The Genom of Homo sapiens.pdf

144 RUDD, SCHUELER, AND WILLARDFigure 3. Repeat content of the junction between the short-arm euchromatin and centromere of the X chromosome. Each line andcolor illustrates a different type of repeat family present in the most proximal 1 Mb on Xp (drawn using rm2parasight; D. Locke, unpubl.).The “satellite junction” indicates an abrupt transition from the euchromatin of Xp and the first pericentromeric satellite sequences.At least three types of satellites are present here: monomeric α satellite, γ satellite, and a 35-bp satellite (HSAT4). The mostproximal annotated genes on Xp (ZXDA and ZXDB) are shown, with the direction of transcription indicated by the arrows. The “arrayjunction” indicates the transition between monomeric α satellite and DXZ1 higher-order repeats, which extend a further ~3 Mb atthe centromere. (Based on Schueler et al. 2001.)quenced (low-pass sequence sampling). BAC 285M22bridges the junction between the D17Z1-B array andmonomeric α satellite; fluorescence in situ hybridizationstudies demonstrated that this junction lies to the shortarm side of D17Z1 (Fig. 4A,C). When we compared thehigher-order repeats in 285M22 and 18L18 (n = 7), allwere 98–99% identical, indicating that they are part of ahighly homogeneous array of α satellite. Notably, however,whereas D17Z1 and D17Z1-B share a similar multimericstructure, they are only 92% identical, demonstratingthat they are distinct yet related higher-orderrepeats. (Such a relationship differs from a number ofvariants of D17Z1 that, although distinctive in theirhigher-order structure and their genomic localizationwithin the large D17Z1 locus, are not distinguished bylevels of overall sequence relatedness [Warburton andWillard 1990, 1995].)Although a contig extending across the full D17Z1 andD17Z1-B arrays remains to be achieved, we have establisheda complete contig linking D17Z1-B to the euchromatinof 17p (M.K. Rudd, unpubl.), essentially using thestrategy developed as part of our Xp work (Schueler et al.2001). The genomic content of this part of chromosome17 is, however, somewhat more complex than that of theX, in that there are three different blocks of monomeric αsatellite located within ~500 kb of D17Z1-B, separatedby regions of genomic sequence populated by a numberof different repeat families (both satellite and non-satellite)and at least some transcribed elements. A similar pictureappears to be emerging on the long arm (17q) side ofthe centromere, although a contig containing stretches ofmonomeric α satellite and proximal 17q sequences hasnot yet been linked to the large D17Z1 array at the centromere(M.K. Rudd, unpubl.).The coexistence within pericentromeric regions of bothhigher-order repeat arrays of α satellite and more limitedstretches of monomeric α satellite without any detectablehigher-order structure appears to be a consistent theme ofa number of human chromosomes (Horvath et al. 2001).Although the organizational distinction between thesetypes of α satellites (i.e., multimeric vs. monomeric) isapparent at short range with standard homology-findingprograms (e.g., Fig. 1B,C), it is also important to addressthe phylogenetic sequence relationships among the individualmonomers populating these different classes of therepeat family.To illustrate this point, we examined ~100 monomersof monomeric α satellite from each of the Xp and 17qcontigs, together with 28 monomers making up the DXZ1and D17Z1 higher-order repeats. As seen in Figure 5, thesequences fall into two distinct phylogenetic clades, correspondingprecisely to their monomeric or multimericorigin. Within the multimeric clade, the DXZ1 andD17Z1 monomers exhibit close sequence relatedness, asestablished previously (Waye and Willard 1986). Notably,the monomeric clade includes monomers from bothchromosomes (Fig. 5); in other words, clusters ofmonomeric α satellite from one chromosome are moreclosely related to monomeric α satellite from the otherchromosome than they are to the multimeric α satellitethat maps only a few hundred kilobases away on the samechromosome.These relationships presumably reflect the highly efficienthomogenization mechanisms that drive and maintainthe high degree of sequence homogeneity withinhigher-order repeat arrays, even across severalmegabases of genomic DNA (Willard and Waye 1987;Durfy and Willard 1989; Schueler et al. 2001; Schindelhauerand Schwarz 2002). However, the phylogeneticdata argue that homogenization mechanisms betweenmonomeric and multimeric α satellite are poorly efficientor nonexistent, even over much shorter genomic dis-