Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12

Abstract

We investigated the organization, architecture, and evolution of the largest cluster (∼4 Mb) of Krüppel-associated box zinc finger (KRAB–ZNF) genes located in cytogenetic band interval 19p12. A highly integrated physical map (∼700 kb) of overlapping cosmid and BAC clones was developed between genetic STS markers D19S454 and D19S269. Using ZNF91 exon-specific probes to interrogate a detailed EcoRI restriction map of the region, ZNF genes were found to be distributed in a head-to-tail fashion throughout the region with an average density of one ZNF duplicon every 150–180 kb of genomic distance. Sequence analysis of 208,967 bp of this region indicated the presence of two putative ZNF genes: one consisting of a novel member of this gene family (ZNF208) expressed ubiquitously in all tissues examined and the other representing a nonprocessed pseudogene (ZNF209), located 450 kb proximal toZNF208. Large blocks of (∼25-kb) inverted β-satellite repeats with a remarkably symmetrical higher order repeat structure were found to bracket the functional ZNF gene. Hybridization analysis using the β-satellite repeat as a probe indicates that β-satellite interspersion between ZNF gene cassettes is a general property for 1.5 Mb of the ZNF gene cluster in 19p12. Both molecular clock data as well as a retroposon-mapping molecular fossil approach indicate that this ZNF cluster arose early during primate evolution (∼50 million years ago). We propose an evolutionary model in which heteromorphic pericentromeric repeat structures such as the β satellites have been coopted to accommodate rapid expansion of a large gene family over a short period of evolutionary time.

[The sequence data described in this paper have been submitted to GenBank under accession nos. AC003973 and AC004004.]