- Open Access
The birth of a human-specific neural gene by incomplete duplication and gene fusion
Genome Biology volume 18, Article number: 49 (2017)
Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The human-specific gene hydrocephalus-inducing 2, HYDIN2, was generated by a 364 kbp duplication of 79 internal exons of the large ciliary gene HYDIN from chromosome 16q22.2 to chromosome 1q21.1. Because the HYDIN2 locus lacks the ancestral promoter and seven terminal exons of the progenitor gene, we sought to characterize transcription at this locus by coupling reverse transcription polymerase chain reaction and long-read sequencing.
5' RACE indicates a transcription start site for HYDIN2 outside of the duplication and we observe fusion transcripts spanning both the 5' and 3' breakpoints. We observe extensive splicing diversity leading to the formation of altered open reading frames (ORFs) that appear to be under relaxed selection. We show that HYDIN2 adopted a new promoter that drives an altered pattern of expression, with highest levels in neural tissues. We estimate that the HYDIN duplication occurred ~3.2 million years ago and find that it is nearly fixed (99.9%) for diploid copy number in contemporary humans. Examination of 73 chromosome 1q21 rearrangement patients reveals that HYDIN2 is deleted or duplicated in most cases.
Together, these data support a model of rapid gene innovation by fusion of incomplete segmental duplications, altered tissue expression, and potential subfunctionalization or neofunctionalization of HYDIN2 early in the evolution of the Homo lineage.
Gene duplication has long been hypothesized to be an important source of evolutionary innovation . The great ape lineage that includes humans has experienced a surge of interspersed segmental duplications over the last 10–15 million years [2, 3]. While large, highly identical duplications sensitize the human genome to recurrent rearrangements associated with disease [4–7], they also have the potential to drive the emergence of novel duplicate genes and functions . The identification of functional duplicate genes, however, is difficult, as these duplications are typically large, highly identical, and clustered into complex mosaic structures juxtaposing sequence blocks of diverse origin . Furthermore, duplicated regions of the genome are frequently misassembled and are the source of extensive copy number variation in human populations [10, 11].
Considerable attention has been focused on the identification of duplicate genes that have emerged since the human–chimpanzee divergence because of their potential to contribute to human-specific traits [6, 12, 13]. Already two such genes, SRGAP2C and ARHGAP11B, have been functionally characterized by heterologous expression studies in mouse suggesting potential roles of the duplicates in increasing dendritic spine density  and expanding the number of cortical neurons , respectively. Both duplicate genes are nearly fixed for copy number in human populations but absent from all non-human primates [15–18]. In addition, both genes carry only a subset of the exons of the ancestral gene due to incomplete segmental duplication of the progenitor locus, supporting the hypothesis that truncation may facilitate neofunctionalization [8, 16].
Chromosome 1q21.1 is one of the largest regions of human-specific segmental duplication blocks in the human genome [6, 19] and, as such, is a reservoir for human-specific transcripts and genes [13, 20]. The presence of large blocks of directly oriented, highly identical duplicated sequence renders this region genetically unstable . Specifically, recurrent deletions and duplications occur at this locus and have been associated with cognitive and motor impairment, articulation abnormalities, and hypotonia [21–23]. Duplication carriers show an increased prevalence of autism spectrum disorder (ASD) and macrocephaly, while deletion carriers show an increased prevalence of microcephaly.
The human-specific gene HYDIN2 was previously mapped to this region of chromosome 1q21 , but because it was contained within an assembly gap in GRCh37/hg19, its role in 1q21 rearrangement syndromes remained uncertain. It was postulated that HYDIN2 might contribute to the reciprocal macrocephaly/microcephaly phenotype , because mutation of the ancestral HYDIN gene leads to hydrocephalus in mouse . In humans, however, recessive mutations in HYDIN were found associated with primary ciliary dyskinesia without hydrocephalus . As such, whether dosage of HYDIN2 plays a role in the 1q21.1 microdeletion/microduplication phenotype has remained unanswered.
With the initial discovery of the HYDIN duplication , two features of the derived locus were noted. First, although the gene duplication was truncated and did not include the promoter, transcription was observed at HYDIN2. Second, HYDIN2 transcripts appeared to derive primarily from neuronal sources, in contrast to the ciliated tissues from which HYDIN transcripts were originally cloned. We sought to investigate the origin and significance of HYDIN2 transcription by reconstructing the evolutionary history of this locus, assessing patterns of human genetic variation in both normal and disease populations, and exploring transcript diversity in human tissues.
Molecular evolution and breakpoint analyses
The ancestral HYDIN gene is notable for its large size—its canonical gene structure occupies 423 kbp of genomic sequence and by homology to mouse is predicted to produce a 15,179 bp transcript encoding a 5121 amino acid protein (Fig. 1a). Comparative sequencing of both human HYDIN paralogs as well as the putative integration or acceptor site in chimpanzee shows that the duplicated sequence is 364 kbp long and shares 99.4% nucleotide identity with its ancestral paralog. The duplication includes 79 coding exons but excludes the sole promoter, as well as the canonical polyadenylation site, though shorter isoforms of HYDIN with earlier polyadenylation sites are recorded. For transcription to occur, this gene segment must have acquired a new promoter and at least one novel polyadenylation site, potentially from flanking sequences.
The ancestral site on chromosome 16q22.2 is flanked by unique sequence, with no indication of a predisposition to rearrangement. In contrast, the acceptor site occurs within a large segmental duplication block on chromosome 1q21 that has been subject to extensive duplication and rearrangement over the last 25 million years of evolution [6, 12, 16, 19]. This includes the hyper-expanded core duplicon for chromosome 1 that carries members of the neuroblastoma breakpoint family (NBPF) and its associated DUF1220 protein domain [27–29]. Copies of NBPF map 36 kbp downstream of the insertion site and represent the nearest protein-coding gene (Fig. 1a, see also Additional file 1: Figure S1). We refined the breakpoint of the duplication integration by targeted sequencing of chimpanzee bacterial artificial chromosome (BAC) clones. A comparison with the high-quality chimpanzee sequence indicates that the insertion at chromosome 1q21.1 occurred at the boundary between LTR and LINE repeats, with concomitant loss of 841 bp of LINE sequence (Fig. 1b) in the human lineage.
To estimate the evolutionary age of the HYDIN duplication, we generated high-quality sequence data for the two human HYDIN paralogs and built a multiple sequence alignment (MSA) using orthologous sequences from chimpanzee (panTro4) and orangutan (ponAbe2) over the 364 kbp duplicated region. Phylogenetic analysis predicts that the duplication occurred approximately 3.17 million years ago (mya; 95% CI: 3.09-3.24 mya, bootstrap method) (Fig. 1c)—a period corresponding to the transition between australopithecines and the genus Homo. The derived HYDIN2 duplication inserted into evolutionarily older segmental duplications shared among great apes (summarized in Fig. 1d). Immediately flanking the large central segment are two blocks, referred to here as the 5' exon block (41 kbp) and the 3' exon block (24 kbp) because they provide exons that form fusion transcripts by joining with exons from within the HYDIN2 duplication. These two blocks were formerly a single segment that was bisected by the insertion of the duplication from chromosome 16.
The segment composed of the 5' exon block and 3' exon block maps to two other locations in the human genome in addition to chromosome 1q21.1 (Fig. 1d): an inversely oriented copy mapping 1.1 Mbp telomerically at chromosome 1q21.2 and another mapping at chromosome 1p22.3. Only the chromosome 1p22.3 locus shares conserved synteny with mouse, where it is found as a single copy and likely represents the ancestral locus. The other two copies on chromosome 1q21 are both associated with NBPF and form a larger homologous segment of ~109 kbp in length. Phylogenetic reconstruction predicts that the first duplication occurred ~21 mya (95% CI: 20.6–21.6 mya, bootstrap method; Additional file 1: Figure S2a), placing the event at the root of the ape lineage after divergence from the Old World monkeys . This is consistent with our observation that this segment is found at single copy in New World and Old World monkeys and at two copies in gibbon and orangutan.
The second duplication, from chromosome 1q21.1 to chromosome 1q21.2, shows greater sequence identity (99.6%) than the HYDIN duplication (99.4%). Although phylogenetic timing predicts a more recent origin for this duplication (2.31 mya; 95% CI: 2.17–2.45 mya; Additional file 1: Figure S2b) than for the HYDIN duplication, it must necessarily have occurred prior to or together with the insertion of the HYDIN segment from chromosome 16 in order for it to have been disrupted by the insertion. It is likely that interlocus gene conversion between human chromosome 1q21.1 and chromosome 1q21.2 copies distorts the timing of this duplication. Longer stretches of conserved synteny between sequenced non-human primate clones and human chromosome 1q21.1 than between the clones and human chromosome 1q21.2 indicate that chromosome 1q21.1 is the more likely ancestral locus. This second duplication extends further upstream to include a segment that provides the new promoter (26 kbp) and further downstream to the segment that includes NBPF12. Altogether, the HYDIN segment is sandwiched by two layers of duplications—the first 21 million years old, and the other 3.2 million years old—providing the genomic substrates for novel HYDIN2 flanking exons and regulatory elements (Fig. 1e).
Copy number diversity and gene conversion in human populations
We assessed HYDIN copy number variation across diverse human populations, archaic hominins, and non-human primate genomes by applying whole-genome shotgun sequence detection and singly unique nucleotide k-mer (SUNK) analysis to obtain aggregate copy number estimates . In contemporary human populations, we observe a narrow distribution of HYDIN copy number, centered on individuals having two diploid copies of each paralog for a total of four aggregate copies (Fig. 2a). As expected from our phylogenetic analysis, all non-human primates have just two diploid copies of HYDIN. Neanderthal and Denisova are believed to have diverged from modern humans approximately 700,000 years ago [31–33]. Consistent with this, we observe the duplication in their genomes as well as in three archaic human genomes (~7000–45,000 years old), though with a greater variability, possibly due to the relatively lower coverage and/or quality of these genomes [34, 35]. In total, our analysis of 2401 human genomes from the 1000 Genomes Project (1KG) and the Human Genome Diversity Project (HGDP; Additional file 1: Figure S3), indicate that the duplication is nearly fixed (99.9%) for diploid copy number in contemporary humans.
For five human samples that showed copy number variation, we performed fluorescent in situ hybridization (FISH) on chromosomal metaphase spreads for validation and cytogenetic characterization (Fig. 2b). In all instances, rare copy number variation is restricted to the duplicate copy, HYDIN2, on chromosome 1q21.1. We designed an orthogonal method to assay HYDIN paralog-specific copy number at a finer scale by designing molecular inversion probe (MIP) assays  to >153 nucleotide differences that distinguish the HYDIN paralogs. We genotyped 6055 DNA samples from controls as well as patients with neurodevelopmental and autism spectrum disorders (Additional file 1: Table S1). Other than patients with the 1q21 microdeletion/microduplication syndrome, copy number variation of HYDIN2 was rare. The assay confirmed rare deletions and duplications of HYDIN2 (described above) as well as rare copy number variants in HYDIN previously detected by array comparative genomic hybridization (CGH) of autism patients . We discovered additional rare internal duplications and deletions, ranging in size from 3 kbp to 289 kbp, affecting both HYDIN paralogs (Fig. 2c and d; see also Additional file 1: Figure S4 and Additional file 1: Table S2). Remarkably, two control individuals showed clear signatures of interlocus gene conversion over a common ~2 kbp region. This event is copy number neutral but clearly shows that HYDIN has served as the donor for the conversion of sequence to HYDIN2. Such events are rare (2/2981 or 0.00067) but indicate non-reciprocal sequence exchange has occurred between HYDIN paralogs on chromosomes 1 and 16.
In summary, we observe no heterozygous deletions in HYDIN in the 1KG or the HGDP genome samples. Pathogenic mutations in the ancestral copy of HYDIN have been observed only in the homozygous state in consanguineous families . The HYDIN duplications (2) and deletions (1) that have been observed in autism cases are large and include other genes . HYDIN2 copy number variation occurs rarely and is largely restricted to individuals carrying chromosome 1q21.1 rearrangements. We have observed no individuals with a loss of both copies of HYDIN2.
HYDIN2 fusion transcripts
We investigated the gene structure of HYDIN2 by first considering an alignment of the theoretical open reading frame (ORF) based on the ancestral HYDIN gene model (Fig. 3). If all duplicated codons were maintained as in HYDIN, the theoretical alignment would yield 21 synonymous and 32 non-synonymous differences between the shared sequence, as well as three deletions (Fig. 3c). The latter includes: a 2095 bp deletion (with intronic sequence) on HYDIN2 that eliminates the splice acceptor for exon 42, a 15 bp in-frame deletion in exon 46, and a 1 bp deletion in exon 69. Due to the deletion of exon 42 and the frameshift in exon 69, a premature stop codon is predicted. As a result of the incomplete gene structure with respect to HYDIN, HYDIN2 is annotated as a pseudogene by both RefSeq and GENCODE.
We identified mapped expressed sequence tags (ESTs), both within and spanning the HYDIN duplication breakpoints, as evidence that transcription might still be occurring, potentially by way of gene fusion to neighboring sequence. To identify the new transcriptional start site, we performed 5' rapid amplification of complementary DNA (cDNA) ends (5' RACE), using fetal brain RNA as starting material. We identified a site 55 kbp upstream, which we define as the HYDIN2 promoter. The high density of spliced ESTs at this location supports this as a site of transcription initiation; we also observe a robust fetal brain DNase1 hypersensitivity peak (Fig. 1e, Additional file 1: Figure S6) consistent with its function as an alternate promoter. Although duplication of HYDIN excluded the canonical polyadenylation site of the longest HYDIN isoform, shorter isoforms of HYDIN that terminate at exons 15, 19, and 20 are also annotated. We identified spliced ESTs supporting exon 19 as an alternative site of polyadenylation in HYDIN. We further investigated alternative polyadenylation through 3' RACE and identified a potential polyadenylation site at exon 43 of HYDIN2.
We amplified by RT-PCR the putative full-length transcripts that spanned from the new HYDIN2 promoter to both the polyadenylation site at exon 19 and the polyadenylation site at exon 43, using fetal brain RNA as a starting material (Fig. 3a). We also designed a series of smaller RT-PCR products extending into the fused 3′ exons. Products were sequenced with single-molecule, real-time (SMRT) sequencing technology, which allowed us to resolve patterns of splicing, although we note that abundance of different isoforms cannot be taken as evidence of messenger RNA (mRNA) expression levels due to the preferential loading bias for smaller isoforms inherent to the sequencing technology. We identified fusion transcripts with both upstream and downstream segments beyond the HYDIN duplication breakpoints. Upstream, these transcripts begin at the promoter identified by 5' RACE and continue into the HYDIN duplication. We observe 13 5'-fused exons, with considerable diversity in alternative splicing. The transcripts that begin with these exons continue into the HYDIN duplication and then generally follow the canonical pattern of HYDIN splicing. Downstream, we also identify fusion transcripts between the HYDIN duplicate exons and the 3′ exon block. These fusion transcripts continue into the neighboring gene, NBPF12, a gene that itself undergoes highly variable splicing, with annotated transcripts in the range of 1831–7061 bp in length.
Transcripts that begin at the new promoter and continue into the duplicated HYDIN exons are predicted to initiate translation consistent with the HYDIN ORF at the ATG located in exon 7 or an alternate ATG mapping to exon 11 (Fig. 3c). Based on sequencing of transcripts, we predict ORFs of 467 and 668 amino acids (transcript termination at exon 19) and an ORF of 1852 (transcript termination at exon 43). These transcripts are designated HYDIN2 isoforms A, B, and F, respectively (Fig. 3b). If translated, these products would represent truncated HYDIN proteins (green bars in Fig. 3c). The 5' and 3' fusion exons (located in NBPF12) do not extend ORFs beyond the HYDIN duplication. We do not find evidence of internal alternative sites of transcription initiation, whether by ESTs, cap analysis gene expression (CAGE), or 5' RACE, although RACE has not been performed exhaustively throughout the 364 kbp duplicated segment.
Our results suggest that HYDIN2 acquired a new promoter and we hypothesize that the novel promoter is responsible for the expression differences between the paralogs. We took advantage of a 15 bp in-frame exonic deletion that distinguishes HYDIN2 from HYDIN to investigate the transcript abundance in different tissues (Fig. 4a). By designing RT-PCR primers that flanked this deletion, we inferred relative expression of the HYDIN paralogs from the differences in signal intensity. Next, we leveraged RNA sequencing (RNA-seq) reads that could be mapped to SUNK differences between HYDIN and HYDIN2 to quantify relative expression levels across a panel of tissues using data from the GTEx project  (Fig. 4b). The latter analysis allowed us to compare expression among the different isoforms characterized by cDNA sequencing as well as quantify differences between paralogs.
We observe that HYDIN is most highly expressed in ciliated tissues, such as the lung and testis, consistent with its known function as a ciliary structural protein . By comparison, HYDIN2 expression is higher in the brain, while also prominent in the ovary. Interestingly, HYDIN2 appears more broadly expressed in fetal tissues with the strongest signal observed in fetal brain. It should be noted that the RT-PCR assay measures expression of exon 46 alone, which is not included in some shorter RefSeq isoforms of HYDIN. Comparison of this assay with SUNK-based mapping of the GTEx data is in close agreement. This is also consistent with the observation that cDNA clones from HYDIN2 were predominantly derived from neuronal sources . With the exception of HYDIN2 isoform F, all three isoforms show moderate levels of expression in cerebellum and cerebral cortex. The longest isoform, HYDIN2 isoform G, with both 5' and 3' fused exons shows a slightly higher level of expression, although we note only that only HYDIN2 isoform A produces a transcript without a large number of 5' untranslated exons due to exon skipping from the first exon to exon 11 of the canonical gene model where an alternate ATG start codon exists.
The predicted HYDIN2 promoter overlaps a DNase I hypersensitivity (DHS) peak (Fig. 1e, Additional file 1: Figure S6) in fetal brain. A number of fetal brain cDNA sequences have been mapped to the duplicated locus of the promoter-containing block on chromosome 1q21.2 [40, 41]. Notably, at the ancestral chromosome 1p22.3 locus (Fig. 1d), where the 5' and 3' exon blocks sit in the absence of the promoter, there are neither annotated transcripts nor spliced ESTs. Within the DHS peak a smaller, higher copy repeat is found, approximately 1113 bp long. A simple BLAT search reveals that this segment has propagated throughout chromosome 1, with ten locations that contain the full-length repeat at a level of identity of 90% or above (Additional file 1: Table S3). Many are clustered at chromosome 1q21 and are found in association with, though not transcriptionally joined to, the NBPF core duplicon. Eight out of ten produce spliced ESTs, many from neuronal tissues, further supporting this segment as contributing to the expression pattern of HYDIN2.
Coding variation and selection in HYDIN and HYDIN2
We investigated whether there was evidence of selection acting on HYDIN2 by comparing the ratio of non-synonymous to synonymous changes between paralogs, using non-human primate HYDIN as an outgroup (Additional file 1: Table S4). We observe moderately strong purifying selection acting on ancestral HYDIN throughout the primate lineage, with an average dN/dS value of 0.29. HYDIN2, in contrast, shows an elevated pairwise dN/dS value in comparison with non-human primates (e.g., 0.39 for human HYDIN2 and chimpanzee HYDIN versus 0.29 for human HYDIN and chimpanzee HYDIN). Branch-based estimates of dN/dS that can detect adaptive evolution after gene duplication  show a similar trend with a consistently elevated dN/dS value for human HYDIN2 when compared to human HYDIN. This result holds if we restrict our analysis to only those exons predicted to be part of the HYDIN2 ORF (HYDIN2 isoform A). Although none of these differences achieve statistical significance due to the limited number of mutational differences occurring within the human lineage, it is interesting that all three mutational changes that occurred within the HYDIN2 ORF result in amino acid changes while only synonymous changes (n = 2) occurred in the corresponding portion of ancestral HYDIN.
As an alternative approach, we sought to characterize and compare deleterious coding variation between HYDIN and HYDIN2 among 3484 probands and 2629 healthy controls from families with autism [43, 44]. We targeted all coding exons with at least five nucleotides of flanking sequence based on the canonical HYDIN gene structure using MIPs. We identified all likely gene-disruptive (LGD) variants (frameshift, stop-gain, stop-loss, or splice-site mutations) and successfully assigned 39% of such deleterious variants to either HYDIN or HYDIN2, made possible by singly unique nucleotides (SUNs) contained within the target sequence of the MIP (Table 1). No common (>1% allele frequency) LGD variants were observed for either paralog. Considering the canonical ancestral gene structure, we initially observed a lower number of LGD mutations for HYDIN (n = 2) when compared to HYDIN2 (n = 10) in controls. Interestingly, if we restrict our analysis to the most likely ORF model (HYDIN2 isoform A), only two HYDIN2 LGD mutations remain and at an allele frequency comparable to what has been observed for HYDIN. Assuming that all unassigned LGD mutations originate from HYDIN2, all higher frequency LGD mutations (>0.15% frequency) correspond to ancestral exonic sequence mapping outside of the HYDIN2 ORF gene model (Additional file 1: Table S5).
HYDIN2 and the chromosome 1q21 microdeletion/microduplication syndrome
Recurrent microdeletions and microduplications at chromosome 1q21 have been associated with a variety of neurodevelopmental phenotypes, including microcephaly and macrocephaly. Loss or gain of HYDIN2 has been hypothesized to underlie these head circumference phenotypes in light of its expression in brain, its inclusion in the typical rearrangement interval, and the association of homozygous losses of HYDIN in mouse with hydrocephalus [22, 24, 25]. To explore this hypothesis, we leveraged our MIP assay (Fig. 5a) to genotype HYDIN paralog-specific copy number in 73 individuals carrying a chromosome 1q21 rearrangement, corresponding to 45 independent rearrangement events (15 duplications and 30 deletions). MIP data revealed that HYDIN2 is usually, but not always, affected by chromosome 1q21 deletions and duplications (Fig. 5b, Additional file 1: Figure S5). Overall, we observe that 87% of duplications (13 of 15) and 93% of deletions (28 of 30) examined include HYDIN2. Targeted array CGH on a subset of patients validated our whole-genome-shotgun-based and MIP-based results in every instance, confirming inclusion or exclusion of HYDIN2 among both 1q21 microduplications and microdeletions (Fig. 5c, Additional file 1: Figure S5).
We also performed comprehensive segmental duplication analysis on the GRCh38 reference haplotype to identify directly oriented duplication pairs with high sequence identity that may confer susceptibility to non-allelic homologous recombination. For typical 1q21 rearrangements, those that include HYDIN2, the most likely candidates are large (247 kbp), highly identical (99.7%) segments that include truncated NOTCH2 duplications (NOTCH2NL) adjacent to members of the NBPF gene family (Fig. 5c, Additional file 1: Figure S5b). For atypical rearrangements, our data are consistent with multiple possible breakpoint locations. Alternatively, these events may have occurred on a still undescribed haplotype structure or originated through a nonrecurrent mechanism.
We examined the phenotype of atypical carriers without copy number variation in HYDIN2. All three atypical 1q21 microduplications excluding HYDIN2 present with macrocephaly and similarly all three patients with atypical 1q21 microdeletions excluding HYDIN2 exhibit microcephaly (Additional file 1: Table S6). These observations suggest that loss or gain of a genomic HYDIN2 copy is not necessary for chromosome 1q21 rearrangement patients to manifest head circumference abnormalities. We cannot rule out the possibilities that these individuals harbor disruptive point mutations in HYDIN2 or that atypical chromosome 1q21 rearrangements dysregulate HYDIN2 expression. Further studies will be necessary to elucidate the potential role of HYDIN2 in brain size and in other aspects of chromosome 1q21 rearrangement phenotypes.
HYDIN2 is a human-specific gene that emerged 3.2 mya, created by incomplete duplication of the ancestral gene HYDIN. Young duplicate genes can rapidly evolve essential functions ; however, unless increased gene dosage is itself beneficial, long-term maintenance of a duplicate gene typically requires mutational change leading to functional innovation or subfunctionalization . Incomplete gene duplication provides one mechanism for rapid functional change because the duplicate differs in structure from its progenitor, with potentially profound functional consequences beyond a simple dosage increase. Such a mechanism has been postulated in the case of the human-specific incomplete duplications of SRGAP2, where the truncated granddaughter paralog, SRGAP2C, has been shown to antagonize the ancestral copy SRGAP2A [14, 16].
Interspersed duplications such as HYDIN have an additional mechanism promoting functional divergence, namely, duplicate copies in new genomic locations are subjected to asymmetric rates of mutation . Because the HYDIN duplication excluded the promoter, naively one would expect the duplicate copy to have been silenced. In contrast, our analysis shows that HYDIN2 is actively transcribed, and more highly expressed than the ancestral paralog in many tissues. The acquisition of a novel promoter effectively created a fusion gene. Thus, the partial duplication was “rescued” by its juxtaposition with active regulatory sequence at chromosome 1q21.1.
The original function of this novel neuronal promoter is not clear, but 2 Mbp away at chromosome 1q21.2 sits an earlier duplication of the HYDIN2 flanking sequences without the HYDIN2 insertion. Here, we observe robust transcription, as evidenced by a number of GENCODE transcripts—all classified as long non-coding RNA and most of which derive from a fetal brain cDNA library . At HYDIN2, this promoter has driven an altered expression pattern, with widespread expression in fetal tissues, decreased expression in testis and lung, and increased expression in brain tissues (cerebellum and cerebral cortex) and ovary being the most prominent changes.
Long-read sequencing of cDNA from both the fetal and adult brain reveals an extraordinary diversity of HYDIN2 isoforms, including the presence of additional 5' and 3' exons within transcripts spanning the duplication junctions. Although we can confirm expression of at least three distinct HYDIN2 isoforms, we favor isoform A as the most likely protein-encoding transcript for several reasons: there is no evidence for a premature termination codon; deleterious coding mutations in the human population are rare; and the other isoforms carry an unusually large number of untranslated exons. The presence of abnormally long untranslated regions (UTRs) or exon junctions downstream of a premature termination codon usually indicates strong signatures for nonsense mediated decay of mRNA . Similarly, a large number of 5' non-coding exons is thought to impede translational efficiency [49, 50].
In the case of HYDIN2 isoform A, intervening untranslated exons are skipped, resulting in a putative 467 amino acid protein with relatively short 5' and 3' UTRs. Although we know little regarding the function of HYDIN2, it is noteworthy that HYDIN has a structural role in motile cilia [39, 51, 52]. Its expression in lung and testis is consistent with the observation that recessive mutations in HYDIN cause primary ciliary dyskinesia, with the primary phenotypes being chronic respiratory infections and male infertility in humans . It is interesting that in addition to these deficiencies, mouse mutants in hy3 (Hydin –/–) show a more severe phenotype, developing lethal hydrocephalus due to impaired ciliary motility and fluid flow in the developing brain. One possible explanation for this phenotypic discrepancy between mutant mice and humans lacking functional HYDIN may be that human HYDIN paralogs have undergone subfunctionalization. In particular, the neuronally expressed HYDIN2 may have assumed some of the ancestral gene’s function during human brain development.
Our copy number analyses reveal that the HYDIN2 duplication has largely fixed in the human population. In fact, HYDIN2 shows the lowest degree of copy number variation in the normal population when compared to other human-specific duplications [8, 13]. While it was speculated that HYDIN2 played an important role in the reciprocal macrocephaly/microcephaly phenotype associated with 1q21.1 duplications/deletions , we have identified rearrangement patients with head size abnormalities lacking altered genomic dosage of HYDIN2. It is plausible that altered expression or point mutations effectively disrupt HYDIN2 in these individuals or, alternatively, that HYDIN2 dysfunction does not contribute to their head circumference phenotypes. Distinguishing these possibilities and determining whether HYDIN2 plays an important role in neurodevelopment more broadly will require further functional studies complemented by large-scale genotyping in various neurodevelopmental disease cohorts and relevant, well-phenotyped controls.
In this study, we characterize the evolutionary history, transcriptional landscape, and potential clinical impact of the human-specific duplicate gene HYDIN2. We show that HYDIN2 was generated by the juxtaposition of multiple segmental duplications culminating with the partial duplication of HYDIN ~3.2 mya. We identify a new promoter that “rescued” the truncated gene duplicate and drives a neuronal pattern of expression. We show that long-read sequencing can be used to understand a previously intractable large and complexly spliced gene and identify transcribed unannotated ORFs. We show that the reciprocal macro/microcephaly phenotypes associated with chromosome 1q21 rearrangements can occur without HYDIN2 copy number changes. Ultimately, we provide a clear example of how juxtaposition of transcriptionally active segmental duplications can lead to the birth of a new gene.
Metaphase and interphase spreads were prepared from lymphoblastoid human cell lines (GM19190, GM19901, GM19201, GM20127, GM19703; Coriell Cell Repository). FISH experiments were performed using fosmid clone WIBR2-3823 N03, directly labeled by nick-translation with Cy3-dUTP (PerkinElmer) as previously described  with minor modifications. Briefly, 300 ng of labeled probe was used for the FISH experiments; hybridization was performed at 37 °C in 2 × SSC, 50% (v/v) formamide, 10% (w/v) dextran sulfate, and 3 mg sonicated salmon sperm DNA, in a volume of 10 μL. Posthybridization washing was at 60 °C in 0.1 × SSC (three times, high stringency). Nuclei were simultaneously DAPI stained. Digital images were obtained using a Leica DMRXA2 epifluorescence microscope equipped with a cooled CCD camera (Princeton Instruments). DAPI and Cy3 fluorescence signals, detected with specific filters, were recorded separately as grayscale images. Pseudocoloring and merging of images were performed using Adobe Photoshop software.
Sequencing and assembly of large-insert clones (BACs)
We searched for discordant BAC-end mappings that spanned the HYDIN2 insertion site at chromosome 1q21.1 in libraries CH251 (chimpanzee) and CH276 (orangutan). One clone was identified for chimpanzee (CH251-231E10) and one in orangutan (CH276-57C3). DNA was isolated from these clones and SMRTbell libraries were prepped and sequenced on the Pacific Biosciences (PacBio) RSII. Inserts were assembled using HGAP and Quiver-polished as previously described .
Orthologous HYDIN sequences in chimpanzee and orangutan were identified using BLAT  in the UCSC Genome Browser . The human chromosome 16 HYDIN shared sequence was used as a query against panTro3 and ponAbe2, respectively. An MSA of these non-human primates as well as the duplicated sequences from chromosomes 1 and 16 (both from CH17) was created using ClustalW . An unrooted phylogenetic tree was constructed in MEGA6  using the neighbor-joining method  with complete-deletion option, yielding a total of 315,349 positions. Genetic distances were computed under the Kimura two-parameter model  with standard error estimates  (n = 500 bootstrap replicates). A Tajima’s relative rate test using chimpanzee as the outgroup failed to reject the hypothesis that both human HYDIN paralogs are evolving at the same rate (p = 0.21). Thus, the timing of the duplication event is estimated by taking the average evolutionary distance between the two HYDIN paralogs as a ratio of the total distance from chimpanzee HYDIN. This yields a timing estimate of 3.17 mya assuming the divergence took place 6 mya. The 95% confidence interval was estimated by the bootstrapping method.
Copy number genotyping
Aggregate and paralog-specific copy number estimates of HYDIN/HYDIN2 were determined using previously described methods . Raw sequences from 236 human individuals from HGDP , 2143 human individuals through Phase 3 of 1KG , 86 non-human primate individuals from the Great Ape Genome Project (including bonobos (n = 14), chimpanzees (n = 23), gorillas (n = 32), and orangutans (n = 17)) , a Denisovan individual , a Neanderthal individual , and three archaic hominids [34, 35] were mapped to the human reference genome using mrsFAST . For aggregate copy number estimates (Fig. 2a) GRCh37 was used. For paralog-specific copy number estimates (Additional file 1: Figure S3) GRCh38 was used, as recent correction to the HYDIN2 locus in the human genome made possible paralog-specific copy number estimates.
Kallisto (v. 0.42.4)  was used to estimate the expression levels of nine transcripts detected and putative HYDIN2 isoforms (see Additional file 2). We added the HYDIN2 sequences to the GENCODE reference transcriptome (release 25)  and generated a new index using kallisto. Transcripts per million values were then calculated using kallisto with default parameters for all of the GTEx RNA-seq samples (dbGaP version phs000424.v3.p1) from the following tissues: cerebellum (38 samples), cerebral cortex (31 samples), lung (133 samples), ovary (six samples), and testis (15 samples).
To experimentally determine relative expression of HYDIN and HYDIN2 in various tissues, we took advantage of a 15 bp deletion in exon 46 of HYDIN. Identical flanking sites were chosen for priming, so that relative expression of transcripts containing exon 46 could be measured in a single reaction. Expected band sizes were 321 bp for HYDIN and 306 bp for HYDIN2. A total of 5 μL of cDNA from various adult and fetal tissues normalized for expression level was used as template (Clonetech Human MTC Panel I, Human MTC Panel II, Human Fetal MTC Panel I (obtained from spontaneously aborted fetuses, aged 16–40 weeks)) and PCR was performed as per manufacturer’s instructions, with GAPDH as a positive control. Reactions were monitored by the level of SYBR Green I (Invitrogen) fluorescence using Bio-Rad MiniOpticon Real-Time PCR System. Reactions proceeded for 31 cycles of amplification (19 for GAPDH reactions) and PCR products were visualized by 20 min of electrophoresis using E-Gel EX Agarose Gels (4%; Invitrogen).
5' and 3' RACE were performed using the FirstChoice RLM-RACE Kit (Ambion) as per manufacturer’s instructions using the nested protocol on poly-A+ RNA derived from fetal brain (Clontech). Spliced ESTs in the HYDIN2 locus were taken as evidence of active transcription, and pileups of ESTs with shared edges were taken as evidence of potential sites of transcription initiation and termination and were chosen as targets for RACE. The ancestral paralog was also targeted as a positive control. PCR products including secondary bands were gel extracted and purified using the QIAquick Gel Extraction Kit (Qiagen) and capillary sequenced. In cases where RACE products did not include unique sequence, PCR products were purified using the QIAquick PCR Purification Kit (Qiagen) and cloned using the TOPO XL PCR Cloning Kit with OneShot TOP10 Chemically Competent E. coli (Invitrogen). Cells were streaked onto agar plates containing 50 μg/mL kanamycin and incubated overnight at 37 °C. Individual colonies were picked and subjected to colony PCR, where the insert was amplified using standard M13 forward and reverse primers. The PCR products were purified and sequenced as before. Unique nucleotide differences were used to infer the paralog of origin. Primers used can be found in Additional file 1: Table S7.
PacBio cDNA sequencing
cDNA was synthesized from poly-A+ RNA using oligo(dT) priming either SuperScript II or SuperScript III reverse transcriptase (Invitrogen) with the following modification: an extra 50 min was added to the reverse transcription incubation time following the addition of another 1 μL of enzyme. A total of 1 μL of from the cDNA synthesis reaction was used as template for nested PCR with Kapa HiFi PCR Kit. PCR amplicons were purified using magnetic beads (Agencourt AMPure XP, 1X concentration). Library preparation for PacBio sequencing of PCR amplicons was performed using standard and approved reagents and protocols. Two SMRT cells were sequenced: the first, which included amplicons spanning from new HYDIN2 promoter to exon 19 was run using P5C3 chemistry, the second, which included amplicons spanning from the new HYDIN2 promoter to exon 43, as well as intermediate fragments from exon 19 through beyond the 3′ duplication breakpoint, was run using P6C4 chemistry. Primers used can be found in Additional file 1: Table S7.
DNase I hypersensitivity (DHS) at HYDIN2 promoter
Chromatin accessibility, as measured by DHS, was assessed for evidence of regulatory activity of the new HYDIN2 promoter [65, 66]. Because standard DHS analysis pipelines discard multi-mapped reads and the HYDIN2 promoter sits in duplicated space, reads corresponding to DHS sites in fetal brain were remapped to a repeat-masked GRCh38 using mrsFAST-Ultra (version 3.3.11)  before being used to determine cut counts. Sample information including GEO accession numbers are shown in Additional file 1: Table S8.
MIP exon sequencing
Human reference sequence (GRCh37) of coding exons from the ancestral paralog only (+/– 5 bp) was used as input to design single-molecule MIPs  using MIPgen . Each MIP was designed to capture 112 bp of genomic sequence and included 40 bp unique to the target region (split between a ligation and an extension arm of the MIP), a universal 30 bp backbone, and a degenerate 8 bp molecular tag included on the extension arm. A total of 240 MIPs were designed to cover HYDIN. MIP phosphorylation, capture, and barcoding were performed as previously described . Briefly, oligos were pooled together at equal concentrations (100 uM), phosphorylated, and an 800:1 excess of oligos was used for the genomic DNA capture (100 ng). Capture reactions were incubated at 60 °C for 18 h. Finished libraries were pooled together and sequenced using either MiSeq (2 × 150 bp) or HiSeq2000 (2 × 101 bp). Probe sequences can be found in Additional file 3: Table S9.
We used the MIPgen data analysis pipeline to map and filter reads in fastq format to a minimal human reference containing only the region containing the ancestral HYDIN paralog (chr16:70821397-71282326) included in our MIP design with the remainder of the genome, including HYDIN2, masked out. This masking ensured reads mapped to only the ancestral paralog for proper variant annotation. Discovery variant calling was performed across the entire ASD cohort per pooled sequence set containing up to 384 samples using FreeBayes (https://github.com/ekg/freebayes) with the following command: freebayes -b < sorted_bams > -f < masked_reference > -t < targeted_regions > -F 0.07 -C 2 -n 4. We removed any variants with the following feature: trinucleotide or homopolymer repeat, read depth ≤10, quality score ≤20, or with no alleles using previously described methods . The resulting variant set was annotated using the Ensembl Variant Effect Predictor (VEP)  using the canonical transcript for each gene. Subsequently, for the ASD study, the complete list of coding variants was used to separately genotype cases and controls to assess overall frequency of events in each cohort: freebayes -b < sorted_bams > -f < masked_reference > -s < sample_list > -@ < variant_vcf > --only-use-input-alleles -F 0.07 -C 2 -n 4 --min-coverage 10.
Tests for selection
The full-length ancestral HYDIN sequence (NM_001270974) was used as a BLAST query to obtain sequenced HYDIN transcripts from other primates. All codons from HYDIN2 that could align with HYDIN were used. An MSA was generated using MAFFT and manually edited for obvious alignment errors. Bases aligning to the 15,366 nt ORF from human HYDIN were selected and a neighbor-joining tree was generated using MEGA. The alignment and tree were input into CODEML  and dN/dS values (omega) were estimated using the Nei-Gojobori method with pairwise deletion . Branch-based tests were performed by allowing additional branches to vary in their dN/dS parameter and comparing the log-likelihood to the nested model. p values were calculated by performing a Chi-square test (df = 2) on twice the difference between the log-likelihood values for different models considered.
HYDIN paralog-specific copy number genotyping using MIPs
HYDIN paralog-specific copy number was genotyped using a previously described method  with single-molecule MIPs . Briefly, MIPs were designed to SUNs distinguishing HYDIN paralogs (Additional file 3: Table S10). MIP capture, library preparation, massively parallel sequencing, and data analysis allowed quantification of reads derived from each HYDIN paralog over each MIP target for each individual. These data were input to a program that output paralog-specific copy number calls and detected duplications, deletions, and interlocus gene conversion events. MIP data for each individual was visualized by plotting paralog-specific HYDIN copy number point estimates across the spatial extent of sequence shared between paralogs. These estimates were calculated at each MIP target by multiplying paralog-specific HYDIN read count relative frequencies by corresponding aggregate HYDIN copy number estimates called by the genotyping program. The algorithmic details of this program have been previously described . In this case, the program considered 25 possible hidden underlying HYDIN paralog-specific copy number states, where both HYDIN and HYDIN2 were allowed to possibly have copy numbers in the range of 0–4 (5 × 5 = 25 combinations). To enable detection of internal events, highest scoring paths through likelihood-based graphs allowing 0, 1, and 2 transitions between copy number states were considered, with the same biologically motivated restrictions on permitted transitions as previously detailed. Prior probabilities were set to reflect the observation that most humans have two copies of both HYDIN paralogs, with log-likelihoods of –15, –7.5, 0, –7.5, and –15 assigned to initial single-paralog copy number states of 0, 1, 2, 3, and 4, respectively. Probe sequences can be found in Additional file 3: Table S10.
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We thank K. Munson and M. Malig for their experimental support with the sequencing of BAC clones and K. Penewit for the experimental support on the MIP-based sequencing assay. We would also like to thank H. Mefford for the helpful discussions and support on analyzing the 1q21 patients. We also thank T. Brown for the critical review of the manuscript.
This work was supported, in part, by the US National Institutes of Health (1R01HG002385 to EEE, F30HG009478 to MLD, and R00NS083627 to MYD) and the UW Medical Scientist Training Program (MLD and MHD). This study was supported by a grant from the Italian Ministry of University and Research-MIUR (Project “Futuro in ricerca” 2010 RBFR103CE3). OP is a recipient of a Human Frontier Science Program postdoctoral fellowship. XN was supported by a US National Science Foundation Graduate Research Fellowship under grant DGE-1256082. EEE is an investigator of the Howard Hughes Medical Institute.
Availability of data and materials
Raw sequencing data from PacBio RT-PCR experiments can be found at the Sequence Read Archive (SRA) under BioProject PRJNA359986. Mapped MIP-based sequencing data can be found under SRA BioProject PRJNA356308. BAC sequences can be accessed under GenBank accession numbers AC275446 (chimpanzee) and AC212876 (orangutan).
Conception and design: MLD, XN, MYD, EEE; Acquisition of data: MLD, XN, CB, LH, MHD, MV, FA, RS, MYD; Data analysis: MLD, XN, OP, BJN, JH, MYD; Manuscript: MLD, XN, EEE. MLD and XN contributed equally to this work. All authors read and approved the final manuscript.
EEE is on the scientific advisory board (SAB) of DNAnexus, Inc. and is a consultant for Kunming University of Science and Technology (KUST) as part of the 1000 China Talent Program (2014-2016).
Consent for publication
Ethics approval and consent to participate
The human samples included in this study did not meet the U.S. federal definitions for human subjects research. All samples were publicly available or encoded, with no individual identifiers available to the study authors. Samples were collected at respective institutions after receiving informed consent and approval by the appropriate institutional review boards. There are no new health risks to participants. Samples that fall within this category include probands with autism and their parents from the SSC, AGRE, and TASC cohorts and individuals from representative human populations from the 1000 Genomes Project.
HYDIN and associated chromosome 1 duplications, Figure S2A. Timing of first duplication of the 5' and 3' segments flanking HYDIN2, Figure S2B. Timing of second duplication of the 5' and 3' segments flanking HYDIN2, Figure S3. Paralog-specific copy number estimates for 236 individuals from the Human Genome Diversity Project (HGDP), Figure S4. HYDIN internal structural variation and interlocus gene conversion, Figure S5. 1q21 rearrangement breakpoint variability, Figure S6. The HYDIN2 promoter corresponds to a peak of chromatin accessibility in fetal brain, Table S1. MIP-based copy-number genotyping of HYDIN2, Table S2. HYDIN duplication, deletion, and interlocus gene conversion events, Table S3. Locations of other copies of the HYDIN2 promoter-associated duplication, their relationship to NBPF, and evidence for transcription, Table S4. Pairwise dN/dS values for HYDIN in primates, Table S5. Likely gene-disruptive events detected in HYDIN/HYDIN2 by MIP-based sequencing of exons, Table S6. Phenotypes for patients having atypical chromosome 1q21 rearrangements, Table S7. Primers used in RACE and RT-PCR experiments, and Table S8. Fetal brain DNase I hypersensitivity samples with GEO accession numbers. (DOCX 5908 kb)
Measured HYDIN2 isoforms (.fasta). Fasta file of transcripts used for expression measurements. (FASTA 34 kb)
Molecular inversion probe (MIP) sequences used for exon sequencing (Table S9) and copy number genotyping (Table S10). (XLSX 74 kb)
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Dougherty, M.L., Nuttle, X., Penn, O. et al. The birth of a human-specific neural gene by incomplete duplication and gene fusion. Genome Biol 18, 49 (2017) doi:10.1186/s13059-017-1163-9
- Segmental duplication
- Duplicate genes
- Gene fusion
- Long-read sequencing
- 1q21 microdeletion/microduplication syndrome