Vol. 61,No. 10
Studies
on
the
Origin-Specific
DNA-Binding
Domain
of
Simian Virus 40
Large
T
Antigen
MICHAEL STRAUSS,tPEDRAM ARGANI, IAN J. MOHR, AND YAKOV GLUZMANt* ColdSpring HarborLaboratory, ColdSpring Harbor, Netw York 11724
Received 23 March1987/Accepted 29 June 1987
Theorigin-specific DNA-bindingdomain of simian virus 40largeTantigenwasanalyzed,and itsC-terminal boundarywasfound to beatorbeforeamino acid 259. This doesnotinclude the zincfingerstructuralmotif locatedatamino acids 302to320(J.M.Berg,Science232:485-486, 1986). Interestingly,N-terminalfragments of 266 and 272 amino acids andlargerdisplayeddramaticallyreducedorigin-binding activity.Inaddition, the specific DNA-binding propertiesof truncated proteins purified from both bacterial and mammalian sources
werecompared.Truncated T antigensfrom mammalian cells bound specificDNAfragmentsmoreefficiently
than did their bacterial counterparts. These results implicate posttranslational modification with a role in regulatingtheDNA-binding activityoflargeT antigen.
The multiple activities ofa single polypeptide chain are
often found sequestered within discrete domains, each of which is responsible for a particular function. The large T antigenencoded bySV40 providesanexcellent opportunity toexaminethisphenomenon. Thismultifunctionalproteinis involved in both lytic infection of permissive cells and malignanttransformation ofavarietyof cells(3,34);
further-more, extensivegenetic analysishas revealed that several of its functions operate independently of each other(4, 6, 10, 12, 13, 21, 22, 30).
Several of the many functions performed by large T antigen, namely initiation of viral DNA replication and autoregulation ofearly transcription (34), are mediated by specific DNA binding to two major sites, one of which
contains the viral origin of replication (5, 23, 31, 33). Previous mutational studies have implicated amino acids between residues 139 and 220 in specific DNA binding (13, 20); however, other genetic data suggest that amino acids beyond residue 300 areinvolved in specific bindingto viral DNAsequences. Whereasfragments containing 399 and 362
N-terminal aminoacids bindtotheviral origin ofreplication,
a smaller fragment containing 341 amino acids lacks this
activity (4). Furthermore, truncated T antigens containing theN-terminal 272 amino acids have been reported to lack specificDNA-binding activity (20, 29). These genetic studies
are complemented by results obtained from partial
proteo-lysis, sinceafragment spanning amino acids 131to371was
produced which retained the ability to bind to viral origin
sequences(27). This 240-amino-acid DNA-binding fragment islarge when compared withotherDNA-bindingdomainsof less than 100 aminoacids in proteinsofeitherprocaryoticor eucaryotic origin (1, 7, 9, 11, 15, 17, 19, 28). It therefore
seemsplausible that the region oflarge Tantigenresponsible forbinding totheviral origin would beofsimilar size. This prompted us toundertake a study aimed atfurther defining the limits of the T-antigen-specific DNA-binding domain,
*Corresponding author.
tPresent address: Zentralinstitut fur Molekularbiologie, 1115 Berlin-Buch, German Democratic Republic.
i Present address: Lederle Laboratories, American Cyanamid Co.,Pearl River, NY 10965.
with the ultimate goal of isolating and characterizing the minimal specific DNA-binding peptide domain.
Construction of BAL 31 deletion series. The ATG codon (nucleotide [nt] 5163) of a cDNA copy of simian virus 40 (SV40) large T antigen-coding sequences was converted to anNdeI site by oligonucleotide-directed point mutagenesis.
This cDNAwasisolatedas anNdeI-BamHIfragment, which
was directionally cloned into a T7 expression vector (32) between the NdeI and BamHI sites. This places the T-antigen cDNA under control of the T7gene10promoterand transcriptional terminator. This construct, pT7Tag,
pro-duces full-length T antigen in Escherichia coli (R. D.Gerard,
I. J. Mohr, M. Strauss, P. Argani, B. Stillman, and Y. Gluzman, manuscript in preparation) and served as the
starting materialforoursetofBAL 31 deletions.
Plasmid pT7Tag (Gerardetal., inpreparation)wascutat its unique PvuII site (SV40 nt 3506), and 5 ,ug of linear plasmid was treated with 1 U of BAL 31 (New England BioLabs)for2, 4, 8,or 12min.Thelongestincubation time
resulted inanaverage size decrease ofabout 600 basepairs. All four fractions were combined, phenol treated, and cut withBamHI toremovetheC-terminal partof thegeneatthe transcription terminator (32), and the endwasfilledwiththe
Klenowfragmentof DNApolymerase Iinthepresenceof all
four deoxynucleotides for 20 min at room temperature. End-filled DNA (0.5
Vg)
was incubated with 1 pLg ofnonphosphorylated Xba stop linker (see below for the
se-quence of this 14-mer; synthesized by Mark Zoller, Cold Spring Harbor Laboratory) and 10 U of T4 DNA ligase overnightat 14°C. CompetentE.coliDH5wastransformed,
and plasmids containingtheXba linkerwere usedto
trans-formtheBL21(DE3) expressionstrain(32). Extracts of 1-ml cultures(preparedbylysozymetreatment)werechecked for
origin-binding activity. Sequencing was done from the
BamHI site (adjacent to and downstream from the Xba linker) by the chemical degradation technique(14).
Constructionofrecombinant adenoviruses. The adenovirus vectorsused contained the coding regionof the truncated T antigens, starting from the HindIII site (nt 5171), covering theXba stop linker, and ending with aBantHI site derived
from pT7Tag. ThisBamnHI site wasfused tothe BclI site of the SV40 BclI-BamHI fragment, which contains the 3326
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NOTES 3327
A A
Al; ( (;I.! - .111 .;6'S J'i. (S irl
t .I_
266r
+-''
cf-
3<-Z t ;Z:,a inc taB 272 266.1 259.3 708
__
E XE H 7
68--
55-
43-
25-FIG. 1. (A) Sequencesof truncated Tantigensin the vicinityof stopcodons. The top shows truncations createdbyfusion ofHindlll
sites atnt 4002 and 3476; the middle and bottom show truncations
generated byBAL 31treatment.Thefirstnucleotideisno.4043(1). CapitallettersrepresentSV40nucleotideoramino acid sequences. Lowercase letters represent nucleotidesequencesderived from the Xba stop linkeroradditional amino acids translatedfrom the linker
nucleotides.Thepresenceof additional amino acids translatedfrom the Xba linker sequence is reflected in the nomenclature of the
truncated proteins. Thus, 259.3 refers to atruncated protein
con-taining the N-terminal 259 amino acids from SV40 large Tantigen
and 3 additional amino acidsprovided byXbalinker sequences. The asterisks indicate carboxy termini of the proteins. (B) Purified T
antigens producedin E. coliand human HeLa cells. Sodiumdodecyl
sulfate-12.5%polyacrylamide gelofproteins (0.5to 1.5 ,ug) purified
from E. coli (E) or HeLa cells (H). The gel was stained with
Coomassie brilliant blue. The numbersonthe left indicate molecular size in kilodaltons.
polyadenylation signal. The HindIII-BamHI fragment was
expressed behind the major late promoter and one late mRNA leaderof adenovirus type5 after insertionintoearly region I ofa nondefective adenovirus vector (Y. Gluzman, manuscript in preparation).
DNA-binding reactions. Plasmid pOS1 contains the HindlIl (nt5171)-to-Ddel (nt 5228) fragment ofSV40DNA cloned between the HindlIl and BanII (nt 489) sites of
pAT153.The DdeI and BanII endswerefilled inby Klenow
polymerase before ligation. An equimolar mixture of three
origin-containing plasmids (pSVO +, which contains the
wild-type [wt] origin, consistingof sites I andII [31];
pOS1,
which contains site I
only;
andpSVOdl3-site
II containsSV40 nt 5209 to 128
[31])
was assembled anddigested
tocompletion
withTaqI.
This enzyme releases intactSV40
origin-containing
sequences and generates severalplasmid-derived
fragments.
The mixture was then labeled with theKlenow
fragment
of DNApolymerase
I,
extracted withphenol
andchloroform,
andprecipitated
with ethanol.Var-iousamounts ofT
antigen
wereincubated with 50 ngof this mixture inorigin-binding
buffer(10
mM HEPES[N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid; pH 7.4],
100 mM
KCI
1 mMMgCl2,
5%glycerol,
50 ,ug of bovine serumalbuminperml)
for60 minat0°C.
PurifiedPab416
(8)
(5 ,ug)
inorigin-binding
bufferwasadded,
andincubationwascontinuedfor an additional 20 minat
0°C.
A 10%(vol/vol)
Protein
A-Sepharose
CL4B(Pharmacia, Inc.) slurry
(100
RIl)
in NET buffer
(50
mM Tris[pH
7.5],
150 mMNaCl,
5 mMEDTA,
0.05% NonidetP-40)
wasadded,
and the reactionswere incubated on a rocker for 50 min at
4°C.
The beadswere
pelleted,
washed three times with NETbuffer,
sus-pended
in1%
sodiumdodecyl
sulfate-25 mMEDTA,
incu-batedat65°C
for 15 min, andelectrophoresed
on6%
nativepolyacrylamide gels
in a Tris-borate-EDTA buffer system.Gels were dried onto DE81 paper
(Whatman, Inc.)
andautoradiographed
on Kodak XAR film.Dephosphorylation
reactions.Dephosphorylation
reactionswere as described in reference 18. T
antigen
in bufferF(10
mM PIPES
[piperazine-N,N'-bis(2-ethanesulfonic acid); pH
7.0],
5 mMNaCl,
0.1 mMEDTA,
10%glycerol,
1 mMdithiothreitol,
0.5 mMphenylmethylsulfonyl
fluoride[26])
wasaddedtorection vessels
containing
30mMHEPES(pH
8.0),
5 ,ugof bovine serum albumin perml,
and 1 mM(final
concentration)
phenylmethylsulfonyl
fluoride.Calf intestinalalkaline
phosphatase
(CIAP;
0.14 U per ,ugofTantigen)
wasadded,
and thereaction mixturewasincubated for12 minat25°C.
One unit ofCIAP
activity
was definedas theactivity
which
hydrolyzed
1,umol
ofp-nitrophenyl phosphate
in 1 minat25°C.
To
begin
toaddress thelimits oftheDNA-binding
domain,
a cDNA copy of
large
T-antigen
coding
sequences wascloned intoabacterial
expression
vectorunder control of thephage
T7promoter(32).
This cDNA clonewasthen usedtogenerateaBAL31deletionseries from the
carboxy-terminal
endof theprotein-coding
sequences. A14-ntXba linker with stop codons in all threereading
frames(5'
CTAGTCT AGACTAG3')
was used toproduce
truncatedproteins
containing
notmorethanfour additional aminoacidsattheircarboxy
termini. The truncatedproteins
produced
in the T7expression
system wereinitially
assayed
fororigin-specific
DNA-binding
activity
in bacterialextracts.Insertion ofthisstop linkerat theBclI site
(a.a.
682)
hadno effect on the
specific
DNA-binding activity
ofthetrun-cated
protein
produced,
whereasinsertion of thesamelinkerinto the PvuII site
(amino
acid436)
resulted ina truncatedprotein
whichdisplayed
slightly
reduced levels ofspecific
DNA
binding (data
notshown).
ThePvuII sitewasthereforechosen as the
starting
point
for the deletion series. Alldeletions between the PvuII and
HindIII
sites(amino
acid272)
produced
truncatedproteins
which eithercompletely
lacked orpossessed
significantly
reduced levels-oforigin-specific
DNA-binding activity
(data
notshown).
Continuedscreening
of smallerproteins,
surprisingly,
revealed the presence of truncated Tantigens
which hadregained
theability
to bind DNAspecifically.
The C-terminal sequences of theseproteins
aredepicted
inFig.
1A.
In addition toexpressing
these truncated Tantigens
in E.coli,
T-antigen
DNA sequencescoding
fortwoofthesetruncatedpolypep-VOL.61, 1987
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[image:2.612.57.296.95.419.2]3328 NOTES
PItOIG. 259.3
H E H
708
F1 t
a
2 3 3 2 3 2 3 2 3 2 '2i
B
5171 128H3 Ddel 39I1 SphI
< < e--v
[image:3.612.62.299.72.363.2]TI
FIG. 2. (A) Origin-specific DNA binding of truncated and full-size Tantigens. Various amounts of each purifiedTantigenwere
incubated withanequimolarmixtureofend-labeledfragments(lane M).After60minat0°C,Tantigenwasimmunoprecipitatedfrom the reactionand theboundDNAfragmentswereelectrophoresedon a
6% nativepolyacrylamide gel. Theamountsof Tantigenpresentin each set of reactions 1, 2, and 3 were 50, 150, and 450 ng,
respectively. The numbers at the top of the figure refer to the individualproteins purifiedfrom E.coli(E)orHeLacells(H). (B)
DNA templates containing SV40 origin sequences. These SV40 DNA fragments were present in equimolar amounts in all DNA-bindingexperiments. They containthewtSV40origin region(w.t.), siteI(), orsite 11(I),andtheirpositionsarenotedtotherightof theautoradiograms in Fig. 2A and 3. Thehorizontalarrows
repre-sentpentanucleotide-bindingsites for Tantigen(3), and the boxes delineatethe various sites(30). Theverticalarrows indicate cleav-age sites forrestriction endonucleases.
information as to the ability of the protein to
transiently
recognize specific sequences within the DNA fragment in
question. DNase footprinting studies have demonstrated
thatthetruncatedproteinsprotect thesameDNAsequences as full-length T antigen, although higher concentrations of
the truncated proteins are required to achieve similar de-grees ofprotection (W. Ryan and Y.Gluzman,
unpublished
data).
Equimolarquantities of DNAfragments containing site I
only (pOS-1), site II
(pSVOdl3),
and the entire wtorigin
(pSVO+) were mixed together to compare directly the
relative strength ofbindingtotheindividual
sites,
aswellas to the natural viral origin (Fig. 2B). Full-length Tantigen
from HeLa cells iscapable ofbindingtoallthree
fragments
in this mixture (Fig. 2A and 3). Itboundefficiently to both
the wt origin and the site I fragment at all concentrations examined;however, itboundtothefragment containing site
II atthe highestconcentration examined.
Interestingly,
the 272 and 266.1-amino-acid truncatedproteins
from E.coli,
originally identified as non-DNA-binding proteins in our
crude-extract screening procedure, bound the wt
origin
fragmentwith low efficiency upon
purification.
Fusionpro-teinsexpressed inE. coli,whichcontain theN-terminal272 amino acids of Tantigenalsobindto wtoriginsequences(D. Lane,
personal communication;
E.Fanning, personal
com-munication). The smaller 259.3
protein produced
in E. coli standsin contrast totheaforementioned truncatedpolypep-tides, sinceitefficiently bindstofragmentscontaining thewt
origin of
replication.
This resurgence of specificDNA-binding activitysuggeststhatanobstructiontoDNA
binding
was removed between amino acids 266 and259. Examina-tion ofprotein-coding sequences between amino acids 266 and 259revealedthe presenceof fouradjacent glutamic acid residues. The presenceofthesenegatively charged residues proximaltotheDNA-binding domainmayaffectthebinding capability ofthefull-length
protein;
furthermore, these res-idues may have more pronounced deleterious effects whenthey are present on the extreme carboxy terminus of the
Tog 259.31HW 259.3(E) 708(H)
CAP 4 - - -1
.~~
_tides (266.1 and 259.3) were cloned into an adenovirus
expression vector and overproduced in mammalian cells (Gluzman, inpreparation). Proteins from both bacterial and mammalian sources were purified to homogeneity by im-munoaffinity chromatography on immobilized PAb419 (26;
Fig. 1B).
The DNA-binding properties of purified, truncated
pro-teinsfrommammalian andbacterialsourceswerecompared
withthoseofwtfull-lengthTantigen frommammalian cells. InthisDNA-bindingassay,theproteinwasincubated witha
mixtureoflabeledDNAfragments andimmunoprecipitated afterallowanceof time for protein-DNAinteraction. Specific DNAfragmentsboundtotheproteinwerethenvisualized by electrophoresis followed by autoradiography (16). The monoclonal antibody used in these studies, PAb 416 (8), recognizes adenaturation-resistant epitope locatednearthe
Nterminus of both truncatedandfull-length proteins. DNA binding, as measured by this assay, reflects formation of
stable, specific protein-DNA complexes but provides no
_
~~4o
-Wt.- _ -I
2 3 2 3 2' 3 2 3 2 3 2 3
FIG. 3. Effect of dephosphorylation on origin-specific DNA
binding. Variousamounts of untreated purifiedTantigen(-) orT
antigen treated with CIAP (+) were incubated with an equimolar
mixture of end-labeled DNA fragments. DNA-binding reactions
wereperformedasdescribed in the legendtoFig.2. Theconditions
for CIAP treatment were as previously described (18). The high-molecular-weight bands appearing on the autoradiogram varied
between experiments and reflect nonspecific binding to protein A-Sepharose.
A
I I
J. VIROL.
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[image:3.612.321.557.472.641.2]NOTES 3329 truncated T antigens. The fact that the purified truncated
proteins from E. coli bound only to fragments containing the wt origin but not to fragments bearing only site I or II at equivalent protein concentrations suggests that cooperativ-ity may exist between binding sites. It is also possible that higher protein concentrations or additional protein se-quences arerequired to recognize these sites individually. In
regard to the latter possibility, it is worth noting that
full-length Tantigen producedin E. coli fails to bind to site II only containing fragments at concentrations at which HeLa cell-produced T antigen binds efficiently (Gerard et
al., in preparation). Footprinting studies in progress will address this question further.
Significant quantitativeandqualitative differencesin
bind-ing were observed when proteins 259.3 and 266.1 purified
from HeLacells were used in this assay and compared with the bacterially produced proteins. Protein 266.1from HeLa cellsboundtofragments containingthe wtoriginatthreefold
reduced concentrations of protein and to fragments contain-ing site II at the highest protein concentrations. Protein 259.3
from HeLa cells bound DNA more efficiently than did
protein 266.1 and about as efficiently as did full-length T
antigen from HeLa cells. Protein 259.3 represents approxi-mately one-third of the length of full-size T antigen;
there-fore, identical-weight amounts ofeachprotein actually rep-resent athreefold molar excessofthe truncatedpolypeptide. Thus, in Fig. 2, lane 2 of259.3 and lane 3 offull-length T
antigen (708 amino acids) represent equivalent molar
quan-tities ofprotein inthe DNA-binding reactions. Full-length T
antigen first forms complexes with wt origin and site I
fragments, whereas site II fragments are bound at higher protein concentrations. However,the truncated mammalian proteins first form complexes with wt origin fragments and then begin to bind site IIfragments. It is possible that the
truncated proteins may be folded in a conformation which
enhances binding to site II fragments. Alternatively,
addi-tional amino acids may be required for certain truncated
proteinsto bind efficiently to site I. The latterpossibility is
unlikely, since truncatedT
antigens
shorter than 259 aminoacidsdisplay efficientbindingtositeI
fragments
(M.Strauss and D. McVey, personalcommunication).
The fact that the truncated
proteins
from bacterial cellsexhibit differentDNA-binding propertiesfromtheir mamma-lian counterparts suggests that
posttranslational
modification provided by amammalian cell may influencespecific
DNAbinding. T
antigen
isphosphorylated
at an amino-terminal cluster and acarboxy-terminal
cluster(24),
andprevious
studieshavedemonstrated that the
phosphorylation
stateof large T antigen affects itsability
toreplicate
SV40origin-containingDNA(18)andbindtoDNA sequencescontained
within the SV40 origin (18, 25, 27a). Upon
partial
dephos-phorylation
oflarge Tantigen
withCIAP,
an up to 20-foldincrease in DNA
replication activity
in vitro was observedundersome
conditions,
concomitant withafour- tofivefoldactivation of
specific
DNAbinding
to site 11(18).
It wastherefore ofinteresttoascertainthe effectofCIAPtreatment
on the
specific
DNA-binding
properties
of these truncatedproteins,which arealso
phosphorylated
inHeLacells(data
not shown). When adenoviral vectors are used to
produce
full-length
Tantigen
in HeLacells,
truncatedproteins
con-taining
approximately
the first 130 amino acids are alsoproduced because of an incorrect
splicing
event. Thesetruncated
proteins
containthe amino-terminalphosphoryla-tion cluster andarealso
phosphorylated. Furthermore,
thesesame
proteins
are also substrates forCIAP-mediated
dephosphorylation.
This demonstrates that truncatedpro-teins which possess
only
asingle phosphorylation
clustercan be
partially dephosphorylated (approximately
80%) by
CIAP
(18).
We arecurrently
examining
theprecise
siteswhichareaffected bythistreatment.
In agreement with
previously published data,
CIAP-treated T
antigen
displayed
aslight
increase inbinding
tofragments
containing
the wtorigin
and site Ionly
and asignificant
increase inbinding
tosite II. Thebinding
proper-ties of 259.3 from E. coli were not altered after CIAP
treatment
(full-length
Tantigen produced
in E. coliisphos-phorylated
to a much lesser extent than HeLaTag;
R. D.Gerard,
I.J.Mohr,
M.Strauss,
P.Argani,
B.Stillman,
andY.
Gluzman,
manuscript
inpreparation).
Similartreatmentof the truncated 259.3
protein produced
in HeLa cells resulted inonly
aslight (if
any) increaseinbinding
tobothwtorigin-
and siteIl-containing fragments.
Twointerpretations
ofthis resultare
possible.
In thefirst, dephosphorylation
of the amino-terminal cluster has no role inmediating
theobserved activation of DNA
binding,
while thecarboxy-terminal clusterof
full-length
Tantigen
isentirely
responsi-blefor this
phenomenon. However,
asecondinterpretation
is
possible,
in which additionalprotein
sequences,whicharenotconstituents of the minimal
DNA-binding
domainorthephosphorylation clusters,
arerequired
to visualize theacti-vation mediated
by
dephosphorylation.
Since bothphos-phorylation
clusters lieoutsidetheregion implicated
in DNAbinding,
removal ofphosphate
groups must thenindirectly
affect or
regulate
theDNA-binding
activity
ofthepolypep-tide.
The
DNA-binding
domain ofTantigen, although
it canfunction
independently,
appears to be a component of asuperstructure which modulates its
activity.
The actualdomainis less than 130 amino acids in size if the C-terminal
boundary
liesproximal
to Pro 259 and the N-terminalboundary
is taken to beLys-131 (29).
Once the domain isreleased from the constraints
imposed by
thelarger
struc-ture, it is free to bind with greater
efficiency,
since the shorter 259.3protein
binds DNA better than does itslonger
truncated counterparts. It is
interesting
that all ofthetrun-cated
proteins
described here aremissing
the zincfinger
structural motif
(Cys-X2-4-Cys-X2>15-His-X24-His)
at amino acids 302 to 320(2).
Although
no functional role for this structure has been demonstratedforlarge
Tantigen,
it hasbeen
suggested
that thesestructuresmaybe involved in theDNA-binding
activities manifestedby
severaleucaryotic
DNA-binding proteins (17;
see reference 2 for areview).
Thus,
thisfinger
structure cannotbeamajor
determinantofbinding
specificity
forlarge
Tantigen;
however,
it still maybe involved in
modulating
theDNA-binding
activitiesofthispolypeptide.
Posttranslational modification isan additional component
ofthis
regulatory
system which wouldsubject
it toan evenfiner level of control. The fact that truncated
proteins
produced
in mammalian cellsdisplay
increased levels ofDNA
binding
supports this notion. Protein259.3, however,
does not
display
the characteristic activation of site IIbinding following
dephosphorylation
exhibitedby
thefull-length
polypeptide.
This suggests that additional sequenceelements,
which are not constituents of the minimalDNA-binding domain,
arerequired
to visualize the activation insite II
binding
brought
aboutby
dephosphorylation.
Thesedynamic
posttranslational
modifications,
which also lieout-side the minimal
DNA-binding
domain,
are excellentcandi-dates foragentswhich would modulate the conformation of the superstructure and thus
change
theaccessibility
oftheDNA-binding
domain.VOL. 61,1987
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3330 NOTES
We thank Bruce Stillman, Ed Harlow, John Anderson, and WinshipHerrfor critically readingthemanuscript,JoanCossettifor excellent technical assistance, and Marilyn Goodwin for help in preparing the manuscript.
This work wasfunded byPublic Health Service grant CA 13106 fromthe National Cancer InstitutetoColdSpring Harbor Labora-tory.
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