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*
Rheumatology Division, Department of Medicine, Washington University School of Medicine, Howard Hughes Medical Institute, St. Louis, MO 63110; and
University of Western Australia, Nedlands, Western Australia, Australia
| Abstract |
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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 |
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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 |
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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 I
). YAC clone
characteristics (i.e., size, stability, chimeric status, and number of
transformant YACs) were assessed as described (9).
|
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
[
-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 [
-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 5090 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 3070 sec and
for smaller YACs (<700 kb), switching times were ramped from
1040 s.
Southern blots
For typing RFLP variants in inbred, recombinant inbred,
backcross, and intra-NKC recombinant congenic inbred mice, 25 µg
liver DNA samples (Mouse DNA Resource, The Jackson Laboratory, Bar
Harbor, ME; Refs. (4, 16) were restricted completely according to
the manufacturers 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
[
-32P]dCTP (Rediprime; Amersham Life
Science) were hybridized to Southern blots. Stringent washing was
performed in 0.2x SSC, 0.1% SDS at 5862°C for typing RFLP
Southern blots, and at 6472°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 |
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Analysis of the Ly49b region
Initially, YACs containing Ly49b genes were
characterized by restriction mapping and STS content analysis.
Ly49b-containing YACs (Table II
) 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. 1
A). 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. 1
B) that did not contain the Ly49a
gene.
|
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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 118)) 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. 2
A). 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. 2
A). 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. 2
A; Ref.
20). Moreover, these YAC inserts were specifically
amplified by Prp M14 gene-specific primers (Table II
).
Southern analysis with a pRML2 vector probe confirmed that
Prp genes do not reside on the pRML2-modified ends of these
inserts (Fig. 2
A). By this analysis, YACs 392D6 and 330B9
could be mapped and aligned in a Prp gene cluster YAC contig
(Fig. 2
B).
|
Notably, the 242D11L2 Southern probe hybridized with the
pRML2-modified YAC insert ends of YACs 242D11, 330B9, and 392D6 (Fig. 2
A). 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 II
).
D6Wum18-specific oligonucleotides specifically amplified
YACs 330B9, 392D6, and 242D11 (Table II
). 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. 2
A). 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 II
). In addition, probe 109B5L hybridization with the
Southern blot represented in Fig. 1
A 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 II
). 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. 1
, A and B, and data not shown). Thus,
D6Wum9 resides
140 kb distal to this MluI site
on YACs 200H7 and 242D11 and the D6Wum916 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 |
|---|
|
|
|---|
2.5 Mb to
4.7 Mb and includes 27 YAC inserts in total,
corresponding to a 0.7-cM genetic interval (Fig. 3
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).
|
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 III
).
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 IV
), 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 112) 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 1318) were identified that are also recombinant in this narrow
NKC region (Ref. 16 ; Table IV
). 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 IV
). 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.
|
|
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 |
|---|
| Footnotes |
|---|
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: ![]()
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. ![]()
Received for publication March 24, 1999. Accepted for publication June 4, 1999.
| References |
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