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The Journal of Immunology, 1999, 163: 1991-1999.
Copyright © 1999 by The American Association of Immunologists

Localization on a Physical Map of the NKC-Linked Cmv1 Locus Between Ly49b and the Prp Gene Cluster on Mouse Chromosome 61

Michael G. Brown2,*, Jun Zhang*, Ying Du*, Janis Stoll*, Wayne M. Yokoyama* and Anthony A. Scalzo{dagger}

* Rheumatology Division, Department of Medicine, Washington University School of Medicine, Howard Hughes Medical Institute, St. Louis, MO 63110; and {dagger} University of Western Australia, Nedlands, Western Australia, Australia


    Abstract
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
The Cmv1 locus controls NK cell-mediated resistance to infection with murine CMV. Our recent genetic analysis of backcross mice demonstrated that the NK gene complex (NKC)-linked Cmv1 locus should reside between the Ly49 and Prp gene clusters on distal mouse chromosome 6. We have aligned yeast artificial chromosome (YAC) inserts in a contig spanning the interval between the Ly49 and Prp gene clusters. This YAC contig includes 13 overlapping YAC inserts that span more than 2 megabases (Mb) in C57BL/6 (B6) mice. Since we have identified genomic clones that span the Ly49-Prp gene region, we hypothesize that at least one should contain the Cmv1 locus. To narrow the Cmv1 critical region, we developed novel NKC genetic markers and used these to genotype informative backcross and intra-NKC recombinant congenic mouse DNA samples. These data suggest that Cmv1 resides on a single YAC insert within an interval that corresponds to a physical distance of ~390 kb. This high resolution, integrated physical and genetic NKC map will facilitate identification of Cmv1 and other NKC-linked loci that regulate NK cell-mediated immunity.


    Introduction
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Cytomegalovirus is a dsDNA virus that establishes chronic infection of its host that is characterized by latency and that persists throughout the lifetime of the host. Normally for the host, this viral infection is asymptomatic. However, latent CMV may reactivate and can lead to life-threatening complications in immunosuppressed or immunocompromised individuals. Human CMV (HCMV)3 infection displays species-specific tropism, and thus it has not been possible to examine HCMV infection in easily manipulated experimental animals such as mice. Murine CMV (MCMV) displays many of the same molecular and pathologic features of HCMV infection, affording experimental analysis in a well-characterized animal model.

Although overall host resistance to MCMV is under multigenic control, regulation of acute viral burden within the spleen is determined by a single autosomal dominant locus designated Cmv1 (1). The mouse Cmv1 locus determines host mortality in different inbred strains following challenge with high titers (>=105 pfu) of MCMV. Moreover, NK cells are required for this Cmv1-dependent protective effect (2). Specifically, C57BL/6 (B6) mouse NK cells possess the Cmv1r resistance allele, which limits splenic viral replication following low dose (103-5 x 104 pfu) MCMV infection. This directly correlates with B6 mouse survival rates following high dose MCMV challenge. In contrast, otherwise functionally competent BALB/c mouse NK cells are unable to limit splenic viral replication, and these MCMV-susceptible (Cmv1s) mice do not survive high dose MCMV challenge.

Recently, the Cmv1 locus was genetically mapped between the chromosome 6 Ly49 and Prp gene clusters by analyzing segregation patterns of splenic viral titers in recombinant inbred (RI) and backcross mice following low dose MCMV challenge (2, 3, 4). The Ly49 gene cluster is characteristic of several NK gene complex (NKC) gene clusters that are expressed predominantly in the NK cell lineage. Ly49, Nkrp1, Cd94, Nkg2, and Cd69 genes encode NK cell receptors that are type II integral membrane proteins homologous to members of the C-type lectin superfamily (reviewed in Ref. 5). By contrast, the Prp gene cluster encodes proline-rich proteins that are expressed in mouse salivary glands (6). This gene cluster was used as an anchor locus for the original mapping of the NKC on mouse chromosome 6 (7, 8). Since the NKC-encoded NK cell receptors specifically recognize target cell ligands and modulate NK cell activity, they are good candidates to regulate NK cell activity in vivo.

Yeast artificial chromosome (YAC) inserts containing most of the known NKC-linked, NK cell-expressed genes have been identified and aligned in a contiguous array spanning more than 2 megabases (Mb) of the NKC with the Ly49 cluster identified as the telomeric-most region (9, 10). Since our backcross analysis demonstrated that the Cmv1 locus should reside in a distal region between the Ly49 and Prp gene clusters, it was unlikely that we had previously identified Cmv1-containing YAC inserts. Therefore, we sought to identify NKC-linked YAC inserts that would span the critical region for the Cmv1 locus.

Interestingly, Ly49b (the most disparate Ly49 gene member) does not reside in the Ly49 gene cluster or anywhere in the previous NKC contig. Rather, we demonstrate here that Ly49b resides telomeric to the Ly49 gene cluster. We have utilized YAC inserts containing the Ly49b gene together with those containing Prp genes to establish a YAC contig spanning the Cmv1 locus. This distal NKC YAC contig spans more than 2 Mb of mouse chromosome 6 and could be aligned to the previous (proximal) NKC YAC contig. One or more of these YAC inserts should therefore contain the Cmv1 locus. We have also developed novel NKC sequence-tagged site (STS) markers that were useful in genetic analysis of backcross and intra-NKC recombinant congenic inbred animals. Two of the novel NKC STS markers that were used in genetic analysis immediately flank the Cmv1 locus. The genetic analysis suggests that Cmv1 resides on a single NKC YAC insert in an interval that corresponds to a physical distance of ~390 kb.


    Materials and Methods
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
YAC library screening

YAC clones were identified by screening the Whitehead Institute/MIT YAC libraries of EcoRI partially restricted B6 mouse DNA inserted into either the vector pYAC4 (the ymWIBR YAC library) or between the vectors pRML1 and pRML2 (the WI/MIT 820 YAC library (11, 12) (Research Genetics, Huntsville, AL) with NKC STS primers (Table IGo). YAC clone characteristics (i.e., size, stability, chimeric status, and number of transformant YACs) were assessed as described (9).


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Table I. Characteristics of NKC STS and Southern probes used in this study

 
YAC clone DNA preparation and PCR analysis

Agarose plugs containing YAC clone DNA (~1 x 108 cells/plug) were prepared from yeast cells grown in selective media according to standard methods (13). For PCR analysis of YAC insert DNA, YAC clone DNA minipreps were prepared and tested by the PCR as described previously (9). For 32P-PCR genotype analysis, forward primers were end labeled with [{gamma}-32P]ATP (sp. act. 3000 Ci/mmol; Amersham Life Science, Arlington Heights, IL) using T4 polynucleotide kinase (NEB, Beverly, MA) by standard methods (14). Labeled forward primers were used in PCR experiments as described for Mouse MapPairs (Research Genetics; Ref. 15). Labeled PCR products and [{gamma}-32P]ATP-labeled DNA m.w. Marker V (Boehringer-Mannheim, Indianapolis, IN) were visualized in acrylamide gels following denaturing PAGE.

Partial restriction of YAC DNA in agarose plugs and pulsed-field gel electrophoresis

Restriction of YAC DNA in agarose plugs was performed by standard methods (13). Pulsed-field gel electrophoresis (PFGE) was performed in either the CHEF DR II or the CHEF Mapper unit (Bio-Rad, Richmond, VA). Agarose plug DNA was separated in 1.0% chromosomal grade agarose (Bio-Rad) run in 0.5x TBE buffer (~14°C), using lambda concatemers (Bio-Rad) and yeast chromosomes (Bio-Rad) as size standards. Intact YAC clone DNA was separated by these PFGE conditions (6 V/cm, 120° angle, linearly ramped switching times from 50–90 sec for 20 h). For partially restricted YAC clone DNA, PFGE-ramped switching times were modified: typically, for larger YACs (>700 kb), switching times were ramped from 30–70 sec and for smaller YACs (<700 kb), switching times were ramped from 10–40 s.

Southern blots

For typing RFLP variants in inbred, recombinant inbred, backcross, and intra-NKC recombinant congenic inbred mice, 2–5 µg liver DNA samples (Mouse DNA Resource, The Jackson Laboratory, Bar Harbor, ME; Refs. (4, 16) were restricted completely according to the manufacturer’s conditions and electrophoresed on ~0.8% agarose gels. YAC clone DNA was prepared and separated as described above.

Southern blots were prepared and analyzed by standard methods (14). DNA was transferred onto Hybond-N membranes (Amersham Life Science) with 20x SSC. Southern probes labeled with [{alpha}-32P]dCTP (Rediprime; Amersham Life Science) were hybridized to Southern blots. Stringent washing was performed in 0.2x SSC, 0.1% SDS at 58–62°C for typing RFLP Southern blots, and at 64–72°C for sequence-specific hybridization on YAC clone Southern blots.

YAC insert end clone isolation

pYAC4-modified YAC insert ends [designated (L) or (R) for pYAC4-left or -right arm-modified ends, respectively] were subcloned by the vectorette method (17), but with minor modification as described (9). Amplified products were subcloned into pBluescript II sk- (Stratagene, La Jolla, CA) and electroporated into Escherichia coli. pRML1- and pRML2-modified YAC insert ends (designated (L1) or (L2) for pRML1- or pRML2-modified ends, respectively) were subcloned by religation of XbaI-, SpeI-, or BamHI-restricted YAC clone DNA and subsequent transformation into E. coli. Transformants were identified by pRML1- and pRML2-specific colony PCR using pRML1-specific primers pRML1.F2, 5'-GAATGTTACCACCTAAATAAG-3', and pRML1.R1, 5'-AGTGAGGGTTAATTT-ACGTAG-3'; or pRML2-specific primers pRML2.F2, 5'-GACAAGAAAAGCAGATT-AAATAG-3', and pRML2.R1, 5'-AATTCGATGTACCCAATTCGC-3'. T7, T3, SK, KS, pRML1.F2, pRML2.F2, and NKC STS primer extension products were sequenced using the ABI Prism Dyedeoxy termination kit (Perkin-Elmer, Foster City, CA) to verify YAC insert ends. Sequence analysis was performed using the Sequencher 3.0 program (Gene Codes, Ann Arbor, MI). YAC insert end probes were also assessed on Southern blots of YAC and mouse genomic DNA restricted with frequently cutting restriction enzymes.

YAC vector Southern probes

pYAC4 vector arm probes were as described (9). pRML1 and pRML2 unique sequences were subcloned as follows: The pRML1- and pRML2-specific amplified products from the respective vectors were TA subcloned into the EcoRV site of pBluescript II sk- as described (9). The 266-bp EcoRI/HindIII fragment of pBSRML1 and the 238-bp EcoRI/HindIII fragment of pBSRML2 were used as Southern probes. Probes were gel purified (Prep-A-Gene; Bio-Rad) and were subsequently verified and quantitated by agarose gel electrophoresis.


    Results
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Previously, we identified and aligned YAC inserts that contained Nkrp1, Ly49, and Cd94/Nkg2 gene clusters but did not contain the Ly49b or Prp genes (9). Ly49b-containing YAC inserts were identified using Ly49b-specific oligonucleotides (Tables I and II) and positioned between the Ly49 and Prp gene clusters (see below). Although B6 mouse YAC clones containing Prp gene cluster microsatellites had been identified previously, they had not been further characterized (15, 18, 19). Since Cmv1 was genetically mapped between Ly49a and the Prp gene cluster previously (4), we sought to identify a complete set of overlapping genomic clones that would span this NKC region and potentially contain the Ly49b gene.

Analysis of the Ly49b region

Initially, YACs containing Ly49b genes were characterized by restriction mapping and STS content analysis. Ly49b-containing YACs (Table IIGo) were Mlu I restriction mapped by Southern analysis of DNA that had been separated by PFGE. A representative composite was produced of MluI-restricted YACs 109F12 and 200H7 on the same nylon membrane successively hybridized with six different Southern probes (Fig. 1GoA). Notably, the Ly-49B cDNA hybridized strongly with a 200-kb MluI fragment and weakly with a smaller MluI fragment from both YAC inserts. This probe did not hybridize with the Ly49a gene-containing YAC insert 52A6 or other 109F12 and 200H7 MluI fragments that were also on the nylon membrane (not shown). These results confirmed the location of Ly49b on YACs 109F12 and 200H7 (Fig. 1GoB) that did not contain the Ly49a gene.


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Table II. Characteristics and NKC marker content of YAC inserts aligned to the distal NKC

 


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FIGURE 1. A physical map of the Ly49b NKC region. A, Agarose plugs containing YAC clones 109F12 (lane 1) and 200H7 (lane 2) were partially (not shown) and completely restricted with MluI, separated by PFGE, and Southern blotted. YAC clone 52A6 was included as a NKC control DNA (not shown). PFGE lanes from this Southern blot containing completely restricted YAC clone DNA and probed successively with six different probes (as indicated) are shown. B, At top, the Ly49b region on mouse chromosome 6 is depicted. Positions of the NKC STS markers D6Wum13, D6Wum12, D6Wum14, and D6Wum9 are indicated on the chromosome map. Below the chromosome map, an MluI restriction site map for this NKC interval is shown. SalI sites that were mapped on YACs 79D7 and 242D11 are also shown. Below the restriction maps, an alignment of YAC inserts 109F12, 200H7, 79D7, and 242D11 are shown. YAC insert orientation to the contig is indicated by the designated YAC ends: pYAC4R (R), pYAC4L (L), pRML1 (L1), or pRML2 (L2). The Ly49b interval (open bar) resides between the mapped MluI sites as indicated.

 
Subsequent successive hybridizations with YAC insert end probes 109F12R, 200H7R, and 200H7L were performed so that placement of MluI sites on these YAC inserts could be completed (Fig. 1GoA). Curiously, probe 200H7R hybridized with more than one fragment of each insert, but not YAC insert 52A6. This probe may contain DNA sequence elements that are common, but restricted, to this NKC region. The 200H7L probe did not hybridize with YAC 109F12 fragments, demonstrating that this locus does not reside on 109F12. Importantly, these left and right YAC end probes hybridized with those fragments also identified by the appropriate YAC vector probes. Similarly, YAC inserts 79D7 and 242D11 could also be aligned to the Ly49b contig by their NKC STS marker content and MluI and SalI restriction profiles (Table IIGo, Fig. 1GoB). Although YACs 452H5, 86F9, and 76B10 also could be aligned to or near the Ly49b region based on STS marker content analysis (Table IIGo), these YAC inserts have not been extensively mapped.

Importantly, a genetic analysis could be performed to confirm and extend these physical findings because the 200H7L Southern probe identified an RFLP (D6Wum9) that distinguishes B6 and BALB/c alleles for this locus. D6Wum9 genotypes of the backcross mice (BALB/c x C57BL/6)F1 x BALB/c No. 37 and (A/J x C57BL/6)F1 x A/J No. 44 and several of the intra-NKC recombinant congenic mice (BALB.B6-Cmv1r(CT 1–18)) confirmed an NKC location for D6Wum9 distal to the Nkrp1 and Cd69 genes (Tables III and IV). Likewise, D6Wum9 genotype analysis of the backcross mouse panels and the intra-NKC recombinant congenic mice confirmed the NKC location for D6Wum9 proximal to the Prp gene cluster. Overall, these analyses confirmed the alignment of the Ly49b-containing YACs to the NKC region between Ly49a and the Prp gene cluster.

Analysis of the Prp region

Likewise, YACs containing Prp genes were restriction mapped with several enzymes and subsequent Southern analysis using probes for the Prp Mp2 gene (20), YAC insert ends 392D6L2 and 242D11L2, and pRML1 and pRML2 YAC vectors (Fig. 2GoA). The Prp Mp2 probe hybridized with 330B9 and 392D6 fragments, but not 52A6 or 242D11 YAC inserts. Although the pRML1 probe may weakly hybridize with a single yeast chromosome sequence in all of the YAC clones tested, it also specifically hybridizes with single restriction fragments from each YAC insert (Fig. 2GoA). Importantly, Prp and pRML1 probes both hybridized with the same size BssHII fragment of 330B9, suggesting that the Prp Mp2 gene resides near the pRML1 end of this YAC insert. An internal 392D6 BssHII fragment hybridizes with the Prp Mp2 probe since it does not hybridize with either of the YAC vector probes, pRML1 or pRML2. Curiously, the Prp gene-containing 392D6 MluI fragment is smaller than the corresponding 330B9 MluI fragment, although the Prp gene-containing 392D6 BssHII fragment is larger than the corresponding 330B9 BssHII fragment. Thus, YAC 392D6 may contain a rearranged or partially deleted DNA insert, or a 330B9 MluI site may have been altered. Nevertheless, members of the Prp gene cluster were mapped to the pRML1 end of YAC 330B9, and this fragment overlaps an internal BssHII fragment of 392D6. This probe may be detecting more than a single gene from the Prp cluster since it hybridized with two similarly sized, SalI fragments of each YAC and since this Prp Mp2 exon 2 genomic probe does not contain an internal SalI site (Fig. 2GoA; Ref. 20). Moreover, these YAC inserts were specifically amplified by Prp M14 gene-specific primers (Table IIGo). Southern analysis with a pRML2 vector probe confirmed that Prp genes do not reside on the pRML2-modified ends of these inserts (Fig. 2GoA). By this analysis, YACs 392D6 and 330B9 could be mapped and aligned in a Prp gene cluster YAC contig (Fig. 2GoB).



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FIGURE 2. A physical map of the Prp Mp2 gene cluster region of mouse chromosome 6. Agarose plugs containing YAC clones 242D11, 330B9, and 392D6 were completely restricted with BssHII (B), MluI (M), and SalI (S). Restricted and uncut (U) DNA samples, including YAC clone 52A6, were separated by PFGE and Southern blotted. A, The Southern blot was probed with a Prp Mp2 exon 2 probe (20 ), YAC end probes 242D11L2 and 392D6L2 (Table IGo), and YAC vector probes pRML1 and pRML2, as designated. Restriction fragment sizes were determined by comparison with yeast chromosome and lambda concatemer mobilities in PFGE. Note that pRML1 weakly hybridized with BssHII (~110 kb), MluI (~80 kb), and SalI (~40 kb) fragments of a yeast chromosome. B, At top, depicted is the mouse chromosome 6 Prp region. Positions for D6Wum12, -20, -18, and -16 are shown. Below the chromosome map, BssHII, MluI, and SalI restriction sites that have been mapped are shown. Note that additional internal BssHII sites on YAC 242D11 and internal MluI and SalI sites on YACs 392D6 and 330B9 may exist that were not mapped by this analysis. Discrepant 330B9 (1 ) and 392D6 (2 ) MluI sites are indicated. Below the Prp region restriction maps, an alignment of YAC inserts 242D11, 392D6, and 330B9 is shown. An interval for the Prp gene cluster (open bar) bounded by the proximal BssHII and distal MluI sites is also shown. YAC insert orientation to the contig is indicated as described for Fig. 1GoB.

 
Overlap of Ly49b, Prp, and the proximal NKC regions

Notably, the 242D11L2 Southern probe hybridized with the pRML2-modified YAC insert ends of YACs 242D11, 330B9, and 392D6 (Fig. 2GoA). Note that SalI fragments were not detected by the pRML2 vector probe since this vector contains a SalI site that resides very close to the vector cloning site for mouse insert DNA. Hence, this end of the Ly49b-containing YAC contig (D6Wum16) must reside between the L2-modified ends of 330B9 and 392D6 and the adjacent SalI site on each of these clones. In support of this alignment, D6Wum16-specific oligonucleotides amplified the expected 337-bp product from YAC 242D11 and three of four Prp containing YAC inserts that were tested, while other NKC YACs were not amplified (Table IIGo). D6Wum18-specific oligonucleotides specifically amplified YACs 330B9, 392D6, and 242D11 (Table IIGo). Southern probe 392D6L2 (D6Wum20) hybridized with the L2-modified ends of YACs 392D6 and 242D11, but did not hybridize with YACs 52A6 or 330B9 (Fig. 2GoA). Finally, a bacterial artificial chromosome (BAC) insert (~65 kb) that contains both D6Wum18 and D6Wum16 has been identified (M. G. Brown, J. Stoll, and W. M. Yokoyama, unpublished data). Taken together, the results suggest that the order for these NKC STS markers is D6Wum20-D6Wum18-D6Wum16 on YAC 242D11 and that D6Wum18 and D6Wum16 should each reside within 65 kb of the other. These findings therefore confirmed the alignment of the Ly49b-containing YAC contig with the Prp-containing YAC contig into an overall distal NKC YAC contig. More importantly, since D6Wum9, D6Wum12, and D6Wum13 must reside centromeric to D6Wum16 and the Prp gene cluster (Tables III and IV), these data provided orientation of this contig on mouse chromosome 6.

To determine whether this distal NKC YAC contig could be aligned with the previously established NKC proximal YAC contig, we surveyed selected YAC clones with the 109B5L Southern probe (D6Wum15), the telomeric-most STS marker from the proximal contig. Importantly, this probe hybridized with YACs 109B5 and 109F12 (a Ly49b-containing YAC) but not other NKC-aligned YAC inserts (Table IIGo). In addition, probe 109B5L hybridization with the Southern blot represented in Fig. 1GoA revealed specific detection of the pYAC4L-modified MluI fragment (240 kb) of YAC 109F12 (data not shown). Moreover, this locus was confirmed on YACs 109B5, 109F12, and 452H5 (Tables I and II) and was found to be tightly linked with the Ly49 genes and the distal NKC marker D6Wum9 (Tables III and IV) using radiolabeled 109B5L-specific oligonucleotides. Thus, these results facilitated the alignment and orientation of the proximal and distal NKC YAC contigs to a region on mouse chromosome 6 that includes the Cmv1 locus.

Assignment of the Cmv1 critical region on the NKC physical map

In our previous backcross analysis in mice, Cmv1 was genetically mapped to a 0.5-cM interval between the Ly49 and Prp gene clusters, but its physical location could not be identified since the physical interval between Ly49 and Prp had not been characterized (4). From the current physical map, this region extends beyond 2 Mb, spanning several YAC clone inserts. We therefore attempted to determine the location of the Cmv1 genetic interval on the NKC physical map before embarking on a gene-screening strategy that would require investigation of multiple large YAC inserts.

Initially, we genotyped backcross and intra-NKC recombinant congenic inbred mice for D6Wum9 alleles (Tables III and IV). Although no animals that contained recombination breakpoints between Ly49a and D6Wum9 were identified, two of the backcross animals contained breakpoints between D6Wum9 and Cmv1. (BALB/c x C57BL/6)F1 x BALB/c mouse No. 21 and (A/J x C57BL/6)F1 x A/J mouse No. 29 contained BALB/c or A/J D6Wum9 alleles, respectively, but each animal contained a B6 Cmv1r allele. Hence, D6Wum9 resides proximal to the Cmv1 locus, thus providing a new centromeric NKC boundary for Cmv1. Likewise, we genotyped the animals described above with D6Wum16. Notably, the D6Wum16 alleles matched the Prp gene alleles in all of the animals tested from each genetic panel (Tables III and IV). Thus, the data support the conclusion that D6Wum16 resides distal to the Cmv1 locus, and therefore D6Wum16 should serve as a novel telomeric boundary for the Cmv1 genetic interval.

From the STS content mapping of genomic clones, it was apparent that the Cmv1 flanking markers D6Wum9 and D6Wum16 reside on YAC 242D11 (Table IIGo). In the alignment of YAC 242D11 with other YAC inserts from the distal NKC contig, the 200H7 telomeric-most MluI site should correspond to the 242D11 telomeric-most MluI site. In support of this alignment, the 200H7L probe hybridized specifically with the pYAC4L-modified 200H7 MluI fragment (~140 kb) and the pRML2-modified 242D11 MluI fragment (~530 kb), but not with the smaller pRML2-modified 242D11 SalI or BssHII fragments (Fig. 1Go, A and B, and data not shown). Thus, D6Wum9 resides ~140 kb distal to this MluI site on YACs 200H7 and 242D11 and the D6Wum9–16 physical interval should span ~390 kb. Since these Cmv1-flanking STS markers both reside on YAC 242D11, we conclude that 242D11 should contain the Cmv1 locus and that the Cmv1 critical region corresponds to a maximum physical distance of ~390 kb on this YAC insert.


    Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
In this report, we have identified, mapped and aligned thirteen new YAC inserts to the NKC on mouse chromosome 6. Overlap of these novel NKC YAC inserts with the adjacent, previously established proximal NKC YAC contig expanded the NKC coverage (A2m-Prp) from ~2.5 Mb to ~4.7 Mb and includes 27 YAC inserts in total, corresponding to a 0.7-cM genetic interval (Fig. 3Go). Since D6Wum15 resides somewhere on the ~240-kb pYAC4L-modified MluI fragment of YAC 109F12, and since the distance between D6Wum18 and D6Wum16 is <=65 kb, the overall physical size estimate for the aligned proximal and distal NKC YAC contigs may be ±310 kb. Using the YAC contig as a backbone, we have physically mapped most known NKC-linked, NK cell-expressed genes and the Prp gene cluster. Recently, McQueen and coworkers identified and mapped five novel Ly49 genes, four of which clearly reside in the Ly49 gene cluster (21). In accord with the data presented here, these genes do not overlap the Ly49b region (21). Conceivably, the NKC could extend beyond the overall YAC contig reported here to include additional gene products that are structurally and/or functionally related to previously reported NKC members (5).



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FIGURE 3. Alignment of the C57BL/6 mouse NKC proximal and distal YAC contigs spanning the Cmv1 locus. At top, mouse chromosome 6 and positions of the proximal NKC gene clusters, Ly49b, and the Prp gene cluster are shown (centromeric-telomeric, respectively). An approximate position for D6Wum15 is shown between the pYAC4L (L) end of YAC 109F12 and the 109F12 adjacent distal MluI site. Proximal (D6Wum9) and distal (D6Wum16) NKC boundaries for the Cmv1 critical region (open bar) on the physical map are shown. Novel NKC STS markers (D6Wum) are shown below the chromosome map. NKC STS markers that distinguish different alleles in inbred mouse strains are underlined. At bottom, an overall NKC YAC contig is shown from which the physical map was established (not all of the NKC aligned YAC inserts are shown). YAC insert orientation to the contig is indicated as described for Fig. 1GoB.

 
Notably, the new distal NKC YAC contig spans the original NKC genetic interval containing Cmv1. Nine novel NKC locus-specific markers, including five that distinguish different inbred mouse alleles, have been positioned on the NKC physical map in this study, including genetic markers that flank the Cmv1 locus. The previous Cmv1 critical region (>2 Mb) now has been narrowed to a fragment of a single YAC insert that corresponds to a physical distance of ~390 kb. This clone should contain the Cmv1 locus, but YACs may be prone to DNA rearrangements and partial deletions. However, we have aligned more than one genomic clone to this NKC region, thus providing multiple coverage to validate the physical map. As an alternative approach, we are now aligning BAC inserts to the Cmv1 critical region and preliminary data corroborates this map. Therefore, we have identified novel NKC-linked genetic markers that enabled us to narrow the Cmv1 locus to an NKC region included on individual genomic clones.

Genetic localization of Cmv1 on the physical map was inherently reliant upon analysis of intra-NKC recombinant mice, especially two informative backcross mice [(BALB/c x C57BL/6)F1 x BALB/c mouse No. 21 and (A/J x C57BL/6)F1 x A/J mouse No. 29], one from each backcross panel containing a recombination breakpoint between D6Wum9 and the Cmv1 locus (Table IIIGo). Importantly, each of these animals was resistant to MCMV infection but contained BALB/c or A/J alleles for proximal NKC markers and the distal NKC marker D6Wum9, respectively. Hence, recombination breakpoints in these animals should have resided between D6Wum9 and Cmv1. Although similar recombinant animals were not identified by Depatie and coworkers or in our intra-NKC recombinant congenic mice (Refs. 16, 22 ; and see Table IVGo), our backcross data are not inconsistent, since it is possible that the additional genetic approaches may have failed to generate animals containing similar low frequency recombination events. In light of this, it is interesting that most of the intra-NKC recombinant backcross mice (six of eight) and four of the original 12 intra-NKC recombinant mouse strains (BALB.B6-CT 1–12) contain breakpoints within the D6Wum9-D6Wum16 (~390 kb) NKC interval. During production of homozygous stock for these "CT" strains, six additional independent intra-NKC recombinant congenic mice (CT 13–18) were identified that are also recombinant in this narrow NKC region (Ref. 16 ; Table IVGo). Moreover, half of the original intra-NKC recombinant congenic "CT" mice (6 of 12) and the intra-NKC recombinant mouse strain B6.BALB-TC1 that was derived from the B6.BALB-Cmv1s congenic strain are recombinant within an ~500-kb interval of the proximal NKC between the Cd69 and Cd94 genes ( Ref. 16 ; Table IVGo). This suggests 1) that two NKC regions, one in the proximal NKC between Cd69 and Cd94, and the other in the distal NKC between D6Wum9 and D6Wum16, may be recombinogenic, and 2) that Cmv1 should reside between boundaries defined by the recombination breakpoints identified in two sets of distal NKC recombinant mice, those that are recombinant between D6Wum9 and Cmv1 and those that are recombinant between Cmv1 and D6Wum16. The recombination hotspots flanking multiple NKC gene clusters that can modulate NK cell function may provide a means to exchange NKC "haplotypes" during meiotic recombination. These haplotypes are predicted to consist of a large number of genes that display polymorphism and influence NK cell function and that segregate with each other. As such, the functions of individual genes may be dependent on alleles in other linked genes.


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Table III. Genotype analysis of informative backcross mice with novel NKC STS markers

 

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Table IV. Genotype analysis of intra-NKC recombinant congenic mouse strains

 
In this analysis, we also identified the precise MluI fragments of different YAC inserts that hybridize with the Ly-49B cDNA. Because this probe also hybridizes weakly to an additional MluI fragment of both YAC inserts, the Ly49b gene may contain an MluI site. Alternatively, the Ly-49B cDNA may be hybridizing with one or more Ly49b-like genes. We hypothesize that such a gene(s) would be Ly49b related since this probe does not hybridize with the Ly49 gene cluster-containing YAC inserts. Hence, an additional gene cluster may reside in the NKC ~1 Mb distal to the Ly49 gene cluster. Importantly, none of the Ly49 genes, including the Ly49b gene, should be considered a Cmv1 candidate gene since the Ly49-D6Wum9 linkage group segregated from the Cmv1 locus in the genetic analysis of the backcross mice. On the other hand, a gene related to Ly49b could be a relevant candidate since the Cmv1 genetic interval is immediately distal to the Ly49b NKC region and the NKC contains several clusters of highly related genes (9, 10, 23).

Likewise, we have physically mapped the Prp Mp2 gene to a presumed telomeric physical boundary for the NKC. This region resides ~2.5 Mb from the Ly49 gene cluster and also appears to contain multiple genes that hybridize with the Prp Mp2 Southern probe. This is not a surprising result given that the mouse Prp gene cluster may contain several different genes that encode proline-rich proteins expressed in the salivary glands of mice (6). For the purposes of this work, Prp gene mapping provided an initial physical boundary for the Cmv1 genetic interval.

Ultimately, this physical map and the novel NKC locus markers that have been derived from it should facilitate positional gene cloning strategies not only for Cmv1, but also for other NKC-linked loci that are defined by immunological phenotypes. These immune function regulators include loci that affect mouse resistance to ectromelia (Rmp1) and possibly also to Leishmania, loci that modulate natural killing of xenogeneic target cells (Chok), and loci that affect non-insulin-dependent diabetes mellitus susceptibility and Bordetella pertussis-induced histamine sensitization (24, 25, 26, 27, 28, 29, 30). The mouse NKC may also contain an orthologue of the rat Nka locus that regulates NK cell-mediated alloreactivity (31). Moreover, the resources described herein should prove invaluable for the localization of these and other mouse chromosome 6 loci that are tightly linked to the NKC, including the Soa locus that affects taste discrimination in mice (32). We suspect that the NKC may also contain genes that have yet to be identified. Hence, this report will provide the framework for the identification of additional NKC-linked genes and regulatory elements that are critical for immune functions.


    Acknowledgments
 
We thank D. M. Carlson for kindly providing the pUMP2BE plasmid. We also thank J. Heusel, B. Plougastel, and E. Ho for critical review of the manuscript.


    Footnotes
 
1 This work was supported in part by the Barnes-Jewish Hospital Research Foundation, by grants from the National Institutes of Health, and by the National Health and Medical Research Council of Australia (Grant 961305 to A.A.S.). M.G.B. was the recipient of a National Research Service Award from the National Institute of Allergy and Infectious Diseases. W.M.Y. is an investigator of the Howard Hughes Medical Institute. A.A.S. also received support from the Department of Industry, Science and Technology under the auspices of the Bilateral Science and Technology Collaboration Program. Back

2 Address correspondence and reprint requests to Dr. Michael G. Brown, Division of Rheumatology, Box 8045, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110. E-mail address: Back

3 Abbreviations used in this paper: HCMV, human CMV; MCMV, murine CMV; B6, C57BL/6; BAC, bacterial artificial chromosome; Mb, megabases; NKC, NK gene complex; PFGE, pulsed field gel electrophoresis; STS, sequence-tagged site; YAC, yeast artificial chromosome. Back

Received for publication March 24, 1999. Accepted for publication June 4, 1999.


    References
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

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