Characterization of two porcine endogenous retrovirus integration loci and variability in pigs

The pig (Sus scrofa) is a potential organ donor for man but porcine endogenous retroviruses (PERVs) represent an important concern for patients, and identification or engineering of PERV-free pigs suitable for xenotransplantation is a major undertaking. Consequently, studies of variability in pigs for the presence of PERVs at specific loci are a prerequisite. We identified genomic flanking sequences of two PERVs cloned in bacterial artificial chromosomes, a replication-competent PERV-A at locus 1q2.4 and a defective PERV-B at locus 7p1.1–2. PERV-A is embedded in the second repeat of a tandem of eight 190 bp repeats. A short duplicated 4 bp cellular motif, AGAC, was found at each flank of PERV-A and a degenerate 4 bp motif was found for PERV-B. At each locus, the PERV flanks matched expressed sequence tags available in public databases. Primer pairs were designed to amplify either genomic flanks or PERV-genomic junctions. Polymerase chain reaction screening was performed on pigs from 11 distinct Chinese breeds and from the European Large White breed. PERV-B at locus 7p1.1–2 was detected in all animals whereas the presence of PERV-A at locus 1q2.4 was variable. Our results suggest that a genetic selection can be designed to identify animals lacking a potentially active PERV at a specific locus and that Chinese and European pig breeds represent large biodiversity reservoirs to explore. Our results point also to the existence of PERVs that might be fixed in the pig genome, and that might not be eliminated by classical genetic selection.Accession numbers: Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under Accession numbers AY160111–AY160114     

Characterizing and mapping porcine endogenous retroviruses in Westran pigs

Since porcine endogenous retroviruses (PERVs) can infect cultured human cells, they are a potential hazard to xenotransplantation. For this reason, endogenous retroviruses from the Westran (Westmead Hospital transplantation) inbred line of pigs were analyzed by using consensus primers for the type A and type B viruses to amplify 1.8-kb envelope gene fragments. After preliminary analysis with restriction enzymes KpnI and MboI, 31 clones were sequenced. Between types A and B, five recombinant clones were identified. Fifty-five percent of clones (17 of 31) had premature stop codons within the envelope protein-encoding region. Endogenous retroviruses in Westran pigs were physically mapped by fluorescence in situ hybridization (FISH) using PERV-A and PERV-B envelope clones as probes to identify at least 32 integration sites (19 PERV-A sites and 13 PERV-B sites). The chromosomal sites of integration in the Westran strain are quite different from those in the European Large White pig. The recombinant clones suggest that defective PERVs could become infective through recombination and further that PERVs might recombine with human endogenous retroviruses in xenotransplants.     

Analysis of natural recombination in porcine endogenous retrovirus envelope genes

Human tropic Porcine Endogenous Retroviruses (PERVs) are the major concern in zoonosis for xenotransplantation because PERVs cannot be eliminated by specific pathogen-free breeding. Recently, a PERV A/C recombinant with PERV-C bearing PERV-A gp70 showed a higher infectivity (approximately 500-fold) to human cells than PERV-A. Additionally, the chance of recombination between PERVs and HERVs is frequently stated as another risk of xenografting. Overcoming zoonotic barriers in xenotransplantation is more complicated by recombination. To achieve successful xenotransplantation, studies on the recombination in PERVs are important. Here, we cloned and sequenced proviral PERV env sequences from pig gDNAs to analyze natural recombination. The envelope is the most important element in retroviruses as a pivotal determinant of host tropisms. As a result, a total of 164 PERV envelope genes were cloned from pigs (four conventional pigs and two miniature pigs). Distribution analysis and recombination analysis of PERVs were performed. Among them, five A/B recombinant clones were identified. Based on our analysis, we determined the minimum natural recombination frequency among PERVs to be 3%. Although a functional recombinant envelope clone was not found, our data evidently show that the recombination event among PERVs may occur naturally in pigs with a rather high possibility.     

Construction of a swine BAC library: application to the characterization and mapping of porcine type C endoviral elements.

A porcine bacterial artificial chromosome (BAC) library was constructed using the pBeloBAC11 vector. It comprised 107,520 clones with an average insert size of 135 kb, representing an almost fivefold coverage of the swine haploid genome. Screening of the library allowed recovery of one to eight clones for 142 unique markers located all over the genome, while it failed for only one marker. About 4% chimeric clones were found. The library was also screened for the protease gene of type C porcine endoviral sequences (PERVs), and 62 clones were recovered, all but two of which contained one protease gene. We found 20 protease sequences (PERV-1 to PERV-20) which, despite differing by point mutations, were all coding sequences. The most frequent sequence, PERV-2, was 100% similar to a protease sequence expressed in the porcine PK-15 cell line. Most of the clones harbored envelope genes. Thirty-three BAC clones were mapped by fluorescence in situ hybridization to 22 distinct locations on 14 chromosomes, including the X and Y chromosomes. These overall results indicate that there is generally one PERV copy per integration site. Although PERV sequences were not tandemly arranged, clusters of integration sites were observed at positions 3p1.5 and 7p1.1. Southern blot experiments revealed 20-30 PERV copies in the Large White pig genome studied here, and variations in PERV content among pigs of different breeds were observed. In conclusion, this BAC collection represents a significant contribution to the swine large genomic DNA cloned insert resources and provides the first detailed map of PERV sequences in the swine genome. This work is the first step toward identification of potential active sites of PERV elements.     

Absence of replication-competent human-tropic porcine endogenous retroviruses in the germ line DNA of inbred miniature Swine

The potential transmission of porcine endogenous retroviruses (PERVs) has raised concern in the development of porcine xenotransplantation products. Our previous studies have resulted in the identification of animals within a research herd of inbred miniature swine that lack the capacity to transmit PERV to human cells in vitro. In contrast, other animals were capable of PERV transmission. The PERVs that were transmitted to human cells are recombinants between PERV-A and PERV-C in the post-VRA region of the envelope (B. A. Oldmixon, J. C. Wood, T. A. Ericsson, C. A. Wilson, M. E. White-Scharf, G. Andersson, J. L. Greenstein, H. J. Schuurman, and C. Patience, J. Virol. 76:3045-3048, 2002); these viruses we term PERV-A/C. This observation prompted us to determine whether these human-tropic replication-competent (HTRC) PERV-A/C recombinants were present in the genomic DNA of these miniature swine. Genomic DNA libraries were generated from one miniature swine that transmitted HTRC PERV as well as from one miniature swine that did not transmit HTRC PERV. HTRC PERV-A/C proviruses were not identified in the germ line DNAs of these pigs by using genomic mapping. Similarly, although PERV-A loci were identified in both libraries that possessed long env open reading frames, the Env proteins encoded by these loci were nonfunctional according to pseudotype assays. In the absence of a germ line source for HTRC PERV, further studies are warranted to assess the mechanisms by which HTRC PERV can be generated. Once identified, it may prove possible to generate animals with further reduced potential to produce HTRC PERV.     

Determinants of high titer in recombinant porcine endogenous retroviruses

Porcine endogenous retroviruses (PERVs) pose a potential stumbling block for therapeutic xenotransplantation, with the greatest threat coming from viruses generated by recombination between members of the PERV subgroup A (PERV-A) and PERV-C families (PERV-A/C recombinants). PERV-A and PERV-B have been shown to infect human cells in culture, albeit with low titers. PERV-C has a more restricted host range and cannot infect human cells. A recombinant PERV-A/C virus (PERV-A14/220) contains the PERV-A sequence between the end of pol and the middle of the SU region in env. The remaining sequence is derived from PERV-C. PERV-A14/220 is approximately 500-fold more infectious than PERV-A. To determine the molecular basis for the increased infectivity of PERV-A14/220, we have made a series of vector constructs. The primary determinant for the enhanced replicative potential of the recombinant virus appeared to be the env gene. Using a series of chimeric env genes, we could identify two determinants of high infectivity; one was an isoleucine to valine substitution at position 140 between variable regions A and B, and the other lies within the proline rich region. Taken together, these results show that the novel juxtaposition of env gene sequences enhanced the infectivity of PERV-A14/220 for human cells, perhaps by stabilization of the envelope glycoprotein or increased receptor binding.     

Evidence and consequence of porcine endogenous retrovirus recombination

The genetic nature and biological effects of recombination between porcine endogenous retroviruses (PERV) were studied. An infectious molecular clone was generated from a high-titer, human-tropic PERV isolate, PERV-A 14/220 (B. A. Oldmixon, et al. J. Virol. 76:3045-3048, 2002; T. A. Ericsson et al. Proc. Natl. Acad. Sci. USA 100:6759-6764, 2003). To analyze this sequence and 15 available full-length PERV nucleotide sequences, we developed a sequence comparison program, LOHA(TM) to calculate local sequence homology between two sequences. This analysis determined that PERV-A 14/220 arose by homologous recombination of a PERV-C genome replacing an 850-bp region around the pol-env junction with that of a PERV-A sequence. This 850-bp PERV-A sequence encompasses the env receptor binding domain, thereby conferring a wide host range including human cells. In addition, we determined that multiple regions derived from PERV-C are responsible for the increased infectious titer of PERV-A 14/220. Thus, a single recombination event may be a fast and effective way to generate high-titer, potentially harmful PERV. Further, local homology and phylogenetic analyses between 16 full-length sequences revealed evidence for other recombination events in the past that give rise to other PERV genomes that possess the PERV-A, but not the PERV-B, env gene. These results indicate that PERV-A env is more prone to recombination with heterogeneous backbone genomes than PERV-B env. Such recombination events that generate more active PERV-A appear to occur in pigs rather frequently, which increases the potential risk of zoonotic PERV transmission. In this context, pigs lacking non-human-tropic PERV-C would be more suitable as donor animals for clinical xenotransplantation.     

Isolation and characterization of an infectious replication-competent molecular clone of ecotropic porcine endogenous retrovirus class C

Xenotransplantation of pig organs is complicated by the existence of polytropic replication-competent porcine endogenous retroviruses (PERV) capable of infecting human cells. The potential for recombination between ecotropic PERV-C and human-tropic PERV-A and PERV-B adds another level of infectious risk. Proviral PERV-C were characterized in MAX-T cells derived from d/d haplotype miniature swine. Three proviruses were cloned from a genomic library. Clone PERV-C(1312) generated infectious particles after transfection into porcine ST-IOWA cells. Electron microscopy revealed the same morphologies of virions in MAX-T cells and in ST-IOWA cells infected with cell-free PERV-C(1312) particles, indicating that MAX-T cells harbor one functional PERV-C provirus.     

Detailed Mapping of Determinants within the Porcine Endogenous Retrovirus Envelope Surface Unit Identifies Critical Residues for Human Cell Infection within the Proline-Rich Region

Replication-competent porcine endogenous retroviruses (PERVs) are either human cell tropic (PERV-A and PERV-B) or non-human cell tropic (PERV-C). We previously demonstrated that PERV in vitro cell tropism is modulated by 2 residues within the C terminus of SU and that the PERV receptor binding domain (RBD) extends beyond the variable regions A and B (VRA and VRB, respectively), to include the proline rich-region (PRR) of SU (M. Gemeniano et al., Virology 346:108-117, 2000; T. Argaw et al., J. Virol. 82:7483-7489, 2008). The present study aimed to identify the specific elements within the PERV RBD that interact with the C-terminal elements of SU to facilitate human cell infection. We constructed a series of chimeric and mutated envelopes between PERV-A and PERV-C and using pseudotyped retroviral vectors to map the human cell tropism-determining sequences within the PERV RBD. We show that the PRR from PERV-A is both necessary and sufficient to allow human cell infection when substituted into the homologous region of the PERV-C envelope carrying two C-terminal amino acid substitutions shown to influence human cell tropism, Q374R and I412V (PERV-Crv). Furthermore, substitution of a single amino acid residue in the PRR of the non-human-tropic PERV-Crv envelope allows vectors carrying this envelope to infect human cells. Receptor interference assays showed that these modified PERV-C envelopes do not bind either of the human PERV-A receptors, suggesting the presence of a distinct human PERV-C receptor. Finally, vectors carrying these modified PERV-C envelopes infect primary human endothelial cells, a cell type likely to be exposed to PERV in clinical use of certain porcine xenotransplantation products.     

Identification of exogenous forms of human-tropic porcine endogenous retrovirus in miniature Swine

The replication of porcine endogenous retrovirus subgroup A (PERV-A) and PERV-B in certain human cell lines indicates that PERV may pose an infectious risk in clinical xenotransplantation. We have previously reported that human-tropic PERVs isolated from infected human cells following cocultivation with miniature swine peripheral blood mononuclear cells (PBMC) are recombinants of PERV-A with PERV-C. Here, we report that these recombinants are exogenous viruses in miniature swine; i.e., they are not present in the germ line DNA. These viruses were invariably present in miniature swine that transmitted PERV to human cells and were also identified in some miniature swine that lacked this ability. These data, together with the demonstration of the absence of both replication-competent PERV-A and recombinant PERV-A/C loci in the genome of miniature swine (L. Scobie, S. Taylor, J. C. Wood, K. M. Suling, G. Quinn, C. Patience, H.-J. Schuurman, and D. E. Onions, J. Virol. 78:2502-2509, 2004), indicate that exogenous PERV is the principal source of human-tropic virus in these animals. Interestingly, strong expression of PERV-C in PBMC correlated with an ability of the PBMC to transmit PERV-A/C recombinants in vitro, indicating that PERV-C may be an important factor affecting the production of human-tropic PERV. In light of these observations, the safety of clinical xenotransplantation from miniature swine will be most enhanced by the utilization of source animals that do not transmit PERV to either human or porcine cells. Such animals were identified within the miniature swine herd and may further enhance the safety of clinical xenotransplantation.     

Comparison of replication-competent molecular clones of porcine endogenous retrovirus class A and class B derived from pig and human cells

Vertically transmitted endogenous retroviruses pose an infectious risk in the course of pig-to-human transplantation of cells, tissues, and organs. Two classes of polytropic type C porcine endogenous retroviruses (PERV) which are infectious for human cells in vitro are known. Recently, we described the cloning and characterization of replication-competent PERV-B sequences from productively infected human cells (F. Czauderna, N. Fischer, K. Boller, R. Kurth, and R. R. Tönjes, J. Virol. 74:4028–4038, 2000). Here, we report the isolation of infectious molecular PERV-A and PERV-B clones from pig cells and compare these proviruses with clones derived from infected human 293 cells. In addition to clone PERV-A(42) derived from 293 cells, four “native” full-length proviral PERV sequences derived from a genomic library of the porcine cell line PK15 were isolated. Three identical class A clones, designated PK15-PERV-A(42), PK15-PERV-A(45), and PK15-PERV-A(58), and one class B clone, PK15-PERV-B(213), were characterized. PK15-PERV-B(213) is highly homologous but distinct from the previously described clone PERV-B(43). PK15-PERV-A(58) demonstrates close homology to PERV-A(42) in env and to PERV-C in long terminal repeat, gag, and pro/pol sequences. All three PERV clones described here were replication competent upon infection of susceptible cell lines. The findings suggest that the pig genome harbors a limited number of infectious PERV-A and -B sequences.A better understanding of the cellular and molecular basis of transplant rejection and the generation of transgenic donor animals bearing genes that mediate protection towards rejection (3, 24, 25) have stimulated approaches to use xenotransplantation, i.e., the therapeutic use of animal cells, tissues, and organs, to overcome the shortage of allogeneic transplants (7). Pigs are preferred as donors for xenotransplants (10).Major concerns have been raised about the possibility of introducing new microbial agents from the animal into the recipient, leading to xenozoonosis (2, 11, 18, 27). Viruses that are germ line transmitted, i.e., porcine endogenous retroviruses (PERV) (21), and DNA viruses that can persist without symptoms in their natural host and are transmitted via intrauterine or transplacentar pathways, e.g., herpesviruses (8), are of particular interest.Approximately 50 integration sites of PERV exist in the genomes of different pig breeds (1, 14, 21), and at least three classes are known (14, 28). Those classes, named PERV-A, -B, and -C (PERV-C is also known as PERV-MSL), display high sequence homology in the genes for group-specific antigens (gag) and polymerase (pol) but differ in the envelope (env) genes which determine the host range. In addition, the existence of multiple other PERV sequences in domestic pigs and their phylogenetic relatives has been described. However, only classes A, B, and C appear to be infectious (22).PERV that are released from different pig cell lines are able to infect human cells in vitro (15, 32, 33). PERV-C (1) is ecotropic compared to PERV-A and PERV-B, which are polytropic as deduced from pseudotype experiments utilizing the corresponding env genes (28).A retrospective investigation of 160 patients who had been treated with porcine cells and tissues showed no evidence for transmission of PERV (20); however, no long-term transplantation of a whole vascularized organ has been attempted so far. In contrast, a recent study utilizing NOD/SCID mice revealed PERV infection in several tissue compartments after transplantation of pig pancreatic islets, indicating the xenozoonotic potential of those retroviruses (31).Recently, we have reported the isolation of replication-competent PERV-B molecular clones derived from human embryonic kidney cells infected with PERV (293 PERV-PK) (5). In this communication, we describe the cloning and characterization of PERV-A and PERV-B proviral sequences derived from the porcine kidney cell line PK15 as well as the characterization of the molecular clone PERV-A(42); isolated from 293 PERV-PK cells (5). [Hereafter, clones derived from cell line 293 PERV-PK will be designated 293-PERV-B(33), 293-PERV-B(43), and 293-PERV-A(42); clones derived from cell line PK15 will be designated PK15-PERV-A(58), and so on.] Three proviruses, one PERV-B and two PERV-A clones, produce infectious and replication-competent particles upon transfection of susceptible cells and subsequent infection of different human cell lines. Thus, this study provides the first functional PERV-A and PERV-B clones isolated directly from the pig genome and allows the comparison of proviral PERV sequences from different origins at the molecular and cellular level.     

猪内源性反转录病毒在中国实验小型猪中的存在与表达

目的对中国实验小型猪中内源性反转录病毒的存在与mRNA的表达进行检测,摸清中国实验小型猪中内源性反转录病毒的携带情况.方法根据已发表的PERV的序列设计并合成了三对引物,分别用于检测PERV核心蛋白基因(gag)、多聚酶基因(pol)及囊膜基因(env)的存在与表达;同时,根据目前通用的env基因分型方法合成了三对用于分型检测的引物env-A、env-B、env-C.应用PCR、RT-PCR扩增的方法,对来自于中国实验小型猪外周血淋巴细胞的DNA和RNA样品进行了检测.结果在6个被检DNA样品中均检出了PERV特异性DNA的存在;同样,在被检RNA样品中均有PERV特异性RNA的表达,且所表达的PERV均为A型和B型,在所有样品中均未检出C型PERV的表达.结论初步表明中国实验小型猪中存在内源性反转录病毒序列,且能以mRNA的形式表达,这一结果为我国特有小型猪的开发、利用及其病毒安全性评价奠定了基础.     

Host Range and Interference Studies of Three Classes of Pig Endogenous Retrovirus

Recent interest in the use of porcine organs, tissues, and cells for xenotransplantation to humans has highlighted the need to characterize the properties of pig endogenous retroviruses (PERVs). Analysis of a variety of pig cells allowed us to isolate and identify three classes of infectious type C endogenous retrovirus (PERV-A, PERV-B, and PERV-C) which have distinct env genes but have highly homologous sequences in the rest of the genome. To study the properties of these env genes, expression plasmids for the three env genes were constructed and used to generate retrovirus vectors bearing corresponding Env proteins. Host range analyses by the vector transduction assay showed that PERV-A and PERV-B Envs have wider host ranges, including several human cell lines, compared with PERV-C Env, which infected only two pig cell lines and one human cell line. All PERVs could infect pig cells, indicating that the PERVs have a potential to replicate in pig transplants in immunosuppressed patients. Receptors for PERV-A and PERV-B were present on cells of some other species, including mink, rat, mouse, and dog, suggesting that such species may provide useful model systems to study infection and pathogenicity of PERV. In contrast, no vector transduction was observed on nonhuman primate cell lines, casting doubt on the utility of nonhuman primates as models for PERV zoonosis. Interference studies showed that the three PERV strains use receptors distinct from each other and from a number of other type C mammalian retroviruses.Pig-to-human xenotransplantation has the potential to alleviate the shortage of allogeneic organs for transplantation (1, 25). In addition, it may also allow the development of novel therapies by providing unlimited supplies of cells and tissues (9, 11, 13, 18). Recently, substantial progress has been made in overcoming immunological barriers to cross-species transplantation (25, 27). At the same time, however, serious concerns that zoonotic infections might occur as a result of xenotransplantation have been expressed (1, 6, 30). Our report that an established pig cell line produces a porcine endogenous retrovirus (PERV) that can infect human cells fueled these concerns (23). Subsequently, the isolation of human tropic PERV from stimulated miniswine peripheral blood lymphocytes (38) has shown that normal pig cells can also produce potentially hazardous virus. PERVs may be difficult to eliminate from donor animals because multiple copies of PERV genomes are present in normal pig genomes (2, 16, 23). PERV infection may have serious impact on the health of not only transplant recipients but also the human population at large, if spread of an undetected infectious agent into the community were to take place (3, 31). To assess the risk posed by the PERVs for pig-to-human transplantation, a greater understanding of the properties of the PERVs is required.Sequence analyses indicate that the infectious PERVs are closely related to one another in their gag and pol genes, with maximum amino acid divergence of around 5% (2, 16a, 23). The PERVs are members of the mammalian type C retrovirus genus showing closest homology to the gibbon ape leukemia virus (GALV) pol gene, with about 70% amino acid identity, and 60 to 70% identity to murine leukemia viruses (MLV). However, three distinct env genes have now been identified in PERV clones. Two of these env genes, PERV-A and PERV-B, were cloned from human 293 cells infected with PK15 virus (16). The third distinct class of PERV env gene, here designated PERV-C, was reported as a part of a full-length PERV genome isolated from miniature swine lymphocytes (PERV-MSL) and from a swine lymphoma (PERV-Tsukuba-1) (2, 32). The three types show marked differences in the VRA, VRB, and PRO regions of SU surface glycoprotein (2, 16). Differences in these regions determine the host range specificity of the different classes of MLV (4, 5). These observations suggest that the PERVs belong to three distinct classes with different host range specificities. To test this idea, the functions of the three types of PERV env gene were examined and correlated to production, infection, and replication of PERVs in cell culture. Recombinant retrovirus vectors bearing PERV Env proteins were developed and their host ranges, cell tropism, and interference with each other as well as with other type C retroviruses were examined. The results of these experiments are the subject of this report.     

FISH physical mapping with barley BAC clones

Fluorescence in situ hybridization (FISH) is a useful technique for physical mapping of genes, markers, and other single- or low-copy sequences. Since clones containing less than 10 kb of single-copy DNA do not reliably produce detectable signals with current FISH techniques in plants, a bacterial artificial chromosome (BAC) partial library of barley was constructed and a FISH protocol for detecting unique sequences in barley BAC clones was developed. The library has a 95 kb average barley insert, representing about 20% of a barley genome. Two BAC clones containing hordein gene sequences were identified and partially characterized. FISH using these two BAC clones as probes showed specific hybridization signals near the end of the short arm of one pair of chromosomes. Restriction digests of these two BAC clones were compared with restriction patterns of genomic DNA; all fragments contained in the BAC clones corresponded to bands present in the genomic DNA, and the two BAC clones were not identical. The barley inserts contained in these two BAC clones were faithful copies of the genomic DNA. FISH with four BAC clones with inserts varying from 20 to 150 kb, showed distinct signals on paired chromatids. Physical mapping of single- or low-copy sequences in BAC clones by FISH will help to correlate the genetic and physical maps. FISH with BAC clones also provide an additional approach for saturating regions of interest with markers and for constructing contigs spanning those regions.     

Mapping dispersed repetitive loci using semi-specific PCR cloning and somatic cell hybrid mapping

A simple and effective method based upon semi-specific PCR followed by cloning has been developed. Chromosomal mapping of the generated fragment on a somatic cell hybrid panel identifies the chromosomal position, and yields a unique sequence tag for the site. Using this method, the chromosomal location of one porcine endogenous retrovirus (PERV) was determined. The porcine genomic sequences were first amplified by PCR using a PERV-specific primer and a porcine short interspersed nuclear element (SINE)-specific primer. PCR products were cloned, and those sequences that contained PERV plus flanking regions were selected using a second round of PCR and cloning. Sequences flanking the PERV were determined and a PERV-B was physically mapped on porcine chromosome 17 using a somatic hybrid panel. The general utility of the method was subsequently demonstrated by locating PERVs in the genome of PERV infected human 293 cells. This method obviates the need for individual library construction or linker/adaptor ligation, and can be used to quickly locate individual sites of moderately repeated, dispersed DNA sequences in any genome.     

An ordered BAC contig map of the equine major histocompatibility complex

A physical map of ordered bacterial artificial chromosome (BAC) clones was constructed to determine the genetic organization of the horse major histocompatibility complex. Human, cattle, pig, mouse, and rat MHC gene sequences were compared to identify highly conserved regions which served as source templates for the design of overgo primers. Thirty-five overgo probes were designed from 24 genes and used for hybridization screening of the equine USDA CHORI 241 BAC library. Two hundred thirty-eight BAC clones were assembled into two contigs spanning the horse MHC region. The first contig contains the MHC class II region and was reduced to a minimum tiling path of nine BAC clones that span approximately 800 kb and contain at least 20 genes. A minimum tiling path of a second contig containing the class III/I region is comprised of 14 BAC clones that span approximately 1.6 Mb and contain at least 34 genes. Fluorescence in situ hybridization (FISH) using representative clones from each of the three regions of the MHC localized the contigs onto ECA20q21 and oriented the regions relative to one another and the centromere. Dual-colored FISH revealed that the class I region is proximal to the centromere, the class II region is distal, and the class III region is located between class I and II. These data indicate that the equine MHC is a single gene-dense region similar in structure and organization to the human MHC and is not disrupted as in ruminants and pigs.