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Molecular and Cellular Biology, December 2000, p. 9203-9211, Vol. 20, No. 24
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
c-Myb Binds to a Sequence in the Proximal Region of
the RAG-2 Promoter and Is Essential for Promoter Activity in
T-Lineage Cells
Qian-Fei
Wang,
Josh
Lauring,
and
Mark S.
Schlissel*
Department of Molecular and Cell Biology,
University of California, Berkeley, California 94720-3200
Received 10 August 2000/Returned for modification 9 September
2000/Accepted 19 September 2000
 |
ABSTRACT |
The RAG-2 gene encodes a component of the V(D)J recombinase which
is essential for the assembly of antigen receptor genes in B and T
lymphocytes. Previously, we reported that the transcription factor BSAP
(PAX-5) regulates the murine RAG-2 promoter in B-cell lines. A
partially overlapping but distinct region of the proximal RAG-2
promoter was also identified as an important element for promoter
activity in T cells; however, the responsible factor was unknown. In
this report, we present data demonstrating that c-Myb binds to a Myb
consensus site within the proximal promoter and is critical for its
activity in T-lineage cells. We show that c-Myb can transactivate a
RAG-2 promoter-reporter construct in cotransfection assays and that
this transactivation depends on the proximal promoter Myb consensus
site. By using a chromatin immunoprecipitation (ChIP) strategy,
fractionation of chromatin with anti-c-Myb antibody specifically
enriched endogenous RAG-2 promoter DNA sequences. DNase I genomic
footprinting revealed that the c-Myb site is occupied in a
tissue-specific fashion in vivo. Furthermore, an integrated RAG-2
promoter construct with mutations at the c-Myb site was not enriched in
the ChIP assay, while a wild-type integrated promoter construct was
enriched. Finally, this lack of binding of c-Myb to a chromosomally
integrated mutant RAG-2 promoter construct in vivo was associated with
a striking decrease in promoter activity. We conclude that c-Myb regulates the RAG-2 promoter in T cells by binding to this consensus c-Myb binding site.
 |
INTRODUCTION |
Antigen receptor genes are assembled
during B- and T-cell development by a series of site-specific DNA
recombination reactions known as V(D)J recombination (58).
The lymphocyte-specific gene products RAG-1 and RAG-2 are essential
components of the V(D)J recombinase complex (38, 44, 51).
Together, they recognize recombination signal sequences which flank
rearranging gene segments and introduce double-stranded DNA breaks
between these signals and gene-containing DNA segments (16).
A null mutation in either gene prevents V(D)J recombination and
completely blocks lymphocyte development at the early progenitor stage
(38, 51).
The RAG-1 and RAG-2 genes are physically linked in the genomes of all
chordates in which they have been studied; they are convergently
transcribed and separated by approximately 8 kb of DNA (50).
Coupled with the recent observation that the RAG proteins have DNA
transposase activity in vitro, these unusual structural features of the
RAG locus have led to the suggestion that RAG-1 and RAG-2 were once
part of a transposable-element system (1, 26, 56).
Transcription of the RAG-1 and RAG-2 genes is limited to specific
stages of B- and T-cell development. Transcription can be detected in
the earliest T- and B-cell progenitors and remains high until the
complete assembly of the T-cell receptor (TCR)
chain gene or the
immunoglobulin (Ig) heavy-chain gene (19, 60, 63). During
the midstages of lymphoid development, RAG transcription diminishes
significantly, coincident with several rounds of cell division. Pre-T
and pre-B cells then exit the cell cycle and increase RAG
transcription, leading to rearrangement of the TCR
or Ig
light-chain loci (19, 63). RAG transcription continues in T
cells until positive selection occurs, at which time expression is
extinguished via a TCR-dependent signal (60). The situation
in B cells is more complex. RAG transcription generally stops when a
complete Ig molecule is expressed on the cell surface (19).
However, if that Ig recognizes self-antigen, RAG expression is
stimulated, and recombination continues in a process known as receptor
editing (15, 35, 57). Thus, regulated RAG expression contributes to self-tolerance of the B-cell repertoire. Finally, the
RAG genes are not expressed in mature peripheral T and B cells; however, there are some data which suggest that transcription [as well
as V(D)J recombination] can be reactivated in B cells during an
antigen-specific immune response (20, 21, 24, 25, 46). Given
the complex regulation and critical involvement of the RAG genes in
lymphocyte development, efforts have been made to decipher the
molecular basis of their transcriptional regulation.
Previous studies performed in our own laboratory and in others have
described the general structure of the murine and human RAG-1 and RAG-2
promoters (13, 31, 32, 65). We reported recently that unlike
the RAG-1 promoter, the murine RAG-2 promoter displays cell-type
specificity in transient-transfection assays (32). A RAG-2
promoter-reporter construct containing the transcription start site and
279 bp of 5' flanking DNA was fully active in both T- and B-cell lines.
Surprisingly, we found that a 5' promoter deletion mutant extending to
nucleotide
71 with respect to the start site retained full activity
in B cells but lost approximately 70% of its activity in T cells.
Further deletion of the promoter to position
45 eliminated nearly all
activity in both B and T cells (32). The DNA sequences of
the murine and human RAG-2 promoters are identical between nucleotides
70 and
50. Within this region, we identified a binding site for the
B-cell-specific transcription factor BSAP (Pax-5) and showed that BSAP
binds this sequence both in vitro and in vivo. Furthermore, mutations
which disrupt BSAP binding greatly diminish B-cell-specific promoter activity. T cells, however, do not express BSAP but still require sequences in the conserved
70 to
50 promoter region for RAG-2 promoter activity (32). Recent reports suggested that c-Myb, a hematopoietic lineage-restricted transcription factor, is
preferentially expressed in developing T but not B cells (2,
11) (see below). In the experiments described below, we have gone
on to determine that c-Myb binds to the RAG-2 promoter and is critical
for RAG-2 promoter activity in T cells.
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MATERIALS AND METHODS |
Cells and cell culture.
Thymocytes used in the chromatin
immunoprecipitation (ChIP) assay were isolated from 3-week-old C57BL/6J
mice (Jackson Laboratory). Jurkat, a mature human T-cell lymphoma line,
and 2017 (54), an Abelson virus-transformed immature murine
T-cell line, were grown at 37°C and 5% CO2 in RPMI 1640 (Mediatech) supplemented with 10% fetal calf serum,
penicillin-streptomycin, L-glutamine, and 50 µM
-mercaptoethanol. 293T, a human embryonic kidney cell line
expressing simian virus 40 T antigen, and HeLa (human cervical carcinoma) cells were grown in Dulbecco's modified Eagle's medium (Mediatech) with 1 g of glucose per liter, supplemented with 10% fetal calf serum, L-glutamine, penicillin-streptomycin, and
50 µM
-mercaptoethanol.
Plasmid constructs.
The RAG-2 promoter constructs used in
the various cotransfection assays have been described previously
(32). The eukaryotic c-Myb expression construct was created
by cloning the murine c-Myb cDNA (a gift from Chi Dang) into the
pEFBneo vector (a modified version of pEF-BOS [37]).
The basic stable-transfection reporter construct consisted of the
PGK-neo drug resistance cassette and the green fluorescent protein
(GFP) cDNA, intron, and polyadenylation signal from pGreenLantern
(Gibco-BRL) separated by the pBSK polylinker. Tandem copies of the
1.2-kb chicken
-globin insulator were excised from pJC13
(10) and cloned into the XbaI site of the
polylinker. The RAG-2 promoter from
279 to +123 was cloned in the
proper orientation upstream of the GFP cDNA. A 4-kb
HindIII fragment containing the E
enhancer core was
cloned into polylinker sites upstream of the promoter and downstream
from the insulator sequences.
Transient-transfection reporter assay.
For cotransfection
experiments, 10 µg of the
279 to +123 reporter, 2 µg of either
empty pEFBneo vector or pEFBneoMyb, and 100 ng of p-CMV-
-gal were
used. 293T cells were transfected with GenePorter reagent (Gene Therapy
Systems) and 2017 cells were transfected with Superfect reagent
(Qiagen) according to the manufacturers' instructions. The cells were
harvested as described previously (32). Luciferase activity
was measured with a luminometer (Analytical Luminescence Laboratories).
-Galactosidase assays were performed with the Galacto-Light Plus Kit
(Tropix) according to the manufacturer's instructions. Luciferase
activity for each sample was normalized to the
-galactosidase assay control.
Stable-transfection reporter assay.
Twenty micrograms of
each linearized construct in 40 µl of sterile phosphate-buffered
saline was mixed with 107 cells resuspended in 800 µl of
culture medium. The cells were in the logarithmic phase of growth. The
mixture of cells and DNA was electroporated at 250 V and 960 µF in a
0.4-cm-gap electroporation cuvette (Bio-Rad). The cells were grown in
50 ml of medium for 48 h without G418, and then 3 × 104 cells were seeded into each well of two 24-well plates
in the presence of 2 mg of G418 (Life Technologies)/ml. After 12 to 14 days of selection, all wells were positive, and they were pooled. This
ensured an adequate number of founder cells, each of which represents
an independent integration event.
G418-resistant cells were subjected to flow cytometry analysis and ChIP
assay. FACStar PLUS and CELLQuest software (Becton Dickinson) were used
for fluorescence-activated cell sorter analysis.
ChIP.
The formaldehyde cross-linking and immunoprecipitation
experiments were done as reported by Boyd and colleagues
(9). In brief, 37% formaldehyde solution (Fisher
Scientific) was added directly to cell culture medium at a final
concentration of 1%. In the case of the mouse thymocytes, the solution
was added to a single-cell suspension of thymocytes in culture medium.
Cross-linking was allowed to occur at room temperature for 10 min. The
cells were lysed, and the nuclei were collected and resuspended in
sonication buffer. Chromatin was sonicated to an average length of 400 to 800 bp, and the suspension was precleared with blocked
Staphylococcus A cells. Chromatin from 4.5 × 107 cells was then incubated with 4 µg of c-Myb-specific
rabbit polyclonal antibody (for Jurkat cells, anti-human c-Myb; for
mouse thymocytes, anti-mouse c-Myb [Santa Cruz]), affinity-purified
rabbit IgG (Jackson Immunoresearch), or no antibody and rotated
overnight at 4°C. The immune complexes were precipitated, washed, and
eluted. After precipitation, supernatant from the "no-antibody"
sample was processed to the cross-link reversal step and analyzed as
unfractionated input chromatin. Cross-links were reversed. After
proteinase K digestion, samples were phenol extracted, and DNA was
ethanol precipitated and resuspended in 30 µl of H2O. Two
microliters of immunoprecipitate or 50 ng of total input DNA was used
for 28 cycles of PCR amplification. PCR products were analyzed by electrophoresis on a 2% agarose gel and visualized by ethidium bromide
staining or denatured and transferred onto a Hybond-N membrane
(Amersham) for Southern blot analysis. The following primers were used
in the ChIP assays: human RAG-2 promoter, hR2U (5'GTGAATTGTGTTGCCATTGTTGC) and humR2P-2
(5'TGTGTGCCTACAGATGTTC); human RAG-2 coding exon,
hRAG-2exon2/F (5'GTTCTTCTGCTGAAAGTTC) and HRAG-2exon2/B
(5'GGTGATGGAAACAACAAAAG); human
-actin, hBA1 (5'CATGTGCAAGGCCGGCTTCG) and hBA2
(5'GAAGGTGTGGTGCCAGATTT); mouse RAG-2 promoter, R2F1
(5'CAACCATCACAGGGGTGCAG) and R2R2
(5'GCCTACAGATGTTCCAGTGAG); and mouse Ig kappa locus, Jk1F
(5'ACCAGATTCTGGCACTCTCC) and JkREV (5'GAGTAAGATTTTATACATCATTTTTAGACA).
DNase I genomic footprinting.
DNase I genomic footprinting
was performed as described by Weinmann et al. (62). In
brief, Jurkat or HeLa cells were harvested and resuspended in cold
NP-40 lysis buffer. Samples were incubated on ice for 5 min, and intact
nuclei were pelleted and resuspended in DNase I digestion buffer.
Genomic DNA was purified from Jurkat cells by proteinase K treatment,
phenol extraction, and ethanol precipitation. DNase I (Boehringer
Mannheim Biochemicals) was added to nuclei (from 3 × 106 cells) or pure genomic DNA (from 8 × 106 cells) to various final concentrations (nuclei, 2 to 10 U/sample; genomic DNA, 0.2 to 0.8 U/sample) and incubated on ice for 5 min. Reactions were stopped and processed for DNA purification. DNA was
resuspended in H2O, and its concentration was determined by spectrophotometry. One microgram of DNA was subjected to
ligation-mediated PCR. The PCR cycles were as follows: for primer
extension, 95°C for 5 min, 59°C for 30 min, and 76°C for 10 min;
for amplification of ligated products, 95°C for 4 min, 60°C for 2 min, and 76°C for 3 min for one cycle, 20 cycles of 95°C for 1 min,
60°C for 2 min, and 76°C for 3 min 15 s/cycle, and final extension
for 10 min at 76°C; for labeling reactions, 95°C for 4 min, 61°C
for 2 min, and 76°C for 10 min for one cycle and two cycles of 95°C for 1 min, 61°C for 2 min, and 76°C for 10 min/cycle. The following locus-specific primers were used: primer extension, 5'
TGCCGCTAAACCAGGTATTAA; amplification, 5'
TTAATTGTCAGCACTTGGGGA; end labeling,
5'ATTGTCAGCACTTGGGGAAGA; and DNA sequencing, 5'
ATCTTTGCCGCTAAACCAGGT. Samples were heated to 90°C for 5 min
and analyzed by electrophoresis on a 6% polyacrylamide-7 M urea
denaturing gel alongside a DNA sequencing ladder. The gels were dried
and exposed to PhosphorImager screens.
 |
RESULTS |
c-Myb activates the RAG-2 promoter in cotransfected cell
lines.
During characterization of the BSAP binding site in the
70 to
50 region of the murine RAG-2 promoter, we generated a series of 5-bp substitution mutations across this interval (Fig.
1A). An analysis of these promoter
mutations suggested that distinct DNA sequences within this small
region were necessary for promoter activity in B- and T-lineage cell
lines (32).

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FIG. 1.
c-Myb transactivates the RAG-2 promoter through a
proximal-region binding site. (A) Critical sequences in the murine
RAG-2 promoter. The major transcription start site is numbered +1. The
boxed regions represent sequences important for promoter activity in
transiently transfected Jurkat T cells (32). The human and
murine proximal-region DNA sequences are shown, with the BSAP binding
site in boldface and a potential c-Myb site indicated by the thin
horizontal bar above the sequence. The thick bar denotes a 20-bp region
of complete identity between murine and human sequences. The sites and
DNA sequences of four substitution mutations (labeled 1, 2, 3, and 4)
are shown in boxes below the sequence. (B) Diagram of the
transient-transfection assay vector for RAG-2 promoter activity. Each
substitution mutation was analyzed in the context of the full 279 to
+123 promoter. The arrow indicates the transcription start site. (C)
Luciferase assay analysis of transient transfections into 2017 murine
pre-T cells. The cells were cotransfected with the RAG-2
promoter-reporter construct and either empty expression vector ( ) or
c-Myb expression vector (+). Two 5' promoter deletion mutants
( 71/+123 and 45/+123) and four 5-nucleotide substitution mutations
(labeled 1 to 4) were also tested. The results are shown as the fold
increase in luciferase activity with c-Myb cotransfection compared to
the activity with empty vector (the actual luminometer unit readings
were 2,759 ± 434 for the wild-type promoter cotransfected with an
empty expression vector and 194,886 ± 228 for the wild-type
promoter cotransfected with the c-Myb expression vector). The data
shown are the average (+ standard deviation) of two experiments, each
performed in duplicate and adjusted for transfection efficiency using
-galactosidase. (D) Luciferase assay analysis of transient
transfections into 293T human embryonic kidney cells as described for
panel C. The actual luminometer unit readings were 1,723 ± 96 for
the wild-type promoter cotransfected with an empty expression vector
and 16,573 ± 67 for the wild-type promoter cotransfected with the
c-Myb expression vector.
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A transcription factor database analysis of the proximal regulatory
region of the murine RAG-2 promoter revealed a perfect match to the
consensus binding site for the hematopoietic lineage transcription
factor, c-Myb (PyAACG/TG [8]) (Fig. 1A). The murine
and human RAG-2 promoter sequences are identical from positions
70 to
50 and contain this consensus c-Myb binding site. Two other potential
transcription factor binding sites in the proximal promoter region (a
second c-Myb site and an Ikaros site) were not located in this region
of identity, and we did not pursue them further.
To test whether c-Myb can transactivate the murine RAG-2 promoter, we
cotransfected cell lines with variants of a RAG-2 promoter-luciferase reporter construct (Fig. 1B) and either an empty expression vector or a
murine c-Myb expression vector. Each transfection was done in
duplicate, and each experiment was performed at least twice. The
reporter construct itself had very little activity in 2017, a mouse
pre-T-cell line which expresses very low levels of endogenous RAG-2 and
c-Myb mRNAs (Fig. 1C) (reference 54 and data not
shown). Cotransfection of the c-Myb expression vector resulted in an
almost 40-fold increase in luciferase activity (Fig. 1C). To localize the DNA sequences responsible for this effect, different truncations of
the promoter were tested in cotransfection experiments. A 5' deletion
extending to nucleotide
71 retained the same sensitivity to c-Myb
coexpression as the wild-type promoter, while further truncation
deleting the proximal region almost abolished the stimulatory effect of
c-Myb on the RAG-2 promoter. We further analyzed our set of 5-bp
substitution mutations across this proximal region in the context of
the full
279 to +123 promoter (Fig. 1A). In the presence of c-Myb,
mutants 1 and 2 still gave an approximately 35- to 65-fold increase in
promoter activity, while mutants 3 and 4, which disrupt the Myb site
and a sequence immediately adjacent to that site, respectively,
resulted in a significant decrease in promoter activity. When 293T, a
human embryonic kidney cell line, was tested in the cotransfection
assay, the same pattern of promoter activity was observed (Fig. 1D).
Overall, c-Myb stimulated the RAG-2 promoter to a greater extent in
2017 cells than in 293T cells. This may be due to the fact that 2017 is
an immature T-cell line, which may provide lymphoid-specific factors to
cooperate with c-Myb, resulting in higher levels of reporter gene expression.
Similar cotransfection studies failed to reveal any stimulatory effect
of c-Myb on RAG-2 promoter activity in Jurkat cells (a human T-cell
lymphoma line which expresses RAG-2 [data not shown] [see below]).
Our previous studies showed that the cloned RAG-2 promoter is very
active in these cells (32). Western blot analysis also
showed that Jurkat cells express a high level of c-Myb protein (data
not shown). Reporter gene expression may already be saturated in this
system without introducing any exogenous activators.
c-Myb binds to the RAG-2 promoter in vivo.
Although Jurkat
cells were reported to lack V(D)J recombinase activity (33,
49), we could easily detect endogenous RAG-2 mRNA in this cell
line by reverse transcription-PCR analysis (Fig. 2) (14). Since both the
endogenous RAG-2 gene and the RAG-2 promoter-reporter construct were
expressed in Jurkat cells, we proceeded to use this cell line to
explore the role of c-Myb in regulating the RAG-2 promoter in vivo.

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FIG. 2.
Jurkat T cells express a readily detectable amount of
RAG-2 mRNA. Total RNA was purified from Jurkat, HeLa, and 293 cells and
converted to cDNA by random-primed reverse transcription. The cDNAs
were analyzed by multiplex PCR for -actin and RAG-2 transcripts. On
top is a digital image of an ethidium bromide (EtBr)-stained gel, and
on the bottom is a phosphorimage of the same gel blotted to a membrane
and probed with an internal RAG-2-specific radiolabeled
oligonucleotide.
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Boyd and colleagues recently adapted a chromatin cross-linking and
immunoprecipitation (ChIP) protocol to characterize the binding of
mammalian transcription factors to a promoter region in intact living
cells (9). Using this ChIP technique, we investigated whether c-Myb binds to the RAG-2 promoter in vivo. Jurkat cells were
treated with formaldehyde. After being sheared to an average length of
600 nucleotides, cross-linked chromatin purified from these cells was
subjected to immunoprecipitation using either c-Myb-specific antibody
or control rabbit IgG. After reversal of the cross-linking,
immunoprecipitated DNA was purified and subjected to PCR analysis using
primers specific for the human RAG-2 promoter and for other control DNA
sequences. As shown in Fig. 3A,
fractionation of chromatin with anti-c-Myb antibody, but not the
control IgG, specifically enriched for endogenous RAG-2 promoter DNA
(the amplified region is from
102 to +9). DNA from the
-actin
locus (data not shown) or the major RAG-2 exon, which is approximately
10 kb away from the promoter, was not enriched with either antibody
(Fig. 3A).

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FIG. 3.
Anti-c-myb antibody specifically enriches RAG-2 promoter
DNA sequences in a (ChIP) assay. Chromatin proteins were cross-linked
to DNA in intact Jurkat T cells (A) and in freshly purified mouse
thymocytes (B) by formaldehyde treatment, and purified nucleoprotein
complexes were fractionated using either anti-Myb antibody (lanes 1),
nonspecific IgG (lanes 2), or no antibody (lanes 3). The precipitated
DNA fractions were analyzed by PCR for the presence of the proximal
RAG-2 promoter region, RAG-2 major exon DNA, or a region of the Ig
kappa locus. In each case, the input DNA was used as a positive control
(lanes 4). Amplification products were analyzed on a 2% agarose gel
and visualized by ethidium bromide staining. IP, immunoprecipitate.
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We further investigated whether c-Myb binds to the endogenous RAG-2
promoter in a primary tissue. A single-cell suspension was made from
whole thymus from 3-week-old mice and subjected to the ChIP assay as
described above. Immunoprecipitated DNA was analyzed by PCR using
primers specific for the mouse RAG-2 promoter (Fig. 1A; the amplified
region is from
163 to
6) and for control DNA sequences. Genomic
sequences from the murine RAG-2 promoter, but not the Ig kappa locus,
were specifically enriched by the c-Myb antibody. We could not detect
precipitation of Ig kappa locus DNA by either anti-c-Myb antibody or
rabbit IgG (Fig. 3B).
The PCR products were also examined by Southern blotting and quantified
by PhosphorImager (data not shown). No signals were detected from mock
precipitation lanes. The signal from anti-c-Myb antibody-precipitated
DNA was compared to that from control antibody-precipitated DNA. The
differences ranged from 70- to 100-fold for the RAG-2 promoter region
and from 0.5- to 7-fold for control regions. These ChIP experiments
provided strong evidence that c-Myb was bound in the vicinity of the
proximal region of the RAG-2 promoter.
In order to determine with higher resolution the site of factor
binding, we performed in vivo DNase I genomic footprinting on Jurkat T
cells and nonlymphoid HeLa cells. Purified intact nuclei or genomic DNA
was treated with increasing concentrations of DNase I, and cleavages
were mapped by ligation-mediated PCR. To test the specificity of the
assay, an RsaI restriction enzyme-treated sample of Jurkat
genomic DNA was first examined. The unique cleavage introduced by the
enzyme in the promoter-proximal region was visualized as a single
intense band migrating at the expected position in a denaturing gel
(data not shown). As shown in Fig. 4, a
DNase-hypersensitive site was detected at position
45 of the human
promoter (which corresponds to position
51 in the mouse promoter),
just on the 3' side of the putative c-Myb binding site, in Jurkat
nuclei but not in the purified Jurkat DNA or HeLa nucleus samples. Two
additional DNase I-sensitive bands were present on the 5' side of the
Myb site at positions
59 and
58. This was distinct from the pattern observed in either pure DNA or HeLa nucleus samples. These data suggested that the c-Myb site may be occupied in vivo in a
lymphoid-cell-specific fashion. When taken together with the ChIP data,
these experiments led us to the preliminary conclusion that c-Myb binds
to the Myb site at positions
54 to
49 of the human RAG-2 promoter
in vivo (corresponding to positions
60 to
55 in the mouse
promoter). Other differences between the various samples in this DNase
footprint analysis suggest that additional factors also bind
specifically to the RAG-2 promoter in vivo (e.g., a hypersensitive site
at position
100).

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FIG. 4.
The RAG-2 promoter proximal region is occupied in the
vicinity of the c-Myb site in vivo. Purified nuclei from Jurkat (lanes
5 and 6) and HeLa (lanes 1 and 2) cells or purified genomic DNA from
Jurkat cells (lanes 3 and 4) were treated with increasing
concentrations of DNase I. DNase-treated DNAs were then repurified and
subjected to linker ligation and PCR amplification. Radiolabeled
extension products were electrophoresed on a denaturing polyacrylamide
gel alongside a DNA sequencing ladder, and the dried gel was analyzed
by phosphorimaging. This ligation-mediated PCR analysis reveals
DNase-sensitive sites on the top strand of the promoter through the use
of a radiolabeled bottom-strand primer. The numbers indicate positions
with respect to the transcription start site. The arrows point to in
vivo DNase I-hypersensitive sites in Jurkat cells, and the position of
the c-Myb binding site is indicated (box). The DNA sequencing ladder
shows the bottom-strand sequence.
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The Myb site is critical for promoter activity and required for
recruitment of c-Myb to the RAG-2 promoter in vivo.
To probe the
functional consequences of the interaction between c-Myb and its
binding site in the proximal RAG-2 promoter in a chromosomal context,
we analyzed a series of Jurkat cell lines stably transfected with
reporter constructs containing the murine RAG-2 promoter.
The design of the reporter construct is shown in Fig.
5A. It consists of a GFP cDNA under the
control of the
279 to +123 region of the murine RAG-2 promoter. The
vector contains a neomycin resistance cassette expressed from the PGK
promoter and separated from the reporter region by two copies of the
chicken
-globin insulator (10). The reporter was stably
transfected into Jurkat T cells, and the G418-resistant transfectant
pool was assayed for GFP expression by flow cytometry. Initial
experiments showed that the RAG-2 promoter-containing construct, in the
absence of an enhancer, gave a fluorescence pattern indistinguishable
from that of untransfected cells (Fig. 5B). We interpreted this
negative result to indicate that either the promoter itself cannot
drive sufficient GFP expression to be detectable above the background or it is unable to overcome the repressive effects of chromatin structure. When the TCR
locus enhancer E
was inserted upstream of the RAG-2 promoter, 30 to 50% of transfectant cells expressed GFP
(Fig. 5B and C). When mutation 3 was introduced into the promoter, less
than 0.5% of transfected cells expressed GFP in the presence of E
(Fig. 5C), leading us to conclude that the Myb binding site was
essential for promoter activity within a chromatin context.

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FIG. 5.
The c-Myb binding site is essential for RAG-2 promoter
activity in an integrated reporter construct in Jurkat T cells. (A)
Reporter construct used in the stable-transfection assay. Linearized
constructs contain a GFP cDNA and the wild-type or mutant 3 RAG-2
promoter ( 279 to +123) in the presence or absence of the TCR locus enhancer (E ). Ins, the 1.2-kb chicken -globin insulator
sequence (10), included to prevent the neomycin resistance
cassette (PGK-neo) from influencing GFP activity. (B and C) Reporter
constructs containing the wild-type or mutant 3 RAG-2 promoter in the
presence or absence of E were transfected into Jurkat cells by
electroporation. Transfected cells were selected as a pool in G418 and
then analyzed by flow cytometry for GFP expression. The
fluorescence-activated cell sorter histograms of untransfected (dashed
line) and wild-type promoter-transfected cells (bold solid line) are
coincident. The thin solid line represents transfectants containing the
wild-type promoter and E , and the dotted line represents the mutant
3 promoter and E .
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Jurkat cells transfected with either the wild-type murine RAG-2
promoter plus E
or the mutation 3-containing promoter plus E
were
also analyzed by the ChIP assay. Immunoprecipitates were analyzed for
the endogenous human RAG-2 promoter and the transfected murine RAG-2
promoter. As shown in Fig. 6, both the
transfected wild-type murine and endogenous human RAG-2 promoter
regions, but not human RAG-2-coding exon DNA (data not shown), were
specifically enriched by c-Myb antibody (Fig. 6A). Furthermore, the
integrated mutant RAG-2 promoter was not enriched in this assay (Fig.
6B), suggesting that this sequence is critical for recruitment of c-Myb to the promoter region in vivo, and this recruitment is well correlated with promoter activity.

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FIG. 6.
The c-Myb site in the proximal region is essential for
in vivo recruitment of c-Myb to the RAG-2 promoter. Pools of
G418-resistant cells containing the wild-type (A) or mutant 3 (B) RAG-2
promoter analyzed in Fig. 5 were subjected to the ChIP assay using
anti-c-Myb antibody (Ab) (lanes 1) or nonspecific IgG (lanes 2). Mock
(lanes 3) indicates samples processed in the absence of antibody, and
input (lanes 4) is DNA prior to immunoprecipitation. Primers specific
for either the transfected or endogenous RAG-2 promoter were used in
PCR analysis of the various precipitated chromatin fractions. Images of
ethidium bromide-stained gels are shown.
|
|
 |
DISCUSSION |
Regulated expression of RAG-1 and RAG-2 is essential for
lymphocyte development. Recent transgenic studies have revealed
distinct DNA sequence requirements for RAG expression in B and T cells. Reporter constructs containing as little as 2 kb of genomic DNA sequence 5' of the RAG-2 promoter are active in B but not T cells, whereas similar constructs containing 9 kb of upstream sequence are
active in both lineages (39). In a separate study, DNA
sequences 5' of the RAG-2 promoter were found to be involved in the
coordinate expression of RAG-1 and RAG-2 in T and B cells while
sequences on the RAG-1 side of the locus were only important for
expression of RAG-1. Perhaps surprisingly, no regulatory elements were
identified in the intergenic region (64). Our own previous
studies revealed distinct requirements for RAG-2 promoter activity in B
and T cells (32). In B-lineage cells, BSAP bound to a
promoter-proximal DNA sequence and was critical for promoter activity.
This factor is not expressed in the T lineage, however. In the present
study, we found that the hematopoietic lineage transcription factor
c-Myb binds to the RAG-2 promoter in T cells, where it is important for
RAG-2 transcription.
We showed that a c-Myb expression vector can transactivate a RAG-2
promoter-reporter construct in a transient-transfection assay (Fig. 1C
and D). When serial deletions and substitution mutations of this
promoter were tested, we found that c-Myb activates luciferase reporter
gene expression through a c-Myb consensus binding site completely
conserved between the mouse and human promoters and located in a region
critical for promoter activity in the transient-transfection assay.
Mutation of a sequence adjacent to the conserved c-Myb site also
interferes with RAG-2 promoter activity and its induction by c-Myb.
This may indicate that c-Myb binds the RAG-2 promoter cooperatively
with a second, adjacently bound factor. We went on to show that c-Myb
was bound to this consensus site in vivo in Jurkat T cells by using a
ChIP assay combined with in vivo DNase I footprinting. Enrichment of
RAG-2 promoter sequences by c-Myb-specific antibody in the ChIP assay provides strong evidence that c-Myb is binding in the vicinity of the
promoter (Fig. 3A). We obtained the same result using mouse thymocytes
(Fig. 3B), which actively express RAG genes. A chromosomally integrated
RAG-2 promoter construct with a mutant c-Myb site was not specifically
immunoprecipitated (Fig. 6B). In a complementary set of experiments, in
vivo DNase footprinting revealed hypersensitive cleavage adjacent to
the c-Myb site in Jurkat cell nuclei but not in non-lymphoid-cell
nuclei or in purified genomic DNA (Fig. 4). This is consistent with the
c-Myb expression pattern as well as the tissue specificity of the
murine RAG-2 promoter.
Using an electrophoretic mobility shift assay and Jurkat cell nuclear
extract, we were unable to detect c-Myb binding to a 40-bp
oligonucleotide probe spanning the RAG-2 proximal-promoter c-Myb
binding site (data not shown). This may be due to the inadequacy of our
in vitro binding and analysis conditions. Alternatively, it may
indicate that c-Myb must cooperate with various other factors to
efficiently bind its site in the RAG-2 promoter. First, as we
demonstrated previously, a DNA sequence located at a distal position
(between positions
156 and
107 [Fig. 1A]) is required for RAG-2
promoter activity in T-lineage cells (32). Whichever transcription factor binds to this region of the promoter may influence
the binding of c-Myb to its site in the proximal region. For example,
c-Myb collaborates with NF-M to induce mim-1 gene expression, which is restricted to differentiating granulocytes (43). In cooperation with core binding factor, c-Myb
regulates the TCR
enhancer (22, 23). A recent report
provided in vitro evidence that GATA-3 may regulate the RAG-2 promoter
as a T-cell-specific factor (30). Further studies will be
required to identify factors which collaborate with c-Myb in the
regulation of the RAG-2 promoter in T cells.
The Myb transcription factor family.
The Myb family of
transcription factors include three members, A-Myb, B-Myb, and c-Myb
(45). Although all three proteins share a highly conserved
DNA binding domain and specifically recognize the same hexanucleotide
consensus sequence, subtle differences exist in the binding preferences
of different members (27, 36). Moreover, studies suggest
that each member interacts with distinct collections of cellular
factors and performs distinct biological functions (42, 45).
A-Myb expression is restricted to male germ cells, ovaries, and
germinal-center B lymphocytes and is not found at significant levels in
immature hematopoietic lineages, including bone marrow cells and T
cells (18). A-Myb homozygous null mutant mice show defects
in spermatogenesis and female breast development, as well as growth
abnormalities (59). These data lead us to believe that A-Myb
is not involved in RAG expression. B-Myb is expressed in dividing cells
of a wide variety of tissues, and it is a key regulator of the cell
cycle (48, 52). B-Myb has been suggested to play a role in
cellular differentiation (45), but its expression closely
parallels cell proliferation rather than differentiation status and
particular cell type (29, 47, 48). For this reason, B-Myb is
less likely to be an activator of RAG expression, since RAG
transcription is diminished in proliferating cells. An antagonistic
relationship between c-Myb and B-Myb has been noted (12,
61). This raises the possibility that B-Myb plays a role in
inhibiting RAG expression, perhaps during active periods of cell
division in early lymphoid cell development. Since Jurkat cells do
express RAG mRNA, a different model system would be needed to test this
hypothesis. c-Myb is prevalently expressed in immature hematopoietic
cells, where genetic analyses have shown that it plays an essential
role in lymphocyte development (see below). In this regard, it is worth
noting that the anti-c-Myb antiserum used in the ChIP experiments
reported here (Fig. 3 and 6) lacks cross-reactivity with B-Myb. Thus,
we conclude that c-Myb, rather than another Myb family member, is
involved in regulating RAG-2 expression.
The Role of c-Myb in T-cell development.
The c-Myb gene is
primarily expressed in immature lymphoid, erythroid, and myeloid cells
(45). This transcription factor is also present in
developing airway epithelium, hair follicles, and gastrointestinal
crypt epithelial cells, as well as tooth buds and the thyroid
primordium during development (11). Within the lymphoid
lineage, mature T and B cells can reactivate c-Myb expression following
in vitro mitogenic stimulation (17). Many tumor cell lines
of T- and B-lymphocyte origin also express high levels of c-Myb
(4, 6, 7). Recent studies of normal developing tissue,
however, suggested that c-Myb is preferentially expressed in the T, but
not B, lineage (2, 11). Primary cells at various stages of
development were examined by reverse transcription PCR for expression
of different transcription factors (2). While pro- and pre-T
cells showed similar significant amounts of c-Myb mRNA, pro- and pre-B
cells totally lacked c-Myb mRNA expression. The same expression pattern
was shared by GATA-3, a T-cell-specific transcription factor, but not
by other factors examined, such as GATA-1 and -2, PU-1, and c/EBP
.
Other workers have characterized c-Myb expression using in situ
hybridization (11). In the developing thymus, high levels of
c-Myb RNA were observed in the cortex, the area populated with immature
thymocytes expressing RAG-1 and RAG-2 and undergoing V(D)J
recombination at TCR loci. When adult bone marrow was examined, a
strong c-Myb signal was noted in only a small percentage of
blastoid-appearing cells, which are likely precursors of erythroid and
myeloid lineages.
Mice which are homozygous for a null mutation in the c-Myb gene exhibit
a specific failure of fetal liver hematopoiesis and die before the
onset of definitive lymphopoiesis (40). The vital role of
c-Myb in T-lymphocyte differentiation was confirmed in a recently
reported study which used homozygous null c-Myb ES cells to generate
chimeric mice using the RAG-deficient blastocyst complementation assay
(3). The chimeric mice were generated by injecting
c-Myb
/
RAG-1+/+ ES cells into blastocysts
generated from RAG-1
/
mice. Since RAG-deficient mice do
not generate mature T and B cells, the authors were able to examine the
ability of c-Myb-deficient progenitors to contribute to T-cell
development in this chimera. They showed that T-cell development was
blocked before the onset of gene rearrangement at the
CD44lo CD25
stage, the beginning of definitive
T-cell differentiation. Thus, in the absence of c-Myb, the V(D)J
recombinase is not expressed in developing T cells. Taken together with
our finding that c-Myb regulates the RAG-2 promoter, these data
strongly suggest that the critical role of c-Myb in early T-cell
development may be, at least in part, due to its ability to regulate
expression of the RAG-2 gene.
In addition to its critical role in the commitment of precursors to the
T-cell lineage, c-Myb also seems to be involved in later stages of
T-cell development. The CD4, TCR
, and TCR
genes, each of which
encodes a protein required for the selection of various T-cell subsets,
have been identified as c-Myb targets (23, 28, 41, 53). A
dominant-interfering c-Myb mutant severely affected thymocyte
maturation in transgenic mice, apparently by interfering with the
expression of antiapoptotic proteins (5, 55), suggesting a
role for c-Myb in late T-cell development. A recent report has
suggested that like B cells, mature T cells might reactivate RAG
expression under very unusual circumstances (34). Regulated
c-Myb expression might also contribute to this phenomenon.
 |
ACKNOWLEDGMENTS |
We thank Peggy J. Farnham (University of Wisconsin) for sharing
the chromatin immunoprecipitation protocol and Kathryn E. Boyd (Yale)
for generous technical assistance with this assay. We also thank
Stephen T. Smale (UCLA) for his DNase I genomic footprinting protocol.
We are grateful to the late Eugenia Spanopoulou for providing us with
293T cells and the pEF-BOS expression vector and Chi Dang (Hopkins) for
sharing with us the murine c-Myb cDNA. We also thank Astar Winoto, Alan
Friedman, Shau-Ku Huang, Laurent Bentolila, Hans Brightbill, Jamie
Geier, and various members of Schlissel laboratory for critical reading
of the manuscript.
This research was funded in part by NIH grants RO1 AI40227 and HL48702
to M.S.S., who also acknowledges the support of a Leukemia Society Scholarship.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Molecular and Cell Biology, 439 LSA (#3200), University of California, Berkeley, CA 94720-3200. Phone: (510) 643-2462. Fax: (510) 642-6845. E-mail: mss{at}uclink4.berkeley.edu.
Present address: Graduate Program in Cellular and Molecular
Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205.
Present address: Department of Medicine, Johns Hopkins University
School of Medicine, Baltimore, MD 21205.
 |
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Molecular and Cellular Biology, December 2000, p. 9203-9211, Vol. 20, No. 24
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Copyright © 2000, American Society for Microbiology. All rights reserved.
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