- Research article
- Open Access
A family history of DUX4: phylogenetic analysis of DUXA, B, C and Duxbl reveals the ancestral DUXgene
BMC Evolutionary Biology volume 10, Article number: 364 (2010)
DUX4 is causally involved in the molecular pathogenesis of the neuromuscular disorder facioscapulohumeral muscular dystrophy (FSHD). It has previously been proposed to have arisen by retrotransposition of DUXC, one of four known intron-containing DUX genes. Here, we investigate the evolutionary history of this multi-member double-homeobox gene family in eutherian mammals.
Our analysis of the DUX family shows the distribution of different homologues across the mammalian class, including events of secondary loss. Phylogenetic comparison, analysis of gene structures and information from syntenic regions confirm the paralogous relationship of Duxbl and DUXB and characterize their relationship with DUXA and DUXC. We further identify Duxbl pseudogene orthologues in primates. A survey of non-mammalian genomes identified a single-homeobox gene (sDUX) as a likely representative homologue of the mammalian DUX ancestor before the homeobox duplication. Based on the gene structure maps, we suggest a possible mechanism for the generation of the DUX gene structure.
Our study underlines how secondary loss of orthologues can obscure the true ancestry of individual gene family members. Their relationships should be considered when interpreting the relevance of functional data from DUX4 homologues such as Dux and Duxbl to FSHD.
Double homeobox genes are exclusive to placental mammals and characterized by two closely spaced homeoboxes of the PRD class. The homeoboxes encode 60 amino acid homeodomains (HDs), an ancient, well studied DNA binding motif found in animals, plants and fungi in many transcription factors including the developmentally important Hox genes. Our particular interest in the DUX family stems from the involvement of one member (DUX4) in the molecular pathogenesis of facioscapulohumeral muscular dystrophy (FSHD). In most cases of this genetic disorder, patients have a contraction of the 3.3 kb D4Z4 tandem repeat array on 4q35. When the genetic linkage between D4Z4 and FSHD was discovered, an intronless open reading frame (ORF) encoding a putative double-homeodomain protein was found to reside within each D4Z4 repeat unit and named DUX4. The DUX4-containing D4Z4 elements are present at high and variable copy number on 4q35 with 11 to >100 repeats in controls. In FSHD, one allele is reduced in size to 1-10 repeats, which is accompanied by a change in chromatin packaging into a less repressive state[7–9]. A near identical tandem array is also present on 10q26, but contractions are not associated with FSHD.
D4Z4 contractions are only pathogenic if they occur on a particular haplotype background ("4qA161")[10, 11]. It has been shown that the DUX4 ORF is discontinuously transcribed, with the ORF of the final repeat unit utilizing a polyadenylation signal in the pLAM region immediately distal to the D4Z4 array. Recently, a landmark paper showed that only chromosomes of disease-permissive haplotypes such as 4qA161 carry this functional polyadenylation signal. This study presents the strongest evidence yet for a DUX4-transcription mediated pathology in FSHD.
DUX4 related sequences are found in primates and Afrotheria and we previously showed that they have been conserved by selection. In mouse, a related ORF known as Dux has been identified, which is also found in a tandem array organization. The predicted Dux protein encoded within this array shares both homeodomains as well as a conserved C-terminal domain with DUX4. In higher apes and humans, many hundreds of D4Z4 related sequences are dispersed throughout the genome, notably on the poorly assembled regions of the acrocentric chromosomes as well as the heterochromatic regions on 1q12[4, 14]. In an interesting case study, the ongoing amplification of intronless DUX sequences has recently been characterized for a DUX4 homologue residing on the Y chromosome (DUXY).
Interrogation of publicly available genome databases has resulted in the discovery of four intron-containing DUX genes (A, B, C and Duxbl = BL). DUXA and DUXB were originally identified in humans[16, 17], but orthologues have also been found in a range of other mammals. DUXC has been described only in armadillo, dog and cow. Before the current study, Duxbl (named after DUXB-like) had been found only in mouse and rat genomes. Independently, gene expression profiling experiments identified Duxbl as one of the genes upregulated in specific stages of mouse thymocyte development. Figure 1 shows gene structures and conserved domains of the four intron-containing DUX homologues as well as the intronless DUX4 and rodent Dux sequences. The two homeoboxes in all four intron-containing genes are split across four exons, with splice junctions within the homeoboxes at equivalent positions.
The in vivo biological function of human DUX4 is still unknown, although a number of groups are addressing this question using experimental approaches based on exogenous expression of DUX genes[19–21]. Studies of DUX homologues may therefore contribute to our understanding of DUX4 function, but if such inferences are to be made with confidence, it is important that we understand how the genes and proteins studied relate to one another. Here, we comprehensively survey the distribution of intron-containing DUX genes in the mammalian class, characterize their gene structures and present data on their phylogenetic relationships. We also identify the putative ancestor of the DUX family and suggest a mutational mechanism that may have created the double homeobox gene structure.
Cataloguing intact and inactive DUXhomologues in placental mammals
We systematically searched all mammalian species in Figure 2 for each of the four known intron-containing DUX genes by tBLASTn. Searches were conducted on whole genome assemblies and separately on syntenic regions. The latter approach allowed the identification of decaying orthologues, whose degenerate amino acid sequences make them hard to identify in whole genome tBLASTn scans. Wherever possible, phylogenetic tree analysis of homeodomains, synteny information and gene structure data were combined to verify that an identified sequence represented the orthologue in that species. Figure 3 shows the relative locations of some of the neighbouring anchor genes used to establish synteny for DUXA, B and BL. For DUXC, no appropriate nearby anchors could be identified. CJ057 encodes a short, highly conserved protein that proved to be particularly useful due to its high conservation and linkage to Duxbl (Additional file 1). Figure 2 provides an overview of all DUX genes catalogued in this study.
DUXA orthologues can be found in most mammalian groups. Rabbits have an intact version, but we could not find any DUXA genes in other Glires. However, squirrel has an intronless DUXA sequence with an ORF spanning both homeoboxes, indicating that DUXA may either be present in an unsequenced region or have had its function maintained by a retrogene (such cases are not without precedent).
DUXA was originally identified as a 6-exon gene in humans. However, our survey of DUXA gene structures shows that the final exon seems to be exclusive to higher primates (Additional file 2). Mouse lemur, rabbit, Laurasiatheria and elephant share a stop codon at the equivalent position in exon 5, just before the location of the splice junction in primates. In dog, exon 5 is extended by 156bp and there is no GT splice donor signal at the position corresponding to that in primates (Additional file 3). Instead, there is an extended ORF, and the additional amino acids encoded by this putative exon share no similarity with the final primate exon. It is unlikely that Glires, Laurasiatheria and elephant have independently acquired a stop codon at the same position in exon 5. Instead, the ancestral DUXA probably contained five exons, with subsequent gain of a sixth exon in primates, effectively creating two DUXA subclasses. The dN/dS ratio of the DUXA C-terminal domain (after HD2) in a pairwise comparison of human, chimpanzee, macaque and orangutan shows an average across all pairs that is below 1 (0.27), indicating that the newly gained sequence has been maintained by purifying selection.
DUXA has spawned a large number of processed pseudogenes in primates as well as other species, indicating germline expression. Booth and Holland recently identified ten such pseudogenes in humans and reported a high number of EST matches for these sequences (DUXAP1-10). In a brief survey of human ESTs we found that some of these expressed sequences have less than 100% sequence identity with either DUXA or any of its known ten pseudogenes (data not shown). This indicates that yet more processed pseudogenes are likely to be dispersed throughout the genome, perhaps residing on the arms of acrocentric chromosomes (which have long been known to house intronless DUX sequences[4, 14]). The presence of an EST sequence for DUXA in the databases has also been noted.
In addition to the previously reported copies of DUXC in armadillo, cow and dog, we have identified closely related homologues in horse, dolphin and megabat (Additional file 4). Interestingly, in all these species DUXC has undergone local duplications and is found in a tandem array organization. The dolphin assembly contains a contig with two intact DUXC copies and one pseudogene as well as the 5' end of a fourth copy, all arranged in tandem in the same orientation with a spacing of less than 5 kb between them. In megabat, one intact and one defective copy (containing a stop codon in HD2) are separated by a spacing of 25 kb. Trace archive sequence data from cow, dolphin, horse and dog also indicate a multi-copy, array-like organization (data not shown).
The previously described conserved C-terminal domain of DUXC is also found in the predicted protein of these newly-identified orthologues. Figure 4 shows an amino acid alignment demonstrating the conservation of this CTD not only between DUXC orthologues but also with human DUX4 and the predicted protein product of the rodent Dux arrays, evidence that they may be functionally related. Maximum Likelihood analysis also clusters the two homeodomains of DUX4 with DUXC (Additional file 5 & 6). Indeed, tBLASTn searches using DUXC as query return DUX4 sequences as top hits in primates. Thus far, we have not found any DUXC orthologues in primates and Glires, so it is possible that this homologue was lost in the common ancestor of the Euarchontoglires after the split from the Laurasiatheria. However, the lack of any suitable anchor genes for DUXC precludes analysis of homologous regions, and some orthologues may thus be missed.
DUXB and Duxbl
Before this study the evolutionary relationship between DUXB and Duxbl was unclear, but our previous phylogenetic analysis suggested that they are not orthologues. Duxbl had only been found in rodents[1, 18], while DUXB sequences had been found in all major mammalian lineages except rodents. Because genome-wide tBLASTn fails to detect decaying orthologues that have been secondarily lost and searches with low stringency pick up more distantly related homeobox genes instead (e.g. MIX), we used synteny information to identify genomic regions that might contain remnants of DUXB and Duxbl (Figure 3).
In mouse and rat, exons four and five of a DUXB-type gene are found next to the TERF2IP anchor, and each of these murine orthologues has a different stop codon mutation in exon five. In guinea pig and cow, exon four is absent but exons two, three and five are still present, again with different stop codon mutations in each species (Additional file 7).
For Duxbl, using CJ057 as an anchor, we found the final exon in guinea pig and decaying Duxbl pseudogenes containing various numbers of exons in primates (Figure 5a). In orangutan, baboon and marmoset, all five exons are present but have stop codons in positions unique to each species.
A recent 10 kb deletion occurred in the ape lineage, removing exons three, four and part of five in human, chimpanzee and gorilla (Figure 5b). It cannot be deduced whether Duxbl was still intact in these apes when the deletion occurred, or whether it was already a pseudogene, perhaps sharing the same stop codon as orangutan. However, the presence of intact (and presumably functional) Duxbl genes in mouse and rat and the relatively undisrupted structure of the primate pseudogenes in combination with independent inactivating mutations indicates that Duxbl was lost only recently in primates. The intact murine Duxbl also implies that the losses in primates and Laurasiatheria were independent events.
Overall, these findings indicate a pattern of reciprocal loss and retention of DUXB and Duxbl in different lineages, although guinea pig is an exception, having lost both genes. The unrooted Maximum Likelihood tree in Figure 6 shows that Duxbl and DUXB cluster together, supporting a relatively recent divergence. We also noted the presence of a protein coding sequence (Cphx, itself encoding a homeodomain) adjacent to mouse Duxbl. Cphx has homologues next to both human DUXB and the human pseudogene orthologue of Duxbl (DUXBLP), indicative of a segmental duplication (Figure 3). This, taken together with the similar gene structure, high homeodomain identity and phylogenetic analysis, indicates that DUXB and Duxbl are paralogues that are probably more closely related to one another than either is to DUXA or DUXC.
Duxbl is also the DUX gene with the strongest experimental evidence for in vivo expression. Duxbl mRNA can readily be detected by RT-PCR in many mouse tissues including brain, liver, lung, kidney (unpublished data and references[18, 24]), while protein expression has been shown in a subset of tissues[18, 24].
Identification of a single-homeobox gene linked to CJ057/ANXA11
In order to search for DUX homologues in more distantly related non-mammalian species, we extended our synteny-based analysis for DUXA, B, and BL to opossum, platypus and chicken. In these three species, the DUXA syntenic region could not be indentified with confidence, and we found no homeobox related sequences in the DUXB region (as defined by ADAT1 and Terf2IP). However, next to CJ057 orthologues, we found a putative Duxbl-related gene in both opossum and chicken, comprising at least two exons that encode a single homeodomain (Figure 7a). The position of the intron within the homeobox is at the equivalent location to that in UXA, DUXB, Duxbl and DUXC (Figure 7b). The large open reading frame in the second exon extends further than in DUXB and Duxbl. Close inspection of the local region did not identify any additional exons that could produce a double-homeobox gene.
Using the predicted ORF of this single-homeobox gene as a tBLASTn query, we also found homologues in platypus and wallaby (although lacking synteny information in either case), as well as anole lizard. Opossum, wallaby and lizard each have more than one copy of these two-exon pairs, in different orientations (Figure 7b). In both the wallaby and lizard assemblies, we found a retrotransposed copy containing both exons (joined at the homeobox splice junction). These retrocopies indicate that in the germline of these species at least, this sequence has been transcribed and spliced to encode a full homeobox. We suggest naming this single-homeobox DUX-related gene sDUX (for "single" homeodomain). Figure 7c shows an amino acid alignment of all sDUX homeodomains identified and includes rodent Duxbl homeodomains for comparison.
Relationship of the intron-containing DUX genes
Despite extensive search efforts, no double-homeobox DUX genes have been identified in non-placental mammals here or previously. Considering the similarity between the homeodomains of the four DUX homologues A, B, BL and C compared to other known homeodomain proteins and their similar gene structures with identical splice positions in both homeoboxes, it is likely that the duplication of the DUX homeobox occurred only once in a single progenitor gene that gave rise to all four members of the DUX family. A Maximum Likelihood tree based not on concatenated but individual homeodomains supports this hypothesis (Figure 6b). For example, the first homeodomains of DUXB, Duxbl and DUXC all cluster together, while the second homeodomains of the same proteins form a separate cluster, suggesting that the two homeoboxes were already duplicated and divergent in the common ancestor of DUXB and DUXC. An analogous observation to such protein domain evolution among different homologues has been made on the level of gene evolution among different species. When relationships between gene homologues (or, in our case, protein domains) are unclear and two homologues (I and II) found in the same species cluster together in phylogenetic analysis relative to a homologue (III) in an outgroup species [(I, II)III], they are most likely paralogues that arose after the speciation event. Conversely, if the homologues cluster as [(I, III)II], gene duplication occurred before speciation. The latter situation can be observed for the two homeoboxes found in the DUX family, which were duplicated before the generation of the different DUX paralogues.
Based on the high similarity in both gene structure and predicted homeodomain sequence compared to other homeobox genes, DUXA probably shares a recent common ancestor with B, BL and C, rather than having evolved the double-homeobox independently. Although the tree clusters DUXA HD1 and HD2 separately from the other homologues, this is most likely due to artefactual long branch attraction caused by the generally higher divergence of DUXA from B, BL and C (note the long branches in Figure 6a).
Assuming our hypothesis that all four DUX homologues are descendants of the same ancestral DUX gene is correct, identifying a single-homeobox gene at the homologous locus of one of these four is informative. If the DUX homeobox duplication had occurred elsewhere (at a locus unlinked to CJ057), the syntenic CJ057/ANXA11 locus in non-placental mammals would be expected to either contain no DUX-related gene at all, or a double-homeobox gene that arrived as a paralogue from the ancestral DUX. We therefore propose that the single-homeobox genes in linkage with CJ057 and ANXA11 in opossum, chicken and lizard are homologues of the ancestral sDUX in mammals. Although we have no synteny information for wallaby and platypus sDUX, we have included these genes in our phylogenetic analysis due to their similar homeodomains and gene structure.
Thus, in the common ancestor of placental mammals, duplication of the homeobox in sDUX gave rise to the ancestral DUX gene, from which all other DUX genes are ultimately descended. Consistent with this, sDUX homologues cluster together at an internal node of our tree, rather than being nested within a particular branch (Figure 6b, Additional file 6).
When human DUX homeodomains (DUX4, DUXA and DUXB) are compared with sDUX and human PRD class homeodomains, sDUX and all DUX proteins cluster together, further supporting their close relationship (Figure 8). Pax3 and Pax7 have been proposed to represent potential competitors for the same DNA binding sites as DUX, a hypothesis based on their similar homeodomain sequences[20, 27]. However, as our tree demonstrates, Pax3/7 are not the only candidates that could be considered in this context, and indeed there are other PRD class homeodomains (e.g. HESX1, TPRX1) that could be just as or more closely related to DUX.
DUX distribution across the mammalian class and divergence of homologues
The DUX family shows patterns of selective loss and retention of different homologues in different lineages. This stands in contrast to the distribution of another recently characterized PRD class homeobox gene, ARGFX, which has survived in humans but has been secondarily lost from most other mammals. One of the most striking features of the DUX family is the loss of Duxbl in all examined species except rodents, with the reverse pattern for its paralogue DUXB.
Aside from exon shuffling and retrotransposition, gene duplication is one of the best understood mechanisms of gene evolution. Following duplication, two paralogues usually meet one of two fates. If the second copy instantly confers a selective advantage ("immediate" model) or can accumulate beneficial mutations before it decays into a pseudogene ("waiting" model), it can be maintained alongside the original gene for sub- or neofunctionalization. Additionally, the different genomic environment of the newly arisen paralogue may result in the use of new promoters with different expression levels or tissue specificity. However, because initial functional redundancy after duplication can relax selection pressure on one of the paralogues, another likely outcome is decay of one of them. This is probably what we observe in the case of DUXB and Duxbl. Which one of the two paralogues was maintained in each mammalian lineage may have been an arbitrary, stochastic decision.
Conversely, the maintenance of DUXA in addition to DUXB/Duxbl in many species argues for functional diversification between these gene lineages. The observed differences in gene structure and the higher homeodomain divergence in DUXA are consistent with this model.
For DUXC and DUX4, the evolutionary history is less clear. We cannot find any evidence for the presence of DUXC orthologues in rodent and primate branches, indicating that this gene may have been lost in the common ancestor of these lineages. In primates at least, the role of DUXC may have been filled by the intronless DUX4-like sequences that encode closely related homeodomains and CTD. Similarly, in the rodent lineage, mouse and rat may have a functional equivalent in Dux. The maintenance of intronless DUX genes alongside DUXA and DUXB/Duxbl (which also lack the conserved DUX4 CTD) supports separate roles for these genes.
Implications for studying DUX4 function in model organisms
The lack of evidence for any double-homeobox DUX genes in non-placental mammals raises questions about some of the experimental approaches that have been employed to investigate DUX4 function. In a recent study, mouse Dux mRNA was injected into Xenopus laevis embryos and gastrulation defects were observed, which was suggested of being supportive of a myopathic role for D4Z4. A very similar experiment using human DUX4 was performed by a different group. In this study, observed developmental defects and increased TUNEL staining in the embryos were interpreted as evidence that in Xenopus there is conservation for a function of DUX4 to induce apoptosis.
The biological relevance of the effects of overexpressing a DUX homologue in an organism of a species lineage that split from the common ancestor of mammals long before the evolution of the double-homeobox gene family is unclear. One might expect that overexpression of a transcription factor in the embryo of an organism whose transcriptional networks cannot have evolved to include double-homeodomain DUX proteins in their regulation can induce cellular stress.
Linking intronless to intron-containing DUX genes
Our data presented here and previously indicate that DUX4 originated from retrotransposition of a processed transcript, most probably DUXC. As such a random integration event results in the loss of linkage with genes flanking the parental locus, there exists no syntenic relationship between intronless and intron-containing DUX genes. It is intriguing that of the four intron-containing DUX homologues, DUXC is the only one consistently found in tandem arrays. Although there are three adjacent copies of Duxbl in mouse, they are part of a much larger macroduplication that includes the neighbouring genes Plac9 and Cphx. Exactly why DUXC and DUX4 (embedded in D4Z4) in particular should have repeatedly undergone duplications and maintained these copies is an unresolved question.
In rodents, the most promising candidate for a functional equivalent of DUX4 is Dux. While there are fewer clues for the origin of the rodent Dux array than for that of DUX4, it probably arose from an independent retrotransposition event of an intron-containing DUXC homologue. We base our opinion of a possible functional equivalence of Dux and DUX4 on their common, conserved C-terminal domain, which they both share with DUXC, and their shared organisation into high-copy number tandem arrays. However, we note that the conserved CTD could have originally been present in all the paralogues and then lost. In that case, Dux could have a parental origin in a different DUX paralogue. Based on our trees, the origins of DUX4 are more likely to lie with DUXC, but a rapid divergence of Duxbl or of DUXA could render the homeodomain clustering of DUX4 with DUXC an artefact of our Maximum Likelihood analysis (Additional file 5 & 6).
However, our data do not support the hypothesis of Wu et al. that mouse Duxbl is the orthologue of human DUX4, which they base on the relatively high amino acid similarity between their respective homeodomains. In a separate study, either human DUXA or DUX4 were suggested as candidates for the human Duxbl orthologue, again based on amino acid identities. Because DUX4 is most likely to have lost its introns through retrotransposition, it cannot be the orthologue of an intron-containing gene such as Duxbl. Here, we have identified the human orthologue of mouse Duxbl, and it is human DUXBLP (a decaying pseudogene), located on 10q22.3. If DUX4 had arisen as a direct descendant of Duxbl by a duplication event that simultaneously resulted in the loss of all introns (in other words, retrotransposition), it could presumably be called a retrogene paralogue of Duxbl. It is interesting to note that after retrotransposition, DUX4 acquired introns in the 3' untranslated region[12, 19, 32]. This is rather unusual, as in most known cases of retrogenes that have acquired introns this has occurred in the 5' UTR, probably because introns distal to the stop codon usually destabilize the transcript via non-sense mediated decay (NMD) and can be selected against. One example of a retrogene with an intron within the 3' UTR is ENSG00000182814. This may represent an example of evolved NMD repression of transcript levels, a mechanism that should not be ruled out for DUX4 regulation.
Orthology and paralogy are entwined concepts defined by two fundamentally distinct evolutionary processes that give rise to the different homologues in a gene family, with important implications for gene function. Orthologues are separated only by speciation events and represent the direct descendants of a gene in a common ancestor, and therefore usually perform equivalent functions in different species. Conversely, paralogues arise by gene duplication within a given species lineage, and it is an intrinsic consequence of the (initial) redundancy between the two copies that one paralogue can be released from purifying selection pressure and evolve to perform related or (crucially) novel functions. So, if DUX4 did indeed originate from DUXC, its relationship to Duxbl can perhaps be described as it being a retrogene paralogue of a paralogue (DUXC) of Duxbl, not an orthologue. These definitions and distinctions are important if the findings of functional studies of one gene (Duxbl) are to be used to infer the putative functions of another gene (DUX4), as suggested in the study cited above. Potential functional divergence between different gene family members would increase the uncertainty of such inferences. Nevertheless, these studies of rodent Duxbl[18, 24] provide the first evidence of in vivo functions of any DUX protein, and are valuable contributions.
Birth of the double-homeodomain ancestor
With sDUX, we have identified a putative single-homeobox homologue of DUX genes in non-placental animals. Based on the similarity between the sDUX and DUX homeodomains and the good synteny information (CJ057 and ANXA11), we deem it likely that in the common ancestor of the eutherian mammals a duplication of homeoboxes occurred in sDUX. This created the ancestral DUX, which ultimately gave rise to all intron-containing and intronless DUX genes. Our data therefore also imply that the origins of DUXA lie with sDUX and the other DUX family members and not with CRX, as suggested previously.
We noticed a consistent feature of our gene structure maps (Figure 5 Additional file 2, 4, 7, 8). In almost all homologues, the intron between the two sets of homeodomain encoding exons (intron 3) is comparatively small. We believe this may be a result of the duplication mechanism.
With sDUX present in multiple local copies in opossum, lizard and wallaby, it is easy to imagine that two closely spaced copies with identical orientations may arise. Two possible mechanisms for this are misaligned homologous recombinational repair and unequal crossing-over, which can be facilitated by repetitive elements such as SINEs. Such tandem duplication cis events have played a major role in the evolution of other homeobox genes, for example the duplications of the NK-like and Hox/ParaHox genes.
A tandem sDUX scenario can indeed be observed at the wallaby locus (Figure 7c, Figure 9). Given such an arrangement, one local deletion could join the two together with a one in three chance of maintaining the reading frame. Provided the extra homeodomain at the N-terminus does not interfere with the function of the joined HD2 and its final exon, one can readily imagine natural selection to allow such a change to occur. A large open reading frame such as that in the final exon of sDUX (mean size of the second exon in ten identified sDUX copies = 989 base pairs) would allow for many possible 5' deletion breakpoints that could all result in an open reading frame. Indeed, the 3' position of the deletion breakpoint may also be variable as long as both the HD2 homeobox and no stop codon are included in the fused exon. The overall mean size of intron 3 across all DUXA, DUXB, Duxbl, and DUXC genes catalogued in our study is only 634 base pairs. We speculate that this may be the consequence of such a mutational mechanism that joined the homeoboxes (Figure 9).
A recent quantitative study analysed 330 independent events of protein domain gain and showed that gene fusion is a major mechanism, preceded by gene duplication in four out of five cases . In the study sample, 71% of events occurred at protein termini and included more than one exon.
Our proposed model for DUX homeobox duplication is a simple mechanism requiring only one deletion, the size of which may be relatively variable and should allow retention of the original splice signals. A similar gene fusion by deletion has been described for the D. melanogaster gene Sdic. A tandem duplication of Cdic (cytoplasmic dynein intermediate chain) and AnnX (annexin X) followed by three local deletions joined several exons of these two genes together to create the novel gene Sdic.
Alternative molecular mechanisms for joining two neighbouring genes include readthrough transcription, which depends on mutation of the stop codon and the transcriptional termination signal in the first copy, and co-transcription by intergenic splicing. In the latter model, pre-existing splice donor and acceptor sites from both neighbouring genes can be used to create a novel fusion gene. In such a case, a gradual erosion of the internal intron 3 could have yielded a DUX like gene structure.
We have characterized the evolutionary history and relationships of the double-homeodomain encoding DUX gene family and identified a likely candidate for its common ancestor. Gene duplication followed by a fusion event most likely created the double homeobox in the last common ancestor of placental mammals as these are the only species where DUX genes have been found. Our study illustrates how the true underlying relationships of homologues in gene families can be obscured by secondary loss of orthologues and thus misunderstood, especially as genomic tBLASTn searches are likely to identify active genes maintained by selection, but miss decaying pseudogenes that may represent the true orthologues. Our data reinforce the view that the inference of relationships between genes should take into consideration synteny information, phylogenetic analysis of amino acid sequence evolution and consider that orthologues may no longer be present in a species. This is particularly important if, as for DUX4, different homologues are studied as models, especially if these studies extend to different organisms. With recently published data clearly linking DUX4 to FSHD pathogenesis, the need to understand DUX4 protein function has become more urgent. Future studies will benefit from a consideration of the evolutionary history of DUX4.
Data collection and DUXgene identification
Previously published data on the DUX gene family[1, 17] was complemented and expanded by systematic interrogation of more than 30 genome databases (ENSEMBL, release May 2010, http://www.ensembl.org/Multi/blastview). Species searched included 25 placental mammals as well as opossum, platypus, chicken, lizard, frog and zebrafish (P. troglodytes, G. gorilla, P. pygmaeus, M. mulatta, P. hamadryas, C. jacchus, M. murinus, T. belangeri, M. musculus, M. norvegicus, S. tridecemlineatus, C. porcellus, O. cuniculus, E. caballus, F. catus, C. familiaris, T. truncates, B. taurus, P. vampyrus, E. europaeus, D. novemcinctus, L. africana, M. domestica, O. anatinus, G. gallus, A. carolinensis, X. tropicalis & D. rerio). Databases were surveyed for annotated DUX genes and searched for DUXA, DUXB, Duxbl and DUXC related sequences by whole-genome ENSEMBL tBLASTn (protein against nucleic acid) using default parameters with a near-exact matches search. For DUXA, DUXB and Duxbl, neighbouring anchor genes (see results section) were used to identify syntenic regions, which were then exported and searched locally for homeodomain-encoding sequences using the NCBI tBLASTn alignment tool with default parameters http://blast.ncbi.nlm.nih.gov/Blast.cgi. For DUXC, no suitable anchor genes could be identified due to incomplete sequence contigs flanking the DUXC loci and a resulting lack of linked sequences. Genes were verified as probable orthologues by considering synteny conservation, and intron-exon boundaries as well as clustering of homeodomain amino acid sequences with already characterized DUX homologues in phylogenetic trees (JalView 2.5 and PHYLIP, see below). For some genes, predicted ORFs were used in nBLAT (Ensembl) to identify any recent pseudogene retrotranspositions to aid exon identification of the intron-containing gene. If no intact orthologue (defined as an intact ORF spanning at least both homeoboxes) was found, but fragments of a decayed DUX gene could be identified in the same region (e.g. with stop codons, frameshifts, or deletion of individual exons), the orthologue was deemed to be not present or secondarily lost in that species. Where a DUX sequence was identified but the gene status (intact or pseudogene) was impossible to determine, e.g. due to local contig gaps, gene status was assigned as unclear.
Sequence alignments and phylogenetic analysis
Predicted amino acid sequences (homeodomains were considered either concatenated or separate) were aligned using ClustalW implemented in JalView 2.5 http://www.jalview.org/. JalView Average Distance or Neighbour-Joining trees based on percent identity or on a BLOSUM62 matrix were calculated initially to confirm clustering of newly identified homologues with the same class of DUX genes. After data collection was complete, phylogenetic analysis was performed with the PHYLIP package version 3.69 http://evolution.genetics.washington.edu/phylip.html. Only homeodomain sequences from intact (and presumably functional) DUX homologues were included in the analysis. Datasets were bootstrapped with Seqboot (100 replicates) and unrooted Maximum Likelihood trees were calculated using Proml (Jones-Taylor-Thornton model, input order jumble = 10, non-rough analysis). Consensus trees were calculated using the majority rule option in Consense, with node bootstrap values representing the percent agreement between the 100 bootstrapped datasets. Proml analysis was then repeated on the original, non-bootstrapped dataset using the consensus tree as an input guide tree. The resulting tree with Maximum Likelihood analysis branch lengths was drawn using iTOL version 1.8.1 http://itol.embl.de/, and consensus bootstrap values were added manually.
Comparative sequence analysis
The deletion breakpoint in the human, chimpanzee and orangutan Duxbl locus was mapped using LAGAN in mVISTA http://genome.lbl.gov/vista/mvista/submit.shtml with species specific repeat masking and default parameters. To calculate dN/dS ratios, nucleic acid sequence was aligned based on translated amino acids using MEGA4 http://www.megasoftware.net/, and ratios were calculated using the MEGA4 implemented Nei-Gojobori method with Jukes-Cantor correction.
Availability of sequences
All relevant sequences are included in the supplemental data (Additional file 9). Genomic loci can readily be found using the data we have provided as query sequences in ENSEMBL tBLASTn searches. Further, all human DUX sequences are summarized in the HomeoDB v2.0 http://homeodb.cbi.pku.edu.cn/.
Clapp J, Mitchell LM, Bolland DJ, Fantes J, Corcoran AE, Scotting PJ, Armour JAL, Hewitt JE: Evolutionary conservation of a coding function for D4Z4, the tandem DNA repeat mutated in facioscapulohumeral muscular dystrophy. Am J Hum Genet. 2007, 81: 264-279. 10.1086/519311.
Gehring WJ, Affolter M, Burglin T: Homeodomain proteins. Annu Rev Biochem. 1994, 63: 487-526. 10.1146/annurev.bi.63.070194.002415.
de Greef JC, Frants RR, van der Maarel SM: Epigenetic mechanisms of facioscapulohumeral muscular dystrophy. Mutat Res-Fund Mol M Mutat. 2008, 647: 94-102. 10.1016/j.mrfmmm.2008.07.011.
Hewitt JE, Lyle R, Clark LN, Valleley EM, Wright TJ, Wijmenga C, Vandeutekom JCT, Francis F, Sharpe PT, Hofker M, et al: Analysis of the tandem repeat locus D4Z4 associated with facioscapulohumeral muscular-dystrophy. Hum Mol Genet. 1994, 3: 1287-1295. 10.1093/hmg/3.8.1287.
Gabriels J, Beckers MC, Ding H, De Vriese A, Plaisance S, van der Maarel SM, Padberg GW, Frants RR, Hewitt JE, Collen D, Belayew A: Nucleotide sequence of the partially deleted D4Z4 locus in a patient with FSHD identifies a putative gene within each 3.3 kb element. Gene. 1999, 236: 25-32. 10.1016/S0378-1119(99)00267-X.
van der Maarel SM, Frants RR, Padberg GW: Facioscapulohumeral muscular dystrophy. BBA-Mol Basis Dis. 2007, 1772: 186-194.
Zeng W, de Greef JC, Chen Y-Y, Chien R, Kong X, Gregson HC, Winokur ST, Pyle A, Robertson KD, Schmiesing JA, et al: Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet. 2009, 5: e1000559-10.1371/journal.pgen.1000559.
Greef JCD, Lemmers RJLF, Engelen BGMV, Sacconi S, Venance SL, Frants RR, Tawil R, Maarel SMVD: Common epigenetic changes of D4Z4 in contraction-dependent and contraction-independent FSHD. Hum Mutat. 2009, 30: 1449-1459. 10.1002/humu.21091.
van Overveld PGM, Lemmers R, Sandkuijl LA, Enthoven L, Winokur ST, Bakels F, Padberg GW, van Ommen GJB, Frants RR, van der Maarel SM: Hypomethylation of D4Z4 in 4q-linked and non-4q-linked facioscapulohumeral muscular dystrophy. Nat Genet. 2003, 35: 315-317. 10.1038/ng1262.
Lemmers R, van der Vliet PJ, van der Gaag KJ, Zuniga S, Frants RR, de Knijff P, van der Maarel SM: Worldwide population analysis of the 4q and 10q subtelomeres identifies only four discrete interchromosomal sequence transfers in human evolution. Am J Hum Genet. 2010, 86: 364-377. 10.1016/j.ajhg.2010.01.035.
Lemmers R, Wohlgemuth M, van der Gaag KJ, van der Vliet PJ, van Teijlingen CMM, de Knijff P, Padberg GW, Frants RR, van der Maarel SM: Specific sequence variations within the 4q35 region are associated with facioscapulohumeral muscular dystrophy. Am J Hum Genet. 2007, 81: 884-894. 10.1086/521986.
Snider L, Asawachaicharn A, Tyler AE, Geng LN, Petek LM, Maves L, Miller DG, Lemmers RJLF, Winokur ST, Tawil R, et al: RNA transcripts, miRNA-sized fragments and proteins produced from D4Z4 units: New candidates for the pathophysiology of facioscapulohumeral dystrophy. Hum Mol Genet. 2009, 18: 2414-2430. 10.1093/hmg/ddp180.
Lemmers R, van der Vliet PJ, Klooster R, Sacconi S, Camano P, Dauwerse JG, Snider L, Straasheijm KR, van Ommen GJ, Padberg GW, et al: A nifying genetic model for facioscapulohumeral muscular dystrophy. Science. 2010, 329: 1650-1653. 10.1126/science.1189044.
Lyle R, Wright TJ, Clark LN, Hewitt JE: FSHD-associated repeat, D4Z4, is a member of a dispersed family of homeobox-containing repeats, subsets of which are clustered on the short arms of the acrocentric chromosomes. Genomics. 1995, 28: 389-397. 10.1006/geno.1995.1166.
Schmidt J, Kirsch S, Rappold GA, Schempp W: Complex evolution of a y-chromosomal double homeobox 4 (DUX4)-related gene family in hominoids. PLoS ONE. 2009, 4: 13-
Booth HAF, Holland PWH: Annotation, nomenclature and evolution of four novel homeobox genes expressed in the human germ line. Gene. 2007, 387: 7-14. 10.1016/j.gene.2006.07.034.
Holland PWH, Booth HAF, Bruford EA: Classification and nomenclature of all human homeobox genes. BMC Biol. 2007, 5: 10.1186/1741-7007-5-47.
Kawazu M, Yamamoto G, Yoshimi M, Yamamoto K, Asai T, Ichikawa M, Seo S, Nakagawa M, Chiba S, Kurokawa M, Ogawa S: Expression profiling of immature thymocytes revealed a novel homeobox gene that regulates double-negative thymocyte development. J Immunol. 2007, 179: 5335-5345.
Dixit M, Ansseau E, Tassin A, Winokur S, Shi R, Qian H, Sauvage S, Mattotti C, van Acker AM, Leo O, et al: DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1. Proc Natl Acad Sci USA. 2007, 104: 18157-18162. 10.1073/pnas.0708659104.
Bosnakovski D, Xu ZH, Gang EJ, Galindo CL, Liu MJ, Simsek T, Garner HR, Agha-Mohammadi S, Tassin A, Coppee F, et al: An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies. EMBO J. 2008, 27: 2766-2779. 10.1038/emboj.2008.201.
Kowaljow V, Marcowycz A, Ansseau E, Conde CB, Sauvage S, Mattotti C, Arias C, Corona ED, Nufiez NG, Leo O, et al: The DUX4 gene at the FSHDIA locus encodes a pro-apoptotic protein. Neuromuscul Disord. 2007, 17: 611-623. 10.1016/j.nmd.2007.04.002.
Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J: Retrocopy contributions to the evolution of the human genome. BMC Genomics. 2008, 9: 10.1186/1471-2164-9-466.
Zhong YF, Butts T, Holland PWH: HomeoDB: A database of homeobox gene diversity. Evo Dev. 2008, 10: 516-518. 10.1111/j.1525-142X.2008.00266.x.
Wu SL, Tsai MS, Wong SH, Hsieh-Li HM, Tsai TS, Chang WT, Huang SL, Chiu CC, Wang SH: Characterization of genomic structures and expression profiles of three tandem repeats of a mouse double homeobox gene: Duxbl. Dev Dyn. 2010, 239: 927-940. 10.1002/dvdy.22210.
Langkjaer RB, Cliften PF, Johnston M, Piskur J: Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature. 2003, 421: 848-852. 10.1038/nature01419.
Bergsten J: A review of long-branch attraction. Cladistics. 2005, 21: 163-193. 10.1111/j.1096-0031.2005.00059.x.
Bosnakovski D, Daughters RS, Xu Z, Slack JMW, Kyba M: Biphasic myopathic phenotype of mouse DUX, an ORF within conserved FSHD-related repeats. PLoS ONE. 2009, 4: e7003-10.1371/journal.pone.0007003.
Li G, Holland PWH: The origin and evolution of ARGFX homeobox loci in mammalian radiation. BMC Evol Biol. 2010, 10: 182-10.1186/1471-2148-10-182.
Long M, Betran E, Thornton K, Wang W: The origin of new genes: Glimpses from the young and old. Nat Rev Genet. 2003, 4: 865-875. 10.1038/nrg1204.
Soskine M, Tawfik DS: Mutational effects and the evolution of new protein functions. Nat Rev Genet. 11: 572-582. 10.1038/nrg2808.
Wuebbles RD, Long SW, Hanel ML, Jones PL: Testing the effects of FSHD candidate gene expression in vertebrate muscle development. Int J Clin Exp Pathol. 2010, 3: 386-400.
Snider L, Geng LN, Lemmers RJLF, Kyba M, Ware CB, Nelson AM, Tawil R, Filippova GN, van der Maarel M, Tapscott SJ, Miller DG: Facioscapulohumeral dystrophy: Incomplete suppression of a retrotransposed gene. PLoS Genet. 2010, 6: e1001181-10.1371/journal.pgen.1001181.
Fablet M, Bueno M, Potrzebowski L, Kaessmann H: Evolutionary origin and functions of retrogene introns. Mol Biol Evol. 2009, 26: 2147-2156. 10.1093/molbev/msp125.
Koonin EV: Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet. 2005, 39: 309-338. 10.1146/annurev.genet.39.073003.114725.
Babushok DV, Ostertag EM, Kazazian HH: Current topics in genome evolution: Molecular mechanisms of new gene formation. Cell Mol Life Sci. 2007, 64: 542-554. 10.1007/s00018-006-6453-4.
Holland PWH, Takahashi T: The evolution of homeobox genes: Implications for the study of brain development. Brain Res Bull. 2005, 66: 484-490. 10.1016/j.brainresbull.2005.06.003.
Buljan MFA, Bateman A: Quantifying the mechanisms of domain gain in animal proteins. Genome Biol. 2010, 11: R74-10.1186/gb-2010-11-7-r74.
Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL: Selective sweep of a newly evolved sperm-specific gene in drosophila. Nature. 1998, 396: 572-575. 10.1038/25126.
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ: Jalview version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009, 25: 1189-1191. 10.1093/bioinformatics/btp033.
Felsenstein J: Confidence-limits on phylogenies - an approach using the bootstrap. Evolution. 1985, 39: 783-791. 10.2307/2408678.
Letunic I, Bork P: Interactive tree of life (iTOL): An online tool for phylogenetic tree display and annotation. Bioinformatics. 2007, 23: 127-128. 10.1093/bioinformatics/btl529.
Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S, Progra NCS: LAGAN and multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 2003, 13: 721-731. 10.1101/gr.926603.
Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007, 24: 1596-1599. 10.1093/molbev/msm092.
Hedges SB: The origin and evolution of model organisms. Nat Rev Genet. 2002, 3: 838-849. 10.1038/nrg929.
This work was funded by grants from the Muscular Dystrophy Association, USA and a PhD studentship from the Muscular Dystrophy Campaign of Great Britain to AL. We would like to thank John Armour and John Brookfield (University of Nottingham) for helpful feedback and discussion.
JEH conceived the study. AL performed database interrogation and phylogenetic analysis and drafted the manuscript. Both authors edited and approved the final version of the manuscript.
Electronic supplementary material
Additional file 5: Concatenated HD tree with DUX4 & mDux. Maximum Likelihood tree based on 120 amino acid concatenated homeodomains. Note the clustering of DUX4 with DUXC and the isolation of the rodent Dux node. (PDF 217 KB)
Additional file 6: Individual HD tree with DUX4 & mDux. Tree based on 60 amino acid individual homeodomains. (PDF 258 KB)
Additional file 9: Homeodomain amino acid sequences. DUX homologue and homeodomain number (1 or 2) before species. Numbers in brackets after species name denote different copies. (PDF 22 KB)
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Leidenroth, A., Hewitt, J.E. A family history of DUX4: phylogenetic analysis of DUXA, B, C and Duxbl reveals the ancestral DUXgene. BMC Evol Biol 10, 364 (2010). https://doi.org/10.1186/1471-2148-10-364
- Placental Mammal
- Syntenic Region
- Deletion Breakpoint
- Stop Codon Mutation
- Large Open Reading Frame