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A Large Expansion of the HSFY Gene Family in Cattle Shows Dispersion across Yq and Testis-Specific Expression

Heat shock transcription factor, Y-linked (HSFY) is a member of the heat shock transcriptional factor (HSF) family that is found in multiple copies on the Y chromosome and conserved in a number of species. Its function still remains unknown but in humans it is thought to play a role in spermatogenesis. Through real time polymerase chain reaction (PCR) analyses we determined that the HSFY family is largely expanded in cattle (∼70 copies) compared with human (2 functional copies, 4 HSFY-similar copies). Unexpectedly, we found that it does not vary among individual bulls as a copy number variant (CNV). Using fluorescence in situ hybridization (FISH) we found that the copies are dispersed along the long arm of the Y chromosome (Yq). HSFY expression in cattle appears restricted to the testis and its mRNA correlates positively with mRNA markers of spermatogonial and spermatocyte cells (UCHL1 and TRPC2, respectively) which suggests that HSFY is expressed (at least in part) in early germ cells.


Introduction
The Y chromosome was originally thought to be devoid of functional genes because of its small size and heterochromatic nature [1]. This theory has since been disproven and now about 78 protein-encoding genes have been assigned to this chromosome in humans, most of which are involved in male growth, development and spermatogenesis [2,3]. The Y chromosome is unique in that the majority of its length does not pair with the X chromosome during meiosis to undergo homologous recombination [2]. This region is known as the male specific region or MSY [2]. The MSY is enriched with multi-copied genes and copy number variants (CNVs) [2,4]. CNVs are DNA segments of at least 1 kb in size that can vary in copy number among individuals through deletions and duplications and in many cases this variation has been linked to gene expression and phenotype [5][6][7][8]. Although there is still a lack of sequence data for the MSY, it has been fully sequenced in both human and chimpanzees and even between these closely related species, it shows enormous (and somewhat unexpected) diversity [9]. This diversity manifests itself in gene structure, content and number of gene copies.
An example of a multi-copied MSY gene is HSFY. It is a member of the heat shock transcriptional factor (HSF) family which are able to bind heat shock elements on heat shock protein (HSP) genes to regulate gene expression [10]. HSPs are important mediators of stress and act as molecular chaperones to regulate cellular homeostasis and promote cell survival in conditions that would otherwise be fatal [11,12].
HSFY contains a heat shock factor type A DNA-binding domain that is similar to that found in other HSF genes, including the X-homologue (LW-1) [13][14][15]. Its three-dimensional conformation, however, is altered so it is unknown if HSFY can act as a transcriptional regulator [13,14]. Its expression is reported to be mainly testis-specific in humans [15]. More specifically, HSFY expression seems restricted to Sertoli and spermatogenic cells [14]. It is likely that HSFY is involved in spermatogenesis but its exact function remains unknown [14][15][16][17].
The copy number of HSFY appears to vary between species. It has been measured in humans and felines and is present in 2 and about 8 copies, respectively [2,18]. HSFY orthologs have been found in a variety of other species including mouse, rat, rhesus macaque, and dogs and appears to be conserved, however, the gene copy number in these species has not yet been characterized [16,19]. Cattle have an HSFY ortholog (HSFY2) and it has been hypothesized that it is present in multiple copies but this theory remains speculative and no attempt has been made to characterize the number of copies [20].
The purpose of this study was to determine the exact genomic copy number of the HSFY family in different individuals, determine its chromosomal location and to determine its expression pattern in Canadian Holstein cattle. We found that bulls contain around 70 copies of the HSFY gene which are dispersed along the long arm of the Y chromosome and we provide evidence that HSFY expression is testis-specific.

HSFY gene analysis and sequencing
A comprehensive search of the sequence database on the NCBI website was carried out in order to find and compare HSFY orthologs among different species. Structural similarities between deduced amino acid sequences among human HSFY sequences (hHSFY1: NP_149099.2; hHSFY2: NP_714927.1), as well as mouse (mHSFYL: NP_081937.1), rat (NP_001012132.1), rhesus macaque (ACL51668.1), cat (NP_001035212.1), and bovine (NP_001070474.1) were determined by multiple sequence alignments carried out using CLUSTAL W software [21]. The current bovine HSFY sequence (HSFY2: NW_001498001.1) is based on the Hereford breed of cattle and was assembled as part of the bovine genome project (Assembly Btau_4.2) [22]. We deduced the HSFY gene sequence in the Holstein breed by sequencing the PCR products that were generated throughout the study (as described below) and the resultant sequence was deposited into GenBank with accession number JF281100. Breed specific differences were analyzed by comparing the predicted Holstein amino acid sequence with the current predicted HSFY amino acid sequence derived from the Hereford breed using CLUSTAL W software.
Sample collection and DNA/cDNA preparation A variety of tissues (blood, heart, kidney, liver, lung, ovary, testis) were obtained from a bank of tissues (L'Alliance Boviteq Inc., St Hyacinthe, Quebec, Canada) collected from a slaughtered Holstein heifer and from 24 slaughtered Holstein bulls. DNA was extracted using methods previously described [23]. Briefly, DNA was extracted from blood samples using standard phenolchloroform methods. Total mRNA was extracted from the remaining tissues using a RNeasy Mini kit (QIAGEN Inc.) and treated with DNAse I (TURBO DNA-free, Ambion Inc.) following

Quantitative PCR
The gene sequences used to design all primer sets were accessed from the sequence database on the NCBI website and their accession numbers are listed in Table 1. Primers were designed for these sequences using Primer3 software [25]. Three sets of primers (designated HSFY8, HSFY10, HSFY16) targeting different regions of HSFY were used relative to the single copy reference gene, SRY, to measure HSFY copy number ( Figure 1, Table 1). A separate set of primers targeting HSFY mRNA (designated HSFYRNA) was designed to span an intron to ensure cDNA specificity ( Figure 1, Table 1). Primers targeting the mRNA specific markers for spermatogonia and spermatocytes, UCHL1 and TRPC2, respectively and the reference gene, GAPDH, were also used in the mRNA experiments [26,27]. To ensure malespecificity, both male and female DNA were run with the HSFY primers as well as an autosomal gene, ZAR1 (Table 1). Melting curve analyses, gel electrophoresis and PCR product sequencing (University of Guelph Laboratory Services, Guelph, ON, Canada) were used to verify amplification of the correct target genes.
1 ng of DNA and 50 ng of the reverse transcription product (cDNA) were analyzed by real time PCR as described previously [23]. Briefly, the real time PCR was performed using a LightCycler 1.5 apparatus (Roche Diagnostics) and a LightCycler Fast Start DNA Master SYBR Green I kit (Roche Diagnostics). The primer and MgCl 2 concentrations were 0.5 mM and 3 mM, respectively. Samples were run in triplicate. The DNA samples were analyzed with two separate PCR runs that were averaged to minimize variability.
A calibrator sample was included in each run to minimize interrun variability [28]. Primer efficiencies were measured according to the equation E = 10 [21/slope] [29]. Normalized ratios were determined for all runs using the 2 2DDCT method (PE Applied Biosystems, Perkin Elmer, Forster City, CA) for DNA runs and the Pfaffl method of quantification for the cDNA runs [30]. HSFY copy number of the calibrator sample was determined with the 2 2DCT method using three sets of primers and averaged.
For statistical analyses all data first underwent the Kolmogorov-Smirnov test of normality. To determine differences between groups, we performed one way analysis of variance (ANOVA). All correlations were analyzed with a Pearson's correlation coefficient. Data is reported as the mean 6 SEM unless otherwise stated. A Figure 1. Schematic bovine HSFY gene and targeted regions of the primers used for the PCR experiments. The numbered boxes represent the gene exons and the adjoining line represents the intron. Primer sets HSFY8F/HSFY8R (111 bp), HSFY10F/HSFY10R (113 bp), and HSFY16F/HSFY16R (102 bp) were used to measure HSFY copy number with real time PCR and target individual exons. Primer set HSFYRNAF/ HSFYRNAR (215 bp) was designed specifically for mRNA amplification: HSFYRNAF targets exon 1 and HSFYRNAR targets exon 2 and together they span an intron to avoid co-amplification of residual DNA. The three primer sets shown below the schematic HSFY gene were used to create PCR probes for the fluorescence in situ hybridization (FISH) experiments and they target the full gene (including both exons and the intron: HSFY-E1F/ HSFY-E2R, 1686 bp), exon 1 (HSFY-E1F/HSFY-E1R, 515 bp) and exon 2 (HSFY-E2F/HSFY-E2R, 752 bp). Primer sequences are listed in Table 1 p-value of less than 0.05 is considered significant. The data was analyzed using GraphPad Prism (version 5.02) software (Graph-Pad Software, Inc., San Diego, CA).
The FISH experiments were performed with standard protocols, briefly: slides were treated with pepsin, dehydrated in ethanol series, denatured at 72uC for 1 minute in 70% formamide (Fisher)/26SSC, then quenched in ice-cold ethanol. Hybridization occurred at 37uC overnight, followed by 5 minute washes in 26SSC, 0.26SSC twice at 37uC and PBS/0.5% Tween 20 at room temperature. Biotinylated signals were visualized by a single layer of FITC-avidin (Vector, 1:400 in PBS/0.5% Blocking Reagent, (Roche)) incubated for 30 minutes at 37uC and washed by 36(PBS/0.5% Tween 20) at room temperature. Chromosomes were counterstained with DAPI (Sigma-Aldrich) and slides were mounted with Vectashield (Vector). Images were captured using a Leica DM5500B fluorescence microscope (Leica), equipped with a Retiga Exi Fast (QImaging) cooled digital camera.

HSFY sequencing
A comprehensive search of the NCBI website revealed a bovine HSFY ortholog, HSFY2 (Entrez Gene ID: 767933). The genomic sequence of this gene was published as part of the bovine genome project (based on Btau_4.2; NW_001498001.1) and derived from the Hereford breed of cattle [22]. The complete mRNA coding sequence (NM_001077006.1) and predicted protein sequence (NP_001070474.1) were also available for Hereford cattle in the database.
HSFY protein sequence alignments had been previously performed in human, mouse and cow, however, detailed percent homologies had not yet been described [16]. For this study, the alignments were expanded to include both copies of HSFY in human (hHSFY1 and hHSFY2) as well as the HSFY sequences of mouse, rat, rhesus macaque, cat and cow. Comparisons of sequence homologies for the complete HSFY protein as well as the conserved HSF-type DNA-binding domain for all species are presented in Table 2. Figure 2 shows the alignment results of the   conserved HSF-type DNA-binding domain among different species. Both copies of human HSFY (HSFY1 and HSFY2) were found to encode identical proteins (100% homology). Overall, cattle show 51% sequence homology with human HSFY and within the conserved DNA-binding domain the homology is increased to 72%. It showed its highest sequence identity with cat, with percent homologies of 58% and 81%, for the complete protein and HSF-type DNA-binding domain, respectively. The complete HSFY gene sequence was deduced in Holstein and submitted to GenBank (accession number: JF281100). The Holstein HSFY genomic sequence was found to differ with the Hereford HSFY sequence by two nucleotides (c.56G.A, c.1192A.C). The published Hereford mRNA sequence, however, also shows the first discrepancy with the Hereford genomic sequence (c.56G.A) and therefore this one mismatch likely represents a genomic sequencing error. Our Holstein genomic sequence matches the Hereford mRNA sequence at this position. The second point mutation we found (c.1192A.C) is consistently different from both the Hereford genomic and mRNA sequences currently deposited on the NCBI database. This mutation results in a substitution from tyrosine (Hereford) to serine (Holstein) at position 266 of the predicted HSFY protein (p.Tyr266Ser). An alignment of the predicted amino acid sequences for both Hereford and Holstein cattle is shown in Figure 3.

HSFY gene copy number
Primer efficiencies were tested and were not found to be significantly different among targets (HSFY8, HSFY10, HSFY16) and the reference gene (SRY). We used the HSFY primers on both male and female DNA samples and as expected we found amplification in the male samples only whereas ZAR1, which is an autosomal gene, was present in both ( Figure 4). Three separate HSFY primers targeting different regions of the gene were used to measure HSFY copy number in the calibrator sample. There were no significant differences in HSFY copy number measured with the three different primers ( Figure 5). The average HSFY copy number of the calibrator sample was 70.860.9 copies. We selected the HSFY8 primers to analyze the full sample set (n = 24) and found that HSFY copy number did not vary significantly from bull to bull (Table 3). The average HSFY copy number amongst all bulls measured was 73.360.8 and this value did not differ significantly with that of the calibrator. All data was normally distributed. The fertility status of the bulls ranged from an NRR of 49.6%-77.3% with an average of 65.9% but showed no significant correlation to HSFY copy number or mRNA levels (Table 3).

Fluorescence in situ hybridization
All three different FISH probes generated an intense, specific, yet dispersed signal on the Y chromosome. The signals were  almost chromosome painting probe-like and labeled the majority of the q-arm of the Y chromosome ( Figure 6). There were no differences in the hybridization pattern between the probes.

HSFY expression
An analysis of a variety of different tissues (heart, kidney, liver, lung, ovary and testis) showed expression only in the testis for both HSFYRNA primers (spans intron 1) and HSFY8 primers (specific to exon 1) (Figure 7). GAPDH was present in all tissues.
For the bulls for which we had testis tissue samples (n = 22) we measured HSFY expression relative to GAPDH. We found significant bull-to-bull variation of HSFY mRNA levels (p,0.0001). We also found significant correlations of HSFY mRNA levels to UCHL1 (r = 0.4832, p = 0.0227) and TRPC2 (r = 0.6966, p = 0.0003) which are mRNA markers of spermatogonial and spermatocyte cells, respectively [26,27]. There was no correlation between HSFY copy number and HSFY mRNA levels (p = 0.3171).

HSFY copy number
The sex chromosomes are thought to have originated from a pair of ancestral autosomes and although the X chromosome still remains highly homologous between species, the Y chromosome underwent a series of drastic inversions and species-dependent rearrangements that led to the current Y chromosome being highly heterogeneous in both size as well as in the genetic makeup among species [9,20,[31][32][33]. Recently it has been shown that even closely related mammals such as humans and chimpanzees show enormous diversity in the MSY of their Y chromosomes for both structure and gene content [9].
One purpose of this study was to characterize the gene copy number of an MSY gene, HSFY, in bulls and determine whether or not it varies between individuals as a copy number variant (CNV). Since this study did not address how many of the copies are actually functional, we classify the copies found here under the common distinction of ''HSFY family''. Since we found no amplification signal in female, we can be sure that the HSFY copies we are analyzing are specific to the Y chromosome and are not found on autosomes or the X chromosome ( Figure 4). This is the first study to estimate the number of HSFY family gene copies in cattle. We found that there are approximately 73 copies of the HSFY family genes on the Y chromosome. Our findings confirm the suggestion that HSFY is multi-copied in cattle [20]. The copy number is greatly expanded when compared to what has been reported in humans (2 functional copies, 4 HSFYsimilar copies (,82% homology to HSFY)) and cat (8 functional copies, unknown HSFY-similar copies) [15,18]. Other species have not yet been characterized.
The fact that we found this gene family to be multi-copied and largely expanded as compared to humans is not unusual for the Y chromosome. TSPY is another example of a multi-copy gene that shows expansion in cattle as compared to humans. Cattle have between 37-200 copies, while humans only vary from 20 to76 copies [2,23,34,35]. It is therefore possible that other genes, like HSFY, could also show expansions in cattle. Interestingly, the Y chromosome of the domestic cat appears to be made up almost entirely of multi-copied genes and even typically single copy genes such as SRY might be present in up to 4 copies [18]. This further demonstrates the extreme heterogeneity of the Y chromosome among species. Not all genes, however, show expansion in cattle. There are some single copy genes present on the bulls' Y chromosome such as SRY, ZFY and EIF1AY that are also found in single copy in humans [20,36,37].
We found that the genomic copy number of HSFY did not change significantly from bull to bull and therefore it does not appear to exist as a CNV. Deletions of HSFY copies in humans have been implicated in cases of male infertility [14,17,38,39]. The bulls in this study had differences in fertilities, as measured by nonreturn rates (NRRs), ranging from low fertility (NRR = 49.6%) to high fertility (NRR = 77.6%), but regardless of the bulls' fertility status, their HSFY copy number stayed relatively constant. The difference may be that humans have only 2 copies of this gene and a deletion in one or both copies can have severe impacts on fertility. Cattle, on the other hand, have about 73 copies of HSFY which may allow for many ''backups'' in case one or more of the copies undergo mutations, thereby minimizing/eliminating harmful effects on fertility.

Localization of HSFY by FISH
Fluorescence in situ hybridization confirmed the results of the molecular copy number determination and localized it on the Y chromosome for the first time. The largest PCR produced probe, spanning the whole gene (1686 bp) generated an intense hybridization signal which covered almost the whole long arm of the Y chromosome ( Figure 6). This suggests amplification of the targeted sequence and the presence of dispersed multiple copies. To test whether the gene specific sequences or an unknown highly repetitive element in the intron caused the observed signal distribution, we amplified the two exons specifically with PCR and used these as FISH probes as well. Both small probes (515 bp and 752 bp) generated the same hybridization pattern (Figure 6), thus we could exlude the contribution of intronic sequences.

HSFY expression
Notably, we found testis-specific expression of HSFY in cattle, as is seen predominantly for human HSFY [2,15]. Both human and feline studies have shown that many multi-copied Y chromosomal genes have acquired testis-specific expression and function so it is not surprising that we also found testis-specific expression of HSFY in cattle [2,19,40,41]. It is theorized that the evolution of multicopied genes in the MSY allows for conservation of genes that enhance spermatogenesis as well as allow for a high level of expression of these genes through gene dosage effects [2,41]. Since we did not find evidence of a connection between HSFY mRNA levels and copy number, there is likely no dosage effects associated with this gene, but it is possible that its multi-copied nature may represent a mechanism of gene conservation. The mRNA levels of HSFY varied significantly between bulls (p,0.0001) and correlated positively with mRNA markers of both spermatogonial and spermatocyte cells. This suggests that HSFY is being expressed in spermatogenic cells, as it is in humans, however further immunohistochemical analysis would be necessary to make firm conclusion about its distribution [14].
In conclusion, we found the HSFY family to be largely expanded as compared to other species studied to date and it is present in about 70 copies. While it does appear to be a multi-copy gene, it does not appear to be a copy number variant, because the gene copy number did not change within our Canadian Holstein bull sample set of over 20 bulls. FISH results showed that the copies are dispersed across the entire long arm of the Y chromosome. An analysis of mRNA showed its expression is testis-specific, like many other MSY genes, and its expression may be localized to spermatogenic cells as it is in humans.