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 to ZNF208. Large blocks of (∼25-kb) inverted ␤-satellite repeats with a remarkably symmetrical higher order repeat structure were found to bracket the functional ZNF gene. Hybridization analysis using the ␤-satellite repeat as a probe indicates that ␤-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 ␤ 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.] Zinc finger (ZNF) genes represent one of the largest gene families in the human genome with an estimated 500-600 members (Hoovers et al. 1992;Becker et al. 1995;Klug and Schwabe 1995). Although the specific function of the majority of ZNF genes remains largely unknown, as a class they are believed to encode transcriptional regulators that in a few instances have been shown to play critical roles in cellular and developmental differentiation processes (Pieler and Bellefroid 1994). ZNF proteins have been implicated in many diverse eukaryotic developmental processes, such as segment pattern formation in the Drosophila embryo (Rosenberg et al. 1986); cellular proliferation in the cerebellar hindbrain of the mouse (Wilkinson et al. 1989); and hematopoietic differentiation among human myeloid precursor cells (Hromas et al. 1991). DNA binding of the encoded proteins is typically mediated by a ZNF motif that consists either of two cysteines and two histidines (Krüppel family or C 2 /H 2 type) or four cysteines alone (steroid receptor or C 2 / C 2 type). The conserved cysteines and/or histidines form a tetrahedral complex around a zinc metal ion, generating a folded loop or ''finger'' of 30 amino acids that is capable of making contact with DNA (Miller et al. 1985)...

Insertion of β-satellite repeats identifies a transmembrane protease causing both congenital and childhood onset autosomal recessive deafness

“…Monomeric, approximately 68-bp repetitive units of β-satellites (or Sau3A repeats) have been detected on the short arms of all human acrocentric chromosomes and chromosomes 1, 9 (centromeric), 19p and Y (refs. [17][18][19]. At least four families of β-satellites have been defined 19 and the β-satellite insertion into TMPRSS3 is likely to be derived from either p21β2 or p21β7 repeats.…”

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

“…3) and very recent, perhaps ape-or human-specific, duplication episodes (the dispersed LLNL1037 clade of pseudogenes share up to 99% sequence identity over variable segmental duplication lengths of <30-160 kb). This mode of duplication, which appears to have been utilized much less frequently than tandem in situ events, has the potential to seed gene clusters at new chromosomal sites (Ohno 1970;Eichler et al 1998). A possible example of this is a monophyletic group of genes including ZNF141 that are clustered together at the telomere of HSA4p (Figs.…”

“…One large cluster of KRAB-ZNF genes located near the centromere of human chromosome 19 (HSA19) is especially interesting because it has long been known to be unique to primates (Bellefroid et al 1995;Eichler et al 1998). Here, we present a detailed analysis of this large subfamily of genes and investigate patterns of evolutionary divergence in clades of recently duplicated primate paralogs.…”

An ORFeome-based Analysis of Human Transcription Factor Genes and the Construction of a Microarray to Interrogate Their Expression

“…This analysis identified 29 regions that passed the criteria. Four of these regions were Hox clusters, and another nine clusters were attributed to zinc finger clusters on chromosome 19 (19p12, 19q13.2, and 19q34;Eichler et al 1998). The remaining 16 clusters had little underlying annotation of their transcript members.…”

“…One of the major issues in designing a microarray of TFs is that many of these genes fall into families that share significant regions of conserved sequence homology. For example, there are >500 TFs that contain zinc finger domains (Eichler et al 1998; this study, see below). To design a probe that will measure the expression of only one gene, it was necessary to identify sequence regions in each gene that were unique to it.…”