Genomic Sequence and Transcriptional Profile of the Boundary Between Pericentromeric Satellites and Genes on Human Chromosome Arm 10p

Abstract

Contiguous finished sequence from highly duplicated pericentromeric regions of human chromosomes is needed if we are to understand the role of pericentromeric instability in disease, and in gene and karyotype evolution. Here, we have constructed a BAC contig spanning the transition from pericentromeric satellites to genes on the short arm of human chromosome 10, and used this to generate 1.4 Mb of finished genomic sequence. Combining RT-PCR, in silico gene prediction, and paralogy analysis, we can identify two domains within the sequence. The proximal 600 kb consists of satellite-rich pericentromerically duplicated DNA which is transcript poor, containing only three unspliced transcripts. In contrast, the distal 850 kb contains four known genes (ZNF248, ZNF25, ZNF33A, and ZNF37A) and up to 32 additional transcripts of unknown function. This distal region also contains seven out of the eight intrachromosomal duplications within the sequence, including the p arm copy of the ∼ 250-kb duplication which gave rise to ZNF33A and ZNF33B. By sequencing orthologs of the duplicated ZNF33 genes we have established that ZNF33A has diverged significantly at residues critical for DNA binding but ZNF33B has not, indicating that ZNF33B has remained constrained by selection for ancestral gene function. These results provide further evidence of gene formation within intrachromosomal duplications, but indicate that recent interchromosomal duplications at this centromere have involved transcriptionally inert, satellite rich DNA, which is likely to be heterochromatic. This suggests that any novel gene structures formed by these interchromosomal events would require relocation to a more open chromatin environment to be expressed.[Supplemental material is available online at www.genome.org and also at

The evolutionary dynamics of α-satellite

“…Higher-order ␣-satellite within an array is extremely homogeneous, and few other sequences have been found embedded within higher-order ␣ arrays (Schueler et al 2001;Ross et al 2005). In contrast, monomeric ␣-satellite is more heterogeneous in sequence and is extensively interspersed with non-␣-satellite sequences (Schueler et al 2001;Guy et al 2003;Kazakov et al 2003;.…”

“…In contrast, monomeric ␣-satellite lacks detectable higher-order periodicity, and its constituent monomers are far less homogeneous than are higher-order repeat units . All normal human centromeres contain large arrays of higher-order ␣-satellite (Warburton and Willard 1996;Alexandrov et al 2001), and, where investigated, these arrays have been found to be bordered by more heterogeneous monomeric ␣-satellite (Wevrick et al 1992;Horvath et al 2000;Schueler et al 2001;Guy et al 2003;. The adjacent organization of higherorder and monomeric ␣-satellite, as well as the fact that lower primates have only monomeric ␣-satellite at their centromeres (Rosenberg et al 1978;Musich et al 1980;Maio et al 1981;Thayer et al 1981;Alves et al 1994), has led to the hypothesis that higher-order ␣-satellite evolved from ancestral arrays of monomeric ␣-satellite and subsequently transposed to the centromeric regions of all great ape chromosomes (Warburton and Willard 1996;Alexandrov et al 2001;Schueler et al 2001Schueler et al , 2005Kazakov et al 2003).…”

Dynamic evolution at pericentromeres

“…Current models of primate pericentromere evolution suggest that the complex intra-and interchromosomal duplications begin with initial euchromatin-derived seeding events, followed by exchange of large duplicated blocks to pericentromeres of nonhomologous chromosomes (She et al 2004;Horvath et al 2005). Although the Brassicaceae duplications do not appear as prevalent as those in primates, in both cases, such events could lead to the evolution of new genes (Guy et al 2003). Indeed, in O. pumila we found a novel hypothetical protein with domains likely derived from three distinct origins (Table 3).…”

Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes

“…Several HSA7 clades contain loci mapping to both chromosome arms (Figs. 2, 3), indicating that subgroup expansion was followed by a series of duplications or inversions around the centromere, as occurred on HSA10 (Tunnacliffe et al 1993;Guy et al 2003). The pericentromeric HSA19 cluster contains a large number of ␤-satellite repeats, and unequal crossing-over between blocks of these repeats has been suggested as a factor in expansion of the cluster (Eichler et al 1998).…”