A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors

Abstract

Krüppel-type zinc finger (ZNF) motifs are prevalent components of transcription factor proteins in all eukaryotes. KRAB-ZNF proteins, in which a potent repressor domain is attached to a tandem array of DNA-binding zinc-finger motifs, are specific to tetrapod vertebrates and represent the largest class of ZNF proteins in mammals. To define the full repertoire of human KRAB-ZNF proteins, we searched the genome sequence for key motifs and then constructed and manually curated gene models incorporating those sequences. The resulting gene catalog contains 423 KRAB-ZNF protein-coding loci, yielding alternative transcripts that altogether predict at least 742 structurally distinct proteins. Active rounds of segmental duplication, involving single genes or larger regions and including both tandem and distributed duplication events, have driven the expansion of this mammalian gene family. Comparisons between the human genes and ZNF loci mined from the draft mouse, dog, and chimpanzee genomes not only identified 103 KRAB-ZNF genes that are conserved in mammals but also highlighted a substantial level of lineage-specific change; at least 136 KRAB-ZNF coding genes are primate specific, including many recent duplicates. KRAB-ZNF genes are widely expressed and clustered genes are typically not coregulated, indicating that paralogs have evolved to fill roles in many different biological processes. To facilitate further study, we have developed a Web-based public resource with access to gene models, sequences, and other data, including visualization tools to provide genomic context and interaction with other public data sets.

Figure 1.

Phylogenetic tree of human KRAB-A motifs. This neighbor-joining phylogenetic tree represents 418 human KRAB-A nucleotide sequences from KRAB-ZNF and SCAN-KRAB-ZNF genes (including some with noncanonical structures). Gene designations are removed from this unrooted phylogram for clarity; a list of the genes including location and aligned KRAB sequences is presented in Supplemental Table S2. Genes from several major physical clusters are colored to show comparisons between physical location and sequence similarity. Loci within a highlighted phylogenetic group that do not map to the same physical cluster as related genes appear as superimposed circles in the appropriate color (or in white for genes that do not belong to any labeled cluster). Genes that also encode SCAN, KRAB-b, KRAB-BL, or KRAB-C motifs are indicated as follows: SCAN, red circles; KRAB-b, orange triangles; KRAB-BL, blue squares; and KRAB-C, green diamonds. The green arrow notes the position of the Xenopus Xfin KRAB sequence, added as a potential outgroup, although the tree is shown unrooted.

Figure 2.

Analysis of expression patterns for KRAB and SCAN-KRAB ZNF genes. Expression levels of members of the human KRAB and SCAN-KRAB genes are represented by red and green boxes (denoting higher and lower expression levels, respectively). Vertical columns of boxes represent different genes, and horizontal rows represent different tissues. We have grouped tissues into the following categories as labeled on the left of each panel: N indicates neural; I, immune; G, glandular; M, muscle; O, other organ; and R, reproductive. In panel A, the 211 analyzed genes are arranged in chromosomal order. Selected genomic clusters are indicated by colored boxes beneath the expression pattern. From left to right, the clusters are (as listed in Supplemental Table S1): 16p13.3, 16p11.2a, 19p13.2, 19p13.2-p13.13, 19q13.12-q13.13, 19q13.31, 19q13.41-q13.42, 19q13.43a, 19q13.43b, 6p22.1b, 7q22.1a, 7q36.1a, and 8q24.3c. In panel B, all selected expression profiles (described in text) have been clustered based on expression pattern similarity. Colored hash marks above the expression profiles indicate the chromosomal cluster from panel A with which each profile corresponds.