- Research article
- Open Access
Evolution of C2H2-zinc finger genes and subfamilies in mammals: Species-specific duplication and loss of clusters, genes and effector domains
© Tadepally et al; licensee BioMed Central Ltd. 2008
- Received: 17 March 2008
- Accepted: 18 June 2008
- Published: 18 June 2008
C2H2 zinc finger genes (C2H2-ZNF) constitute the largest class of transcription factors in humans and one of the largest gene families in mammals. Often arranged in clusters in the genome, these genes are thought to have undergone a massive expansion in vertebrates, primarily by tandem duplication. However, this view is based on limited datasets restricted to a single chromosome or a specific subset of genes belonging to the large KRAB domain-containing C2H2-ZNF subfamily.
Here, we present the first comprehensive study of the evolution of the C2H2-ZNF family in mammals. We assembled the complete repertoire of human C2H2-ZNF genes (718 in total), about 70% of which are organized into 81 clusters across all chromosomes. Based on an analysis of their N-terminal effector domains, we identified two new C2H2-ZNF subfamilies encoding genes with a SET or a HOMEO domain. We searched for the syntenic counterparts of the human clusters in other mammals for which complete gene data are available: chimpanzee, mouse, rat and dog. Cross-species comparisons show a large variation in the numbers of C2H2-ZNF genes within homologous mammalian clusters, suggesting differential patterns of evolution. Phylogenetic analysis of selected clusters reveals that the disparity in C2H2-ZNF gene repertoires across mammals not only originates from differential gene duplication but also from gene loss. Further, we discovered variations among orthologs in the number of zinc finger motifs and association of the effector domains, the latter often undergoing sequence degeneration. Combined with phylogenetic studies, physical maps and an analysis of the exon-intron organization of genes from the SCAN and KRAB domains-containing subfamilies, this result suggests that the SCAN subfamily emerged first, followed by the SCAN-KRAB and finally by the KRAB subfamily.
Our results are in agreement with the "birth and death hypothesis" for the evolution of C2H2-ZNF genes, but also show that this hypothesis alone cannot explain the considerable evolutionary variation within the subfamilies of these genes in mammals. We, therefore, propose a new model involving the interdependent evolution of C2H2-ZNF gene subfamilies.
- Zinc Finger
- Tandem Duplication
- Zinc Finger Motif
- Zinc Finger Gene
- Homologous Cluster
The sequencing of the human genome uncovered that a large number of gene families are often arranged in a clustered organization [1–3]. C2H2 zinc finger (C2H2-ZNF) genes make up ~2% of all the human genes and represent the second largest gene family in humans after the odorant receptor family [4–7]. The first identified members of the C2H2-ZNF family were Xenopus TFIIIA and Drosophila Kruppel and thus genes of this family are often called zinc finger genes of the TFIIIA or Kruppel type [6, 8].
Most of the characterized C2H2-ZNF genes code for transcription factors which bind DNA through their zinc finger region; others bind RNA and their exact function is as yet unknown [9, 10]. The zinc finger region is composed of a basic structural unit of 28 amino acids (CX2–4CX3FX5LX2HX3–4HTGEKPYX, where X is any amino acid), called the zinc finger motif that is often repeated in tandem. The two cysteines and two histidines in this motif interact with a zinc ion, stabilizing the proper folding of this motif [11–13]. C2H2-ZNF proteins often contain an effector domain that is always located N-terminal to the zinc finger region, such as the KRAB (Kruppel-Associated-Box), SCAN (SRE-ZBP, CTfin51, AW-1 and Number18 cDNA) and BTB (Broad-Complex, Tramtrack and Bric-a-bric) domains. The first two domains are vertebrate-specific [14–16], while BTB is also present in insects. The KRAB domain includes the KRAB A box (~38 amino acids) involved in transcriptional repression, and often a second box, usually KRAB B (~32 amino acids) or in a few cases KRAB b or KRAB C (~21 amino acids) box [17–20]. The KRAB A box and the second KRAB B, b or C boxes are encoded by separate exons often prone to alternative splicing. The SCAN, also called the leucine-rich (LeR) domain (~84 amino acids) , mediates protein-protein interactions through dimerization [22, 23]. The BTB domain (~120 amino acids) is a dimerization domain that also acts as a repression domain in some cases . In contrast to the SCAN and KRAB domains, which are only present in C2H2-ZNF proteins, the BTB domain is also found as a part of actin-binding proteins . C2H2-ZNF proteins are grouped into different subfamilies based on the type of N-terminal effector domain present.
Initial studies on the C2H2-ZNF gene family focused on human chromosome 19, which is particularly enriched in clusters of these genes [25, 26]. More recent studies dealt more specifically with the KRAB subfamily [18, 27–29]. The current view is that C2H2-ZNF genes have undergone a massive expansion during vertebrate evolution, primarily by tandem duplication [18, 27, 29–32]. Yet, this view may be biased, because it is extrapolated from subsets of C2H2-ZNF genes.
In this report, we reconstruct a global picture of the evolution of the C2H2-ZNF gene repertoires during mammalian speciation that is based on a comprehensive catalogue of all human C2H2-ZNF genes and their syntenic counterparts present in clusters in other mammals. Our study clearly demonstrates that this gene family expanded and contracted not only in human but across mammals, and in a lineage-specific fashion. In addition, we discovered evolutionary change of individual C2H2-ZNF orthologs involving both differential duplication of zinc finger motifs and loss of N-terminal effector domains. This led us to propose a model for the interlinked evolution of SCAN, SCAN-KRAB and KRAB subfamilies, underlining the importance of comparing complete gene repertoires rather than specific subfamilies for gaining insights into the possible orthologous relationships between genes from various genomes. Our data indicates that during speciation of mammals, divergent evolutionary trends at the level of individual C2H2-ZNF genes as well as the entire family characterized the evolution of the C2H2-ZNF genes.
Compilation of a comprehensive catalogue of human C2H2-ZNF genes
Clustered organization of human C2H2-ZNF genes
It was reported earlier that human chromosome 19 is particularly rich in tandemly duplicated C2H2-ZNF genes and that KRAB C2H2-ZNF genes are also found in clusters on several other chromosomes [32, 34]. In order to trace the duplication history of the entire C2H2-ZNF repertoire, we studied the distribution of these genes across the whole human genome. Two consecutive C2H2-ZNF genes were considered to belong to a cluster if the distance between them is ≤ 500 Kbp, regardless of the presence of other genes or pseudogenes within the cluster (see Methods). Using this definition, we identified 81 human C2H2-ZNF clusters accounting for 72% of the total number of C2H2-ZNF genes (518 of the 718) (see Additional Files 2 and 3). The remaining genes are dispersed as singletons. Among these clusters, 31% include exclusively tandemly organized C2H2-ZNF genes with no other intervening genes (see Figure 2B and Additional File 3). The number of C2H2-ZNF genes per cluster ranges from 2 to 76 with an average of 6. As illustrated in the Figure 2B, about 75% of the total numbers of C2H2-ZNF clusters have between two to six genes. Consistent with previous reports, chromosome 19 not only has the largest number of C2H2-ZNF clusters (see Additional File 2) but also hosts the largest clusters (>12 genes) (see Figure 2B and Additional File 3).
We find that the large majority of KRAB (89%) and SCAN (90%) types of C2H2-ZNF genes are arranged in clusters (see Figure 2A and Additional File 2). This contrasts with the BTB subfamily of C2H2-ZNF genes or those lacking effector domains, which occur more often as singletons in the genome. An analysis of the composition of individual clusters revealed that two-third of the clusters contains a mixture of various C2H2-ZNF subfamilies (see 'mixed clusters', Additional File 3). The few clusters made up of a single C2H2-ZNF gene subfamily ('pure clusters') are of small size (< 4 genes).
Identification and comparison of syntenic C2H2-ZNF clusters across mammals
With the ultimate goal to study the evolution of zinc finger genes, we identified and compiled clusters in completely sequenced mammalian genomes (i.e., chimpanzee, mouse, rat and dog) that are syntenically homologous to those of human. Syntenically homologous clusters were identified by the genes flanking each cluster. All the C2H2-ZNF genes found within the delimited syntenic regions were then identified using a TBLASTN search (see Methods). The 81 human C2H2-ZNF clusters and their syntenic counterparts in other mammals are listed in Additional File 4, which also includes information on the orientation of the genes in the clusters, their associated domains, the number of zinc finger motifs and the flanking genes.
Comparing individual syntenic clusters in the mammalian genomes
To distinguish whether differences in the number of C2H2-ZNF clusters are due to species-specific gene gain or loss, we systematically compared individual syntenic clusters in the five mammalian genomes studied. The results of this analysis point to a differential evolutionary history in mammals. About 60% of the human clusters (49) have syntenically homologous counterparts in all the species studied, indicating that these C2H2-ZNF clusters predate the divergence of dog, rodents and primates (see Additional File 4 and Additional File 5). In addition, we found (i) primate specific clusters (14, including 2 human specific clusters), (ii) clusters, present in primates and dog, that were lost in rodents (8 clusters including 3 present in mouse but absent in rat) and (iii) clusters present in primates and rodents but absent in dog (10 clusters) (examples in Figure 3B). Essentially all the primate clusters have larger number of genes than rodent or dog clusters, which reflect a global primate-specific expansion of C2H2-ZNF genes (see Additional File 5). Further, in 40% of all primate clusters, those from human contain more C2H2-ZNF genes than those from chimpanzee. This indicates that most of the evolutionary changes (duplication and/or loss) occurred late in the primate branch. A similar pattern was seen in rodents, where almost all mouse C2H2-ZNF clusters exhibit more genes than their syntenic rat clusters. While these results illustrate that the C2H2-ZNF gene family is rapidly and independently evolving within different lineages, insights into the role of gene duplication and loss in the history of this gene family required rigorous phylogenetic analysis as described below.
Phylogeny of C2H2-ZNF clusters in mammalian genomes
A detailed analysis of the tree revealed four clades that underwent species-specific expansion, and two clades, with gene loss in some species. For example, a dog-specific expansion is seen in the monophyletic Group I, which includes three clustering genes from human (hZNF331), chimpanzee (pZNF331) and dog (cZNF331), which in turn grouped within a larger clade containing nine additional C2H2-ZNF genes from dog. In addition, this clade indicates a loss in rodents, due to the absence of any mouse or rat genes. Group I alone illustrates how both species-specific duplication in dog and loss in rodents can account for the higher number of genes seen in dog C2H2-ZNF clusters as compared to rodents.
Group II shows more pronounced expansion in human as seen in several clusters. For example, one of the primate-specific clades includes 17 human genes and 7 chimpanzee C2H2-ZNF genes (see Figure 5). Of the 17 human genes present in the clade, only 6 genes show a one-to-one orthologous pairing with chimpanzee genes. Another well supported clade (100% bootstrap) includes a single human gene (hZNF677) clustered with two dog genes (LOC484331 AND LOC476394). In this clade, the absence of a chimpanzee or rodent counterparts to these three genes suggests a loss in these species. For chimpanzee, however, loss by pseudogenization is possibly involved (see physical maps described below); note that the percentage of C2H2-ZNF genes annotated as pseudogenes was higher in chimpanzee than in human C2H2-ZNF clusters (see Additional File 4: '62 chimpanzee vs. 25 human pseudogenes').
In Group III, the relationship of the four rodent genes with the dog and primate genes could not be resolved (bootstrap < 95%). Still, a rodent-specific clade revealed a duplication exclusively in mouse (to the exclusion of rat), and also exhibited a higher number of genes in mouse, as seen in several other cases in our study.
Superimposition of the phylogenetic trees on the physical maps of clusters
Group II mainly contains primate-specific C2H2-ZNF genes that cluster on the phylogenetic tree in two well supported clades (≥ 97% bootstrap), plus a sub-group with weaker support (93% bootstrap). Almost all these genes also cluster physically together on the chromosome. Human orthology assignments for ten of the twelve chimpanzee genes from Group II (underlined in Figure 6) were corroborated by two lines of evidence i.e. from the phylogeny, and from the topology on the chromosome. Noticeably, only 7 out of 10 of the C2H2-ZNF ortholog pairs from this primate-specific cluster exhibit the same number of zinc finger motifs and the same type of N-terminal domain, suggesting that gain or loss of zinc finger motifs and effector domains often occurs within orthologs.
Species-specific variation in the number of finger motifs and the presence of N-terminal conserved domains
Comparative studies in genome research have focused on the extensive similarities existing between the human genome and the genomes from various other model organisms, which provide valuable insights into the biological function and the aetiology of human diseases. However, differences among genomes have received less attention, in spite of the importance they may have in the physiological, morphological and behavioural traits that distinguish species. A few studies on various gene families, such as the odorant receptor family, pointed to some differences existing between genes of closely related species [35–39]. Our comprehensive study of the C2H2-ZNF gene family reveals that there is an extensive variation of the C2H2-ZNF gene content and organization, as well as in the domain composition of orthologous genes among mammals. We also provide the first clear demonstration of the contribution of gene loss in the C2H2-ZNF family during evolution, which occurs at the level of clusters, genes and their functional domains. We also provide the first genome-scale confirmation of the rapid evolution of C2H2-ZNF gene clusters that occurs independently within related mammalian species, which also supports conclusions drawn from smaller-scale studies on individual genes, clusters and C2H2-ZNF subfamilies [27, 29, 30, 32]. Altogether our data led us to propose a new model for the interdependent evolution of the main C2H2-ZNF subfamilies (see Figure 8B) as discussed below. Although it is possible that the release of improved genome assemblies of non-human sequences may lead to the detection of a few new C2H2-ZNF genes or of incorrectly assembled C2H2-ZNF loci, these are unlikely to change any conclusions drawn from this study.
Substantial variation in family size and clustering of C2H2-ZNF genes across mammals
We report here the first complete catalogue of all human C2H2-ZNF gene clusters and their syntenic homologs in chimpanzee, mouse, rat and dog. This catalogue reveals that in human, a large proportion of the genes from the C2H2-ZNF family (>70%) are organized in clusters. Comparative studies of the five mammalian genomes indicated that the total number of genes found in clusters varied considerably, from 172 in rat to 518 in human. Significantly, human and mouse have a larger number of clustered C2H2-ZNF genes (>30%) as compared to chimpanzee and rat, respectively, indicating that independent evolutionary events occurred after the divergence of the two primates (within the last ~6–10 million years) and two rodents (within ~30–46 million years). We distinguish two kinds of events: first, a variation in the number of C2H2-ZNF genes in syntenically homologous clusters and second, the existence of lineage- and species-specific clusters in primates, rodents and canines. This can be accounted for by independent evolution of C2H2-ZNF genes in these closely related species. Previous studies focusing on KRAB C2H2-ZNF genes from human chromosome 19 had identified and analyzed a primate-specific cluster  including members of the primate-specific ZNF91 subfamily of C2H2-ZNF . Other studies on the KRAB C2H2-ZNF subfamily also identified a differential expansion between a human KRAB C2H2-ZNF cluster and its syntenic counterpart in mouse , and more recently other species-specific expansions have been found, from analyses based on draft sequences of various mammalian genomes . Here, we illustrate and confirm at a larger scale the existence of an on-going process of genome dynamics including several lineage- and species-specific rearrangements and a continuous repertoire expansion taking place independently in all evolutionary branches, particularly in primates. This finding was only possible through the analysis of a complete catalogue of all the subfamilies of C2H2-ZNF clusters and their syntenic counterparts in five mammalian species.
Gene duplication and loss: two counteracting forces in the evolution of C2H2-ZNF genes
An overview of the 81 human C2H2-ZNF clusters identified here revealed that a third of them are pure clusters (containing 2 to 24 C2H2-ZNF genes), i.e., they are not interspersed with other genes. Earlier observations of pure C2H2-ZNF gene clusters have led to the hypothesis that C2H2-ZNF genes in primates have expanded massively by tandem duplication [25–27, 40–42]. We revisited this question based on our catalogue of human C2H2-ZNF clusters and their syntenic counterparts in chimpanzee, mouse, rat and dog. Based on a reconciliation of both the superimposition of gene trees onto the known species trees  and the physical maps, we confirm gene duplication and loss. Our results clearly show that both gene gain and gene loss events have occurred multiple times and independently in all the mammals studied. Combined with physical map data, our phylogenetic studies indicate that the expansion of C2H2-ZNF genes that occurred during the evolution of the five species studied, results from the combined action of single-gene duplication and multiple gene duplication (for instances, duplication of all or part of the genes within a cluster). These duplication events were, however, counteracted by the loss of individual genes or clusters as exemplified in several cases where related genes or clusters found in primates and canids were absent in one or both of the two rodents studied. Our study represents the first clear demonstration of the involvement of gene and cluster loss in the evolution of C2H2-ZNF genes and suggests that during mammalian evolution the duplication events outnumbered the loss events. Furthermore our results provide convincing support to the idea that the C2H2-ZNF gene family evolved according to a "Birth and Death" model as proposed by Nei and colleagues [44, 45]. According to this model, new genes are created by duplications, including tandem duplication and block (multigene) duplication (birth). While certain copies remain relatively unchanged in the genome for a long time, others diverge functionally by acquiring a new function. Some are deleted from the genome or become pseudogenes following deleterious mutations (death through elimination or inactivation). In the case of C2H2-ZNF genes, pseudogenization seems to be limited as suggested by expression studies and statistical analysis, which showed positive selection based on the analysis of specific clusters [27, 40]. This sets the C2H2-ZNF family apart from other gene families such as the olfactory receptor gene family [36, 46]. Noticeably, gene loss by pseudogenization is prominent in the olfactory receptor family, with humans accumulating a higher number of pseudogenes as compared to other primates and mouse [37–39]. These variations in the numbers of pseudogenes and functional genes have been associated with the differential chemosensory dependence in these species [47, 48]. In comparison, beyond their role as transcription regulators, only a few C2H2-ZNF proteins have known functions . Further studies of C2H2-ZNF genes in mammals are needed to shed light on the functional consequences of different repertoires of these genes in different species. Until now, the clustered organization of these genes has made knock-out studies in animal models inefficient, likely due to redundancy. However, based on a better knowledge of the organization/content of C2H2-ZNF genes in the various genomes, large chromosomal deletions of pure C2H2-ZNF clusters or other types of gene disruption or targeting approaches could provide insights into the functions of these genes in various animals.
Evolution of C2H2-ZNF genes through gain and loss of finger motifs and N-terminal effector domains
Evidence of the variation in the numbers of zinc finger motifs among orthologs was previously reported for a subset of C2H2-ZNF genes on human chromosome 19 and their mouse homologs . It was shown that this variation is due to both differential duplication of finger motifs and loss by degeneration. In our study, such variation in the number of zinc finger motifs among orthologs was observed repeatedly among all five mammals. Since the zinc finger motifs are flexible, with the ability to bind DNA, RNA and/or proteins, changes in the sequences of zinc finger motifs and their number could differentially alter binding specificities and thus protein function. Changes in both the number of C2H2-ZNF genes and in the number of finger motifs in orthologous genes may be important determinants of species-specific functions.
The rapid evolution of the C2H2-ZNF genes observed in the mammalian lineage was not limited to the variation in the number of genes and zinc finger motifs. Variation was also observed in the presence of N-terminal effector domains, such as SCAN or KRAB, which could be accounted for by either gain or loss of these motifs in the various species. Loss by sequence degeneration of both the SCAN and the KRAB sequences was confirmed in several cases in our study. In certain cases, loss or gain could not be distinguished. A puzzling question that remains, however, is whether gain of KRAB and SCAN sequences occurred multiple times within C2H2-ZNF genes. It is indeed difficult to explain why these effector domains are always found in association with and N-terminal to the zinc finger motifs of C2H2-ZNF proteins, and that the SCAN domain is always positioned N-terminally to the KRAB domain of SCAN-KRAB C2H2-ZNF proteins. Interestingly, by analyzing the exon-intron structure of C2H2-ZNF genes from all clusters, we found that most SCAN and SCAN-KRAB C2H2-ZNF genes have each a typical exon-intron structure (see Figure 7C and Figure 8A). This suggests that the acquisition of SCAN and KRAB sequences by C2H2-ZNF genes are most likely singular events. This led us to propose a new model described in Figure 8. Considering that the SCAN domain is present in all vertebrates and is more ancient than the KRAB domain which is only present in tetrapods, we suggest that first, a SCAN-C2H2 ZNF gene was formed in an ancestor of vertebrates through the gain of SCAN sequence and that later, after the emergence of the tetrapods, the gain of a KRAB sequence gave rise to a SCAN-KRAB C2H2-ZNF gene (Figure 8B). These two gain events possibly occurred through an exon-shuffling mechanism. Diversification of the C2H2-ZNF repertoires from each subfamily then occurred through on-going gene duplications, and loss by deletion or degeneration of the SCAN and/or KRAB sequences. As implied by this model, the birth of the SCAN-KRAB C2H2-ZNF subfamily occurred earlier than that of the KRAB C2H2-ZNF subfamily. This is consistent with previous data showing that SCAN-KRAB-ZNF genes do not group together onto one evolutionary clade but intermix with KRAB-ZNF genes in phylogenetic trees of the KRAB sequence [18, 27, 27]. On the whole, our model is in agreement with the fact that C2H2-ZNF orthologs often belong to different C2H2-ZNF subfamilies as defined by domains and with our observation of intermingling within many C2H2-ZNF clusters of C2H2-ZNF genes from the SCAN, KRAB and SCAN-KRAB subfamilies. Our study clearly indicates that the evolution of C2H2-ZNF subfamilies is tightly linked and stresses that the assignment of proper orthology requires comprehensive analysis of all C2H2-ZNF genes rather than the individual analysis of specific C2H2-ZNF subfamilies. It also points to the importance of loss/contraction, whose role in the dynamics of evolution is often underestimated. The underlying mechanisms in the expansion of C2H2-ZNF genes and the functional consequences of variation in their repertoires across mammals are yet unclear. It may be that these variations contribute to changes in the control of gene expression/chromatin compaction leading to species-specific morphogenetic programs or cognitive functions in animals.
Collection of human C2H2 zinc finger genes
We conducted an extensive similarity search to identify the complete repertoire of C2H2-ZNF genes in the human genome (assembly NCBI 36). First, we identified all the genes annotated as C2H2 and/or Kruppel zinc finger genes by performing an initial text term search via Entrez . Second, we used PROSITE  to identify all the proteins which had a zinc finger motif of the C2H2 type as well as the N-terminal effector domain, if present.
From these searches, the genomic coordinates, chromosome number, position on the chromosome, number of fingers and identified domains were collected for each of the gene and protein sequences (initial dataset). A TBLASTN  search (e-value cutoff 1e-3) was done against the genome using each of the gene sequences from the initial dataset as a query. The blast hits were used to generate the final dataset of all the identified C2H2-ZNF genes (see Additional File 1).
Identification of C2H2-ZNF gene clusters in the human genome
We analyzed the relative positions of C2H2-ZNF genes in the human genome in order to identify the C2H2-ZNF clusters. A distribution of the distances between neighboring C2H2-ZNF genes in the human genome is presented in Additional File 6. Two consecutive C2H2-ZNF genes are said to belong to a cluster if the distance between them is ≤ 500 Kbp regardless of the presence of other genes within the cluster, a threshold classically used in gene family studies . Clusters were determined for each human chromosome. For the cluster name, the first number corresponds to the chromosome number on which the cluster is found and the second to the number attributed to the cluster.
Identification of mammalian C2H2-ZNF clusters syntenically homologous to human clusters
We searched for clusters homologous to the human C2H2-ZNF clusters (i.e. syntenically homologous clusters) in other mammals for which complete genome sequences are available. The assemblies used for Pan troglodytes, Mus musculus, Rattus norvegicus and Canis familiaris were chimpanzee Pan Tro- 2.1, mouse NCBI m36, rat RGSC 3.4 and dog Can Fam 2.0. We used the linkage maps of Ensembl ; assignment of syntenic clusters is based on the genes flanking each human cluster and which were mapped in all the species. Four flanking genes at each extremity were mapped in most instances. Then, we conducted TBLASTN analysis of the syntenic regions comprised between the flanking genes, using as queries the amino acid sequence of the zinc finger region from all the human C2H2-ZNF genes from the corresponding region identified in this study. A hit with e-value ≤ 1e-4 confirmed the respective homologous clusters in the five mammalian genomes. A comprehensive catalogue of the human C2H2-ZNF clusters and their syntenic counterparts in other mammals is compiled in Additional File 4.
Phylogenetic analysis was conducted using the amino acid sequences of the zinc finger region (identified using PROSITE) of C2H2-ZNF genes from selected human clusters and their syntenically homologous clusters in chimpanzee, mouse, rat and dog. Genes containing less than three zinc finger motifs were not considered in the phylogenetic analysis (noise is expected to be too high if sequences of only 56 amino acids corresponding to 2 fingers motifs or less were included-yellow goes to methods). All multiple sequence alignments of the zinc finger regions of the C2H2-ZNF genes were generated using the program MUSCLE . To resolve the challenging issue of comparing sequences containing multiple copies of a repeated finger motif sequence, that vary in copy number from gene to gene and whose patterns of duplication may differ from one species to the other, we used the following procedure. As a first step, we performed a multiple alignment of all the zinc finger regions of the C2H2-ZNF genes of interest; we removed all the sequences that were not unambiguously alignable and generated a new alignment allowing to visualize sequence similarity between the finger motifs of the various genes. As a second step, we performed individual pair-wise alignments of all the genes used in the first step. Then, we conducted a multiple alignment of the individual finger motifs from all C2H2-ZNF genes, to then determine if the similar finger motifs from a given C2H2-ZNF gene group together. The final alignment was derived from the above three alignments combined and then edited to remove gaps using the program GBLOCKS . Maximum Likelihood (ML) and Bayesian Inference (BI) methods were used to infer the phylogenetic trees and estimate the clade support. For ML analysis, the program RAxML (RAxML-VI-HPC Version 2.2.1)  employing the WAG model of amino acid substitution was used to reconstruct the best tree. Bootstrapping of 100 datasets was implemented. The posterior probabilities were determined by a Bayesian MCMC method implemented in the program Mr. Bayes v.3.1  to test the robustness of the topology of the tree inferred through ML. One million generations were run and the trees were sampled after every 10 generations.
To determine an appropriate outgroup for our analysis, we searched the nr database to look for close homologs in non-mammals using TBLASTN (e-value cut off 1e-4). In addition to the Xfin sequence from Xenopus laevis, we obtained a set of zinc finger genes from Chicken (Gallus gallus, Assembly WASHUC2) specifically selected for each human C2H2-ZNF cluster based on an extensive similarity search. To select the chicken outgroup, a TBLASTN (e-value cutoff 1e-4) search was done against the chicken genome using each of the human C2H2-ZNF sequences derived from the selected cluster of interest as a query. The top 10 hits for each query sequence were all analysed using a CD-HIT analysis (Identity threshold = 100%, 95% and 90%)  to produce a final set of non-redundant representative chicken sequences, all used as a part of the outgroup.
Sequence analysis to confirm the loss of domains
In the case where loss of a domain was suspected, we conducted an extensive sequence analysis to rule out the possibility that these domains had remained undetected either due to a frame-shift or inadequate exon-intron splicing of the gene and thus inappropriate translation, preventing recognition by PROSITE . Firstly, for each particular C2H2-ZNF genes where loss of an N-terminal domain was suggested, we systematically collected the nucleotide sequence of the region ranging from the stop of translation of the previous gene to the start of translation of the next gene. We conducted a TBLASTN search of this region using the amino acid sequence of the domain of interest (present in the corresponding orthologs and the consensus of the domains selected from randomly selected sequences) as a query to confirm the absence of the domain in the C2H2-ZNF gene of interest. Secondly, we obtained the exon-intron structure of these genes using the Ensembl Genome Browser , in order to search for exonic or intronic sequences which may exhibit significant identity with the nucleotide sequence of the domain of interest. For this purpose, we conducted a BLAST analysis of the individual exon and intron sequences with the nucleotide sequence of the various domains that are present in the corresponding orthologs.
Flowchart of the study
Figure 1 summarizes the flowchart of the procedure for the analysis of C2H2-ZNF genes and clusters in mammals.
The authors thank B. Franz Lang for suggestions and help in phylogenetic analysis and Nicolas Lartillot for constructive comments on tree building and datasets. We also acknowledge Hervé Philippe, Henner Brinkmann and Amy Hauth for critical discussions, Allan Sun for assistance in hardware and software installations, and Nicolas Lartillot, Sébastien Lemieux and Martine Raymond for critical reading of the manuscript. This work was supported by a grant from Natural Sciences and Engineering Research Council of Canada (to M.A). HDT received a one year biT studentship for excellence from a Canadian Institutes of Health Research strategic training program grant in bioinformatics. M.A is a Chercheur National of the Fonds de la Recherche en Santé du Québec (FRSQ) and G.B is an associate of CIFAR (Canadian Institute for Advanced Research, Program in Evolutionary Biology).
- Thornton JW, DeSalle R: Gene family evolution and homology: genomics meets phylogenetics. Annu Rev Genomics Hum Genet. 2000, 1: 41-73. 10.1146/annurev.genom.1.1.41.View ArticlePubMedGoogle Scholar
- Venter JC, et al: The sequence of the human genome. Science. 2001, 291 (5507): 1304-51. 10.1126/science.1058040.View ArticlePubMedGoogle Scholar
- Ohta T: Evolution of gene families. Gene. 2000, 259 (1–2): 45-52. 10.1016/S0378-1119(00)00428-5.View ArticlePubMedGoogle Scholar
- Lander ES, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409 (6822): 860-921. 10.1038/35057062.View ArticlePubMedGoogle Scholar
- Messina DN, et al: An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression. Genome Res. 2004, 14 (10B): 2041-7. 10.1101/gr.2584104.PubMed CentralView ArticlePubMedGoogle Scholar
- Schuh R, et al: A conserved family of nuclear proteins containing structural elements of the finger protein encoded by Kruppel, a Drosophila segmentation gene. Cell. 1986, 47 (6): 1025-32. 10.1016/0092-8674(86)90817-2.View ArticlePubMedGoogle Scholar
- Bellefroid EJ, et al: The human genome contains hundreds of genes coding for finger proteins of the Kruppel type. DNA. 1989, 8 (6): 377-87.View ArticlePubMedGoogle Scholar
- Miller J, McLachlan AD, Klug A: Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. Embo J. 1985, 4 (6): 1609-14.PubMed CentralPubMedGoogle Scholar
- Theunissen O, et al: RNA and DNA binding zinc fingers in Xenopus TFIIIA. Cell. 1992, 71 (4): 679-90. 10.1016/0092-8674(92)90601-8.View ArticlePubMedGoogle Scholar
- Grondin B, Bazinet M, Aubry M: The KRAB zinc finger gene ZNF74 encodes an RNA-binding protein tightly associated with the nuclear matrix. J Biol Chem. 1996, 271 (26): 15458-67. 10.1074/jbc.271.26.15458.View ArticlePubMedGoogle Scholar
- Rhodes D, Klug A: Zinc fingers. Sci Am. 1993, 268 (2): 56-9. 62–5.View ArticlePubMedGoogle Scholar
- Klug A, Rhodes D: Zinc fingers: a novel protein fold for nucleic acid recognition. Cold Spring Harb Symp Quant Biol. 1987, 52: 473-82.View ArticlePubMedGoogle Scholar
- Lee MS, et al: Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science. 1989, 245 (4918): 635-7. 10.1126/science.2503871.View ArticlePubMedGoogle Scholar
- Bellefroid EJ, et al: The evolutionarily conserved Kruppel-associated box domain defines a subfamily of eukaryotic multifingered proteins. Proc Natl Acad Sci USA. 1991, 88 (9): 3608-12. 10.1073/pnas.88.9.3608.PubMed CentralView ArticlePubMedGoogle Scholar
- Rosati M, et al: Members of the zinc finger protein gene family sharing a conserved N-terminal module. Nucleic Acids Res. 1991, 19 (20): 5661-7. 10.1093/nar/19.20.5661.PubMed CentralView ArticlePubMedGoogle Scholar
- Collins T, Stone JR, Williams AJ: All in the family: the BTB/POZ, KRAB, and SCAN domains. Mol Cell Biol. 2001, 21 (11): 3609-15. 10.1128/MCB.21.11.3609-3615.2001.PubMed CentralView ArticlePubMedGoogle Scholar
- Urrutia R: KRAB-containing zinc-finger repressor proteins. Genome Biol. 2003, 4 (10): 231-10.1186/gb-2003-4-10-231.PubMed CentralView ArticlePubMedGoogle Scholar
- Looman C, et al: KRAB zinc finger proteins: an analysis of the molecular mechanisms governing their increase in numbers and complexity during evolution. Mol Biol Evol. 2002, 19 (12): 2118-30.View ArticlePubMedGoogle Scholar
- Looman C, Hellman L, Abrink M: A novel Kruppel-Associated Box identified in a panel of mammalian zinc finger proteins. Mamm Genome. 2004, 15 (1): 35-40. 10.1007/s00335-003-3022-0.View ArticlePubMedGoogle Scholar
- Witzgall R, et al: The Kruppel-associated box-A (KRAB-A) domain of zinc finger proteins mediates transcriptional repression. Proc Natl Acad Sci USA. 1994, 91 (10): 4514-8. 10.1073/pnas.91.10.4514.PubMed CentralView ArticlePubMedGoogle Scholar
- Stone JR, et al: The SCAN domain of ZNF174 is a dimer. J Biol Chem. 2002, 277 (7): 5448-52. 10.1074/jbc.M109815200.PubMed CentralView ArticlePubMedGoogle Scholar
- Sander TL, et al: Identification of a novel SCAN box-related protein that interacts with MZF1B. The leucine-rich SCAN box mediates hetero- and homoprotein associations. J Biol Chem. 2000, 275 (17): 12857-67. 10.1074/jbc.275.17.12857.View ArticlePubMedGoogle Scholar
- Schumacher C, et al: The SCAN domain mediates selective oligomerization. J Biol Chem. 2000, 275 (22): 17173-9. 10.1074/jbc.M000119200.View ArticlePubMedGoogle Scholar
- Melnick A, et al: Critical residues within the BTB domain of PLZF and Bcl-6 modulate interaction with corepressors. Mol Cell Biol. 2002, 22 (6): 1804-18. 10.1128/MCB.22.6.1804-1818.2002.PubMed CentralView ArticlePubMedGoogle Scholar
- Bellefroid EJ, et al: Clustered organization of homologous KRAB zinc-finger genes with enhanced expression in human T lymphoid cells. Embo J. 1993, 12 (4): 1363-74.PubMed CentralPubMedGoogle Scholar
- Eichler EE, et al: Complex beta-satellite repeat structures and the expansion of the zinc finger gene cluster in 19p12. Genome Res. 1998, 8 (8): 791-808.PubMedGoogle Scholar
- Huntley S, et al: A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res. 2006, 16 (5): 669-77. 10.1101/gr.4842106.PubMed CentralView ArticlePubMedGoogle Scholar
- Mark C, Abrink M, Hellman L: Comparative analysis of KRAB zinc finger proteins in rodents and man: evidence for several evolutionarily distinct subfamilies of KRAB zinc finger genes. DNA Cell Biol. 1999, 18 (5): 381-96. 10.1089/104454999315277.View ArticlePubMedGoogle Scholar
- Shannon M, et al: Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters. Genome Res. 2003, 13 (6A): 1097-110. 10.1101/gr.963903.PubMed CentralView ArticlePubMedGoogle Scholar
- Hamilton AT, et al: Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. Genome Res. 2006, 16 (5): 584-94. 10.1101/gr.4843906.PubMed CentralView ArticlePubMedGoogle Scholar
- Hamilton AT, et al: Lineage-specific expansion of KRAB zinc-finger transcription factor genes: implications for the evolution of vertebrate regulatory networks. Cold Spring Harb Symp Quant Biol. 2003, 68: 131-40. 10.1101/sqb.2003.68.131.View ArticlePubMedGoogle Scholar
- Dehal P, et al: Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. Science. 2001, 293 (5527): 104-11. 10.1126/science.1060310.View ArticlePubMedGoogle Scholar
- Kim SS, et al: A novel member of the RING finger family, KRIP-1, associates with the KRAB-A transcriptional repressor domain of zinc finger proteins. Proc Natl Acad Sci USA. 1996, 93 (26): 15299-304. 10.1073/pnas.93.26.15299.PubMed CentralView ArticlePubMedGoogle Scholar
- Rousseau-Merck MF, et al: The KOX zinc finger genes: genome wide mapping of 368 ZNF PAC clones with zinc finger gene clusters predominantly in 23 chromosomal loci are confirmed by human sequences annotated in EnsEMBL. Cytogenet Genome Res. 2002, 98 (2–3): 147-53. 10.1159/000069802.View ArticlePubMedGoogle Scholar
- Gilad Y, Man O, Glusman G: A comparison of the human and chimpanzee olfactory receptor gene repertoires. Genome Res. 2005, 15 (2): 224-30. 10.1101/gr.2846405.PubMed CentralView ArticlePubMedGoogle Scholar
- Niimura Y, Nei M: Evolution of olfactory receptor genes in the human genome. Proc Natl Acad Sci USA. 2003, 100 (21): 12235-40. 10.1073/pnas.1635157100.PubMed CentralView ArticlePubMedGoogle Scholar
- Niimura Y, Nei M: Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene. 2005, 346: 13-21. 10.1016/j.gene.2004.09.025.View ArticlePubMedGoogle Scholar
- Lapidot M, et al: Mouse-human orthology relationships in an olfactory receptor gene cluster. Genomics. 2001, 71 (3): 296-306. 10.1006/geno.2000.6431.View ArticlePubMedGoogle Scholar
- Sitnikova T, Su C: Coevolution of immunoglobulin heavy- and light-chain variable-region gene families. Mol Biol Evol. 1998, 15 (6): 617-25.View ArticlePubMedGoogle Scholar
- Schmidt D, Durrett R: Adaptive evolution drives the diversification of zinc-finger binding domains. Mol Biol Evol. 2004, 21 (12): 2326-39. 10.1093/molbev/msh246.View ArticlePubMedGoogle Scholar
- Elemento O, Gascuel O: An efficient and accurate distance based algorithm to reconstruct tandem duplication trees. Bioinformatics. 2002, 18 (Suppl 2): S92-9.View ArticlePubMedGoogle Scholar
- Bertrand D, Gascuel O: Topological rearrangements and local search method for tandem duplication trees. IEEE/ACM Trans Comput Biol Bioinform. 2005, 2 (1): 15-28. 10.1109/TCBB.2005.15.View ArticlePubMedGoogle Scholar
- Page RD, Charleston MA: From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol Phylogenet Evol. 1997, 7 (2): 231-40. 10.1006/mpev.1996.0390.View ArticlePubMedGoogle Scholar
- Nei M, Gu X, Sitnikova T: Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc Natl Acad Sci USA. 1997, 94 (15): 7799-806. 10.1073/pnas.94.15.7799.PubMed CentralView ArticlePubMedGoogle Scholar
- Nei M, Kumar S: Molecular Evolution and Phylogenetics. 2000, New York: Oxford University Press, 17-203.Google Scholar
- Glusman G, et al: The complete human olfactory subgenome. Genome Res. 2001, 11 (5): 685-702. 10.1101/gr.171001.View ArticlePubMedGoogle Scholar
- Sharon D, et al: Primate evolution of an olfactory receptor cluster: diversification by gene conversion and recent emergence of pseudogenes. Genomics. 1999, 61 (1): 24-36. 10.1006/geno.1999.5900.View ArticlePubMedGoogle Scholar
- Quignon P, et al: Comparison of the canine and human olfactory receptor gene repertoires. Genome Biol. 2003, 4 (12): R80-10.1186/gb-2003-4-12-r80.PubMed CentralView ArticlePubMedGoogle Scholar
- Krebs CJ, et al: Regulator of sex-limitation (Rsl) encodes a pair of KRAB zinc-finger genes that control sexually dimorphic liver gene expression. Genes Dev. 2003, 17 (21): 2664-74. 10.1101/gad.1135703.PubMed CentralView ArticlePubMedGoogle Scholar
- Entrez. [http://www.ncbi.nlm.nih.gov]
- PROSITE: Database of protein domains, families and functional sites. [http://ca.expasy.org/prosite/]
- Gertz EM, et al: Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol. 2006, 4: 41-10.1186/1741-7007-4-41.PubMed CentralView ArticlePubMedGoogle Scholar
- Ensembl Genome Browser. [http://www.ensembl.org]
- Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32 (5): 1792-7. 10.1093/nar/gkh340.PubMed CentralView ArticlePubMedGoogle Scholar
- Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, 17 (4): 540-52.View ArticlePubMedGoogle Scholar
- Stamatakis A, Ludwig T, Meier H: RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics. 2005, 21 (4): 456-63. 10.1093/bioinformatics/bti191.View ArticlePubMedGoogle Scholar
- Huelsenbeck JP, Ronquist F: MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001, 17 (8): 754-5. 10.1093/bioinformatics/17.8.754.View ArticlePubMedGoogle Scholar
- Li W, Jaroszewski L, Godzik A: Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics. 2001, 17 (3): 282-3. 10.1093/bioinformatics/17.3.282.View ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.