Chromosomal distribution, GC content, and repeat content of 614-kb DNA sequence surrounding the 2q13–2q14.1 fusion site (2qFus). (A) Each black line indicates the sequence coverage of finished Bacterial Artificial Chromosome (BAC) clones assembled into the 2qFus contig on the basis of their 99.9%–100% identity in regions of overlap. BAC RP11–559H14 is unfinished (gray line); it overlaps RP11–480C16 and –395L15 with 99.7% identity, thereby confirming their overlap. Clone names are followed by chromosomal locations determined by fluorescence in situ hybridization; accession numbers are given below the lines. RP11–432G15 extends 35 kb off the right side of the map. Note that final GenBank entries for some of the BACs have been trimmed to remove overlap among clones exceeding 2 kb. The green vertical line marks the location of the inverted degenerate telomere repeats at the fusion site. The fusion site is immediately flanked by a telomere-associated repeat, TAR1, a repeat that is commonly found in close association with terminal telomere arrays and sometimes found near interstitial degenerate telomere repeats. (B) The G + C trace shows a graph of %GC content with window sizes of 500 bp for local content. Red, blue, and green regions represent H3, H1–H2, and L isochores, respectively, as defined by GESTALT using a 30-kb sliding window. The location, strand, age, and type of interspersed repetitive elements are shown in the third trace, also generated with GESTALT (Long Interspersed Elements [LINEs], green; Alus, red; Mammalian-wide Interspersed Repeats [MIRs], purple; all other repeats including retroviruses, Long Terminal Repeats [LTRs], Mammalian Apparent LTR-retrotransposons [MaLRs], etc., brown). The age of each element is indicated by the height of the feature; taller features represent evolutionarily more recent insertions. (C) Chromosomal distributions of sequence homologous to the 2qFus region as determined by PCR assays on a monochromosomal hybrid panel. Filled and open circles denote positive and negative PCR assays, respectively. The precise locations of the PCR assay are indicated by the vertical tick marks. The colored bar delineates regions with different chromosomal distributions. The light gray block within gray block indicates sequence duplicated within chromosome 2 (see Fig. 3).

Summary of regions of homology with portions of the 614-kb sequence surrounding the fusion site on 2q13–2q14.1 that were identified by BlastN searches of finished genomic sequence publicly available as of February 28, 2002. Table 1 gives the clone names and accession numbers for the paralogous segments. For simplicity, only one of the sequences with homology with only the 68-kb region immediately surrounding the fusion site is shown. Red solid lines indicate the regions with >95% average identity to the 2qFus sequence. These lines are drawn with reference to the 2qFus sequence; the actual lengths of the paralogous segments may be slightly longer or shorter than those drawn because of distributed insertions and deletions. Red dotted lines indicate adjoining regions with no available sequence, but that were shown by PCR to be homologous to 2qFus (see Fig. 1). Different colors are used to indicate divergent sequence, with solid lines indicating the extent of contiguous sequence coverage, and dotted lines indicating either unavailable sequence or neighboring sequence that lacks homology with any of the other segments shown. Blocks 9p11.2-A and -B map to the pericentromeric region of 9 by fluorescence in situ hybridization and hybrid panel analyses and are tentatively assigned to 9p11.2. Orientation indicated in parentheses is tentative; the presence of alpha-satellite-like repeats in the right-most portion of the 9p11.2-A sequence indicates that it runs telomere to centromere as drawn. (<?) Indicates that 2qFus homology could extend farther in direction of arrowhead. The small red symbols on stalks indicate the most recent Alu insertions in the 2qFus region and/or its paralogs. The most recently active families, AluYb8 and AluYa5, are indicated by squares and triangles, respectively, and circles indicate the older class of AluY elements. Filled and open symbols indicate that the particular element is present or absent, respectively. The partially filled symbol in 9pter indicates that this AluYb8 element is not present in all 9pter alleles (see text). The asterisks mark the position of a highly variable SATR1 repeat common to at least four of the paralogous segments; it is 15,109 bp long in 9q13, 15,021 bp in 9p11.2-B, 4919 bp in 9pter, and 3881 bp in 2qFus.

Estimated timing of duplications, inversions, and relocations of 2qFus-paralogous blocks based on sequence identity measures and fluorescence in situ hybridization analyses of hominids. (A) Phylogeny of hominids. The branch lengths and estimated speciation dates are based on sequence analyses of 53 autosomal intergenic nonrepetitive DNA segments analyzed by Chen and Li (2001). The speciation dates are drawn at the midpoint of estimated ranges: human–chimpanzee, 4.6–6.2 Mya; human–gorilla, 6.2–8.4 Mya; human–orangutan, 12–16 Mya. MRCA marks the estimate of the time of the most recent common ancestor of all modern humans (Yu et al. 2001). The average ± SD percent sequence substitution (Jukes-Cantor model, excluding indels) between human and each of the three other hominids is given at the right (Chen and Li 2001). (B) Estimated timing of events involving 2qFus-paralogous blocks. The blocks are identified by their current positions in humans (i.e., 2qFus-Dist and 2qFus-Prox are the regions forming the distal and proximal sides of the 2q fusion site, respectively; both were at chromosome tips when the duplicative transfers occurred). Ancestral and derived states, when indicated, are inferred from breaks that disrupt genes, specific repetitive elements, or isochore patterns; the copy carrying the full-length gene/element and/or lacking an isochore transition at the breakpoint is assumed to represent the ancestral version.

Summary of fluorescence in situ hybridization (FISH) analyses of hominid chromosomes using BACs RP11–480C16 (green), RP11–395L14 (blue), and RP11–432G15 (red) derived from the ancestral fusion site in human 2q13–q14.1. Data for chromosomes 2, 9, and 22, which carry the major blocks of paralogy in human, are shown in the top panels so that the banding patterns are not obscured by the FISH signals. Other chromosomes are shown in the bottom panel. A total of at least six metaphase spreads were examined for each probe in each species (one individual each). Hybridization signals seen at each location were scored from digitized images on an intensity scale of 1–4 on each probe in each species. The cumulative scores were normalized to that of the location with highest cumulative score in each experiment. The area of each dot is proportional to this normalized score. Dots are aligned with the midpoint of observed FISH signals for each location. The asterisk indicates where hybridization was seen on one homolog only. Ideograms are redrawn from Yunis and Prakash (1982). Accession numbers for the three clones are given in Fig. 1. Human 2p- and 2q-specific clones, RP11–90H11 and RP11–47E6, respectively, were used to verify the identity of hominid chromosomes orthologous to 2p and 2q (i.e., chimpanzee 12 and 13, respectively) (not shown).

Disruption of isochore, L1 repetitive element, and PGM5 gene by the breakpoint of duplication between 9q13 and 2qFus. (Green) L isochore; (blue), H1–2 isochore. The regions shown correspond to nucleotides 381651 to 423067 in the 2qFus contig and, for 9q13, from nt 139050 in RP11–561023 to nt 9713 in RP11–88I18. The breakpoint of homology (dotted line) was determined by cross_match (http://www.genome.washington.edu/phrap_documentation.html) analysis, the L1PBa repeat was identified by RepeatMasker, and the GC-content and isochore classification were determined by GESTALT. The vertical bars are exons of the PGM5 gene (see Fan et al., 2002 for more details).