected, one of them interrupted by the centromere.

Figure 3

Summary and interpretation of the hybridization of tree shrew chromosome 6- (green), 7- (red), 24- (blue), and 28- (yellow) specific paints on ring-tailed cat, pig, tree shrew, prosimians (lemur), Old World monkey (macaque), Bornean orangutan, African great apes, and human chromosomes. Uncolored chromosome segments represent apomorphic translocations. The segment homologous to human 21 is shown hatched. Red lettering indicates phylogenetic landmarks. The ancestral order of chromosome segments for carnivores, artiodactlys, and primates is found in the ring-tailed cat and prosimians. The origin of Old World monkeys, apes, and humans is marked by a synapomorphic fission of homologs to chromosomes 21 and 3 and an inversion. The Bornean orangutan has conserved the ancestral order for all higher Old World primates. From this Old World monkeys are derived by a synapomorphic inversion. African apes and humans are phylogenetically linked by two inversions.

Figure 4

Examples for comparative fine-mapping experiments in higher primates using YACs and human subregional painting probes. For abbreviations of species names see Fig. 2. (A) Hybridization signals observed with YAC 3 and 12 (yellow) on human chromosome 3 and various primate homologs counterstained in red. (B) Partial primate metaphases (blue) after hybridizations with two YACs each (green/red). Note that YACs 4 and 7 are chimeric, giving additional signals on other chromosomes. (C) Multicolor FISH experiments with YACs and subchromosomal painting probes derived from somatic cell hybrids (see Fig. 1, for probe location on human chromosomes). Chromosomal counterstain is false colored in gray, hybridization signals in green and red, and yellow in case of probe overlap.

Figure 5

The most parsimonious reconstruction of chromosome 3 rearrangements in higher primates. Blue bars within a chromosome represent the hybridization signals obtained with a painting probe specific for human chromosome 3q. Yellow and red bars show the hybridization signals obtained with African green monkey chromosome 15 and 22 paints, respectively. The horizontal lines show inversion break points and the arrows the direction of changes. Numbers indicate the location and order of YAC signals. The red boxes frame the assumed ancestral condition for all higher Old World primates as found in the Bornean orangutan. (Upper) To derive the homologs of human/African great apes from that of Bornean orangutan two overlapping inversions are necessary. First YACs 8–10 and 1 would have to be inverted, leading to an intermediate chromosome type. In a second inversion a fragment including YACs 2–7, the centromere, and YACs 8–10 were inverted. The signal derived from African green monkey chromosome paints are split in two segments each. The Sumatran orangutan homolog can be derived from that of the Bornean orangutan by a single pericentric inversion involving breakpoints between YACs 1 and 10 and the telomere. (Lower) A centromere inactivation/activation and a single pericentric inversion is needed to derive the ancestral Old World monkey homolog as seen in both the macaque and snub-nosed monkeys from that of the Bornean orangutan. For better comparison the orangutan homolog has been inverted. C. aethiops homologs can be derived from the ancestral Old World monkey homolog by a fission between YACs 3 and 4 and the activation of a new centromere.