Supplementary Methods
Plasmids and Expression Vectors
The c-Myc expression vectors pRcCMV-Myc2 and retroviral pWZLneo-Myc2
have been previously described30, 13. To generate Myc-YFP, the EcoR1-BamHI cMyc fragment was removed from pBabepuro-Myc2ER13 and subcloned into
EcoR1-BamH1-digested pEYFP-N1 (Clontech), resulting in fusion of Yellow
Fluorescent Protein (YFP) to the C-terminus c-Myc. To generate pBabepuroARF, the EcoR1 fragment digested from pCMV5-ARF (containing mouse p19ARF)
was inserted into the EcoR1 site of the retroviral pBabepuro vector. For pBabehygro-Myc2ER, the EcoRI fragment was digested from pBabepuro-Myc2ER was
inserted into the EcoRI site of the retroviral pBabehygro vector. All constructs
were verified by sequencing. The luciferase and SEAP reporter constructs, htertSEAP, cul1-luc, gadd45-luc and pdgfr-luc, have been previously described8, 10, 11,
12.
pRL-TK was obtained from Promega. c-Myc deletion constructs were made
using PCR-mediated mutagenesis (Advantage 2 PCR system; Clontech). All
mutations were confirmed by DNA sequencing. To generate c-Myc N ( 1-167),
an ATG in optimal Kozak consensus sequence (ACCATGG) was introduced at
amino acid 168 by PCR amplification using the primers 5’
AAGCTTACCATGGGGCACAGCGTCT 3’ and 5’
GCGTCTAGATAGGTCAGTTTATGCACCAGAG 3’ and the cDNA was
transferred to pGEM-T Easy Vector (Promega) followed by subcloning into
pcDNA3 (Invitrogen). To generate c-Myc C (368-439), a TAA stop codon with
XbaI site was introduced at amino acid 368 by PCR amplification using the
primers 5’ CTACCAGGCTGCGCGCAAAGAC 3’ and 5’
CGTCTAGACTATTACCTCCTCTGACGTTCC 3’ and the PCR product was
transferred to pGEM-T Easy Vector followed by SacII/XbaI digestion. The SacIIXbaI c-Myc fragment from pRcCMV-Myc2 was then substituted by the SacIIXbaI c-Myc C fragment. To generate c-Myc N+C (167 + 368-439), the
HindIII-BfaI fragment of c-Myc C was substituted by the HindIII-BfaI fragment
of c-Myc N. To generate c-Myc 1-144, an ATG start codon in Kozak consensus
sequence with EcoRI site was introduced at the N-terminus and a TAA stop
codon with EcoRI site was introduced at amino acid 145 using the primers 5’
GAATTCGCCACCACGATGCCCCTC 3’ and 5’
CTAGTGATTTTACAGCTTGGCAGCGGC 3’. The PCR product was then
subcloned into the EcoR1 site of pCMV-Tag2 (Stratagene). For generation of cMyc 250-367, the same strategy was employed using the primers 5’
GAATTCGCCACCATGGACTCTGAAGAACAA 3’ and 5’
GGCCTCGAGCTATTAGTTCCTCCTCTGACG 3’.
Cell Culture, Transfection, and Retroviral Infection
Cos-7 cells, p53-/- MEFs, ARF-/- MEFs, p53/ARF double null (DKO) MEFs and
REF112 cells were cultured in DMEM with 10% calf serum. Wild-type MEFs
from day 14 embryos were isolated and maintained on a 3T9 protocol and
propagated in DMEM with 10% fetal calf serum (FCS). HO16 (c-myc-/-) cells
were maintained as previously described13. Cos-7 cells were transfected using
the calcium phosphate method, and MEF cells using Fugene 6 (Roche), with the
indicated plasmids. Cells were subjected to analysis approximately 48 hr after
transfection. The p53-/- MycER MEFs and DKO MycER MEFs were generated
using the retroviral expression vector pBabehygro-Myc2ER as described
previously13. Rat1a stably expressing c-MycER with or without ARF were
generated as described previously13 using the retroviral expression vectors
pBabepuro-ARF and pWZLneo-c-Myc2ER.
PCR primers
Quantitative Real-Time PCR
Nucleolin
fwd: 5’ ACACCAGCCAAAGTCATTCC 3’
rev: 5’ ATCCTCATCACTGTCTTCCTTC 3’
CDK4
fwd: 5’ GCAGTCTACATACGCAACAC 3’
rev: 5’ TCGTCTTCTGGAGGCAATC 3’
eIF4E
fwd: 5’ GGACGGGATTGAGCCTATGTG 3’
rev: 5’ CAGCAGTGTCTCTAGCCAGAAG 3’
htert
fwd: 5’ ATGGCGTTCCTGAGTATGG 3’
rev: 5’ TGAGTGTCCAGCAGCAAG3’
Cul1
fwd: 5’ GCTTGTGGTCGCTTCATAAAC 3’
rev: 5’ TGTCTTCTAGTTCTGCCTCTTC 3’
gadd45
fwd: 5’ GCTGGCTGCTGACGAAGAC 3’
rev: 5’ CGGATGAGGGTGAAATGGAT 3’
p15INK4b
fwd: 5’GGTTCCCTCCGCCTTCTG 3’
rev: 5’ GCCCTCTTCGTGCTTGCA 3’
ChIP
eIF4E
fwd: 5’ AGAGGCCTAAATCCAACTCGGCA 3’
rev: 5’ AAGGCAATACTCACCGGTTCCACA 3’
Nucleolin
fwd:5’ GGCGATCTGCTGTCTCTG 3’
rev: 5’ CAACTGCTTCCCACTTCTC 3’
Northern Blot Analysis
Total RNA was prepared from cells with TRIzol reagent (Invitrogen). Ten µg of
total RNA was separated on 1% agarose, 5.4% formaldehyde denaturing gels and
transferred to Hybond-N+ membranes (Amersham). Blots were then UV crosslinked, prehybridized, hybridized, and washed according to the manufacturer’s
instructions (ULTRAhyb; Ambion). cDNA probes were labeled with [32P]-dCTP
(ICN) using the PrimeIt II random labeling kit (Stratagene).
Cell Proliferation and Apoptosis Assays
One day after seeding at 5x104/35 mm dish in media containing 10% FCS, p53-/MycER and DKO MycER MEFs were treated with 1 M OHT as indicated and
refed with media containing 1 M OHT daily. The number of attached cells
(living cells) and floating cells (apoptotic cells) was determined in triplicate at the
indicated times. Apoptosis was confirmed by detection of caspase-3 activation
using a specific antibody (Pab CM1; BD PharMingen). Each time course was
representative of at least two different monoclonal cell lines. For growth rate
analysis of Rat1a MycER or Rat1a MycER+ARF monoclonal cell lines, cells were
seeded and treated as described above except cells were shifted into media
containing 20%FCS and 0.25 M OHT. For the apoptosis assay, Rat1a MycER
cell or Rat1a MycER+ARF cell lines were plated at 2.5x105/35 mm dish and
shifted 48 hr later into media containing 0.5% serum without or with 1 M OHT
for 4 days. The number of floating (apoptotic) and attached (living) cells was
determined in triplicate at the indicated times. Apoptosis was confirmed using
DNA fragmentation analysis as described previously13. The data was converted
to ratio of apoptotic cells to living cells and plotted over time. Representative
data is shown from experiments using four different monoclonal cell lines.