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

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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, andZNF37A) 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 ZNF33Aand ZNF33B. By sequencing orthologs of the duplicatedZNF33 genes we have established that ZNF33A has diverged significantly at residues critical for DNA binding butZNF33B 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 atwww.genome.org and also at http://www.ncl.ac.uk/ihg/10p11.htm. The sequence data from this study have been submitted to EMBL under accession nos. AL391686, AL161931, AL133350, AL121927, AL132657,AL135791, AL132659, AL117337, AL117339, AL132658, AL133217,AL133216, AJ245587, AJ245588, AJ251655, AJ275023–AJ275036,AJ250940–AJ250950, AJ275024–AJ275036, AJ492195, AJ492196,AJ491691–AJ491697. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: W. Amos.]