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Vol. 17, No. 5, pp. 591-596, March 1, 2003
Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 67404 Illkirch Cedex, Strasbourg, France
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ABSTRACT |
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The GATA factor Pannier activates proneural achaete/scute (ac/sc) expression during development of the sensory organs of Drosophila through enhancer binding. Chip bridges Pannier with the (Ac/Sc)-Daughterless heterodimers bound to the promoter and facilitates the enhancer-promoter communication required for proneural development. We show here that this communication is regulated by Osa, which is recruited by Pannier and Chip. Osa belongs to Brahma chromatin remodeling complexes and we show that Osa negatively regulates ac/sc. Consequently, Pannier and Chip also play an essential role during repression of proneural gene expression. Our study suggests that altering chromatin structure is essential for regulation of enhancer-promoter communication.
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Introduction |
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Transcription factors must gain access to their
target sites in vivo to regulate gene expression and this implies
alteration of chromatin structure around regulatory regions by
chromatin remodeling complexes. In Drosophila, the
polycomb group of genes maintains repression of homeotic genes
like Ultrabithorax, presumably by inducing a repressive
chromatin structure (Pirotta 1997
). In contrast, some members of the
trithorax group of genes were identified by their ability to
suppress dominant polycomb phenotypes (Kennison and Tamkun
1998
). The osa trithorax group gene encodes a large ubiquitously expressed protein with an ARID domain
(A/T-Rich Interaction Domain; Treisman et al. 1997
; Collins et al. 1999
) that
binds AT-rich DNA sequences, and a C-terminal domain, the
eyelid homologous domain (EHD) whose function is not known.
The EHD is conserved in multicellular organisms including
Caenorhabditis elegans and humans but is not present in yeast.
Osa is a component of Brahma (Brm) chromatin remodeling complexes
(Treisman et al. 1997
; Collins et al. 1999
), the Drosophila
homologs of the yeast SWI/SNF. These Brm complexes are believed to play
a crucial role during gene expression by regulating chromatin
structure. However, how these complexes are recruited to specific genes
remains poorly understood.
The patterning of the large sensory bristles (macrochaetae) of the
thorax of Drosophila is a classical model to study how a
specific pattern is generated during development. There are only 11 sensory organs on each heminotum and they occupy stereotyped positions.
The development of the bristle precursor depends on expression of the
achaete/scute (ac/sc) proneural genes (Modolell 1997
). Genes of the ac/sc complex encode basic
helix-loop-helix proteins that heterodimerize with Daughterless (Da)
to activate downstream genes required for neural fate. Transcription of
ac and sc appears to be initiated by enhancers
(Gomez-Skarmeta et al. 1995
; Garcia-Garcia et al. 1999
) and the
expression is maintained throughout development by autoregulation
mediated by (Ac/Sc)-Da heterodimers binding to E boxes within the
ac/sc promoters (Martinez and Modolell 1991
; Van Doren et al.
1991
). Each enhancer interacts with specific transcription factors and
promotes proneural expression in only one or a few proneural clusters.
These factors, expressed in broader domains than the proneural
clusters, define the bristle prepattern. Pannier (Pnr) belongs to the
GATA-1 family of transcription factors (Ramain et al. 1993
; Heitzler et
al. 1996
) and activates proneural expression required for development
of the dorsocentral (DC) sensory bristles through binding to the DC
enhancer (Garcia-Garcia et al. 1999
) located at 4 and 30 kb from
ac and sc, respectively. Consequently, the loss of
function pnr alleles fail to activate ac/sc and lack
DC sensory bristles. Chip is a ubiquitous nuclear protein required for
maximal activation by diverse remote enhancers (Morcillo et al. 1996
,
1997
; Torigoi et al. 2000
). It was shown that it physically interacts
both with Pnr and the (Ac/Sc)-Da heterodimers and facilitates
enhancer-promoter communication (Bulger and Groudine 1999
; Dorsett
1999
) during Pannier-driven neural development (Ramain et al. 2000
).
In our current study, we present genetic interactions between osa, pnr, and Chip that reflect direct interactions between Osa and Pnr and between Osa and Chip. We show that Osa negatively regulates neural expression because loss of osa function exhibits increased expression of ac/sc and an excess of DC sensory bristles. Pnr and Chip have been previously identified as essential proteins of a proneural complex that activates ac/sc during neural development. Our study reveals that Pnr and Chip are also essential in recruiting Osa during neural repression. Hence, our study provides insights into how chromatin remodeling activity might be targeted to specific promoter sequences to regulate enhancer-promoter communication during development.
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Results and Discussion |
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ChipE is a viable allele of Chip that
is associated with a point mutation in the LIM-interacting domain
(LID), which specifically reduces interaction with the bHLH proteins
Ac, Sc, and Da. As a consequence, the ChipE mutation
disrupts the functioning of the proneural complex encompassing Chip,
Pnr, Ac/Sc, and Da (Ramain et al. 2000
). A homozygous
ChipE mutant shows thoracic cleft and loss of the DC
bristles, similar to loss of function pnr alleles (Fig.
1B).
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To identify new factors that regulate this proneural complex, we screened for second-site modifiers of the ChipE phenotypes (I. Biryukova and P. Heitzler, unpubl.). We found one allele of osa (osaE17) among the putative mutants. OsaE17 corresponds to a loss-of-function allele, and homozygous embryos die with normal cuticle patterning. Both osaE17 and null alleles of osa (osa616 or osa14060) enhance the cleft but suppress the loss of DC bristle phenotypes of ChipE flies. Indeed, ChipE flies with only one copy of osa+ (ChipE;osa616/+) are weak and sterile but show wild-type DC bristle pattern (Fig. 1C).
These genetic interactions suggest that Osa can antagonize the function
of Pnr. Moreover, overexpressed Osa
(+/UAS-osa;Gal4-pnrMD237/+) induces a thoracic cleft
and the loss of DC bristles (Collins et al. 1999
; our current study)
similar to the loss-of-function pnr alleles (Heitzler et al.
1996
; Garcia-Garcia et al. 1999
). In contrast, loss-of-function
osa alleles display an excess of DC bristles similar to
overexpressed Pnr (Haenlin et al. 1997
). For example,
(osa14060/+), (osa616/+), and
(osaE17/+) flies exhibit respectively
2.35 ± 0.12, 2.38 ± 0.12, and 2.43 ± 0.17 DC bristles per
heminotum (Oregon wild-type flies have 2.00 DC bristles/heminotum).
Furthermore, transallelic combination of osa14060
with the hypomorphic osa4H
(osa4H/osa14060) accentuates the excess of
DC bristles (Fig. 1D) compared with (osa14060/+).
(osa4H/osa14060) flies display
4.17 ± 0.19 DC bristles per heminotum. On the other hand,
(osa4H/osa4H) flies display 2.50 ± 0.11
DC bristles per hemithorax. The development of the extra DC bristles
revealed by phenotypic analysis was compared with the positions of the
DC bristle precursors detected with a LacZ insert, A101, in
the neuralized gene (Boulianne et al. 1991
) that exhibits
staining in all sensory organs (Huang et al. 1991
). In
(osa14060/osa4H) discs, additional DC
precursors are observed that lead to the excess of DC bristles (Fig.
1E). The pnrD alleles encode Pnr proteins carrying a
single amino acid substitution in the DNA binding domain that disrupts
interaction with the U-shaped (Ush) antagonist (Cubadda et al. 1997
;
Haenlin et al. 1997
). Consequently, PnrD constitutively
activates ac/sc, leading to an excess of DC bristles. We found
that this excess is accentuated when osa function is simultaneously reduced (pnrD1/osa616 in
Fig. 1F).
As osa shows genetic interactions with trithorax
group genes encoding components of the Brm complex like moira
(mor) and brm (Collins et al. 1999
; Crosby et al.
1999
; Vazquez et al. 1999
), we investigated whether mutations in
mor and brm suppress the ChipE
phenotype. We found that loss of one copy of brm+ in
(ChipE; brm2/+) flies suppresses the lack
of DC bristles observed in ChipE flies (Fig. 1G),
similar to loss of one copy of osa+ (Fig. 1C). This
shows that brm and osa both act during Pnr-dependent patterning, in agreement with the fact that they have been shown to be
associated in the Brm complex. In contrast, reducing the amount of Mor
by half [(ChipE;mor1/+) flies] is not
sufficient to modify the ChipE phenotype (data not
shown). This does not definitely exclude the possibility that
mor is directly or indirectly involved, via the Brm complex,
in Pnr-dependent patterning.
The complete osa open reading frame of 2715 amino acids and the intronic splicing signals were PCR amplified from genomic DNA prepared from homozygous embryos (osaE17 and osa14060) and homozygous first instar larvae (osa4H). For osa14060 and osa4H, the sequence analysis revealed a single mutation in the N terminus that causes a glutamine to stop codon substitution (Q n°251 for osa14060; Q n°1281 for osa4H; Fig. 1H). The conceptual translation of osa14060 leads to a truncated Osa protein lacking both functional domains, whereas Osa4H retains the ARID domain but lacks the C-terminal EHD (Fig. 1H). Wild-type osa function is necessary for patterning of the DC bristles. Although osaE17 behaves as a stronger allele than osa14060 and osa4H, we were unable to molecularly identify the mutation. Hence, the osaE17 phenotype may result from a mutation in regulatory sequences that affects osa expression.
We have previously shown that a complex containing Pnr, Chip, and the
(Ac/Sc)-Da heterodimer activates proneural expression in the DC
proneural cluster and promotes development of the DC macrochaetae
(Ramain et al. 2000
). Osa and Pnr/Chip have antagonistic activities
during development because loss of osa function
(osa4H and osa14060) displays
additional DC bristles. However, as our current study reveals that
osa genetically interacts with pnr and Chip,
we asked whether Osa physically interacts with the Pnr and Chip
proteins. We performed immunoprecipitations of protein extracts made
from Cos cells cotransfected with expression vectors for tagged Osa and
either Pnr or tagged Chip (Fig. 2B,C).
Because Osa is a large protein, we used several expression vectors
encoding contiguous domains of Osa (Fig. 2A, domains A-F). Osa
coimmunoprecipitates with Pnr and Chip (Fig. 2B,C) and can be detected
on Western blots with appropriate antibodies. The interactions appear
to require the overlapping domains Osa E (His1733/Glu2550) and Osa F
(Ala2339/Ala2715; Fig. 2B,C) corresponding to the EHD.
Enhancer-promoter communication during proneural activation and
development of the DC bristles requires regulatory sequences scattered
over large distances and appears to be negatively regulated by
interaction of Pnr and Chip with Osa through the EHD. Interestingly,
the EHD is not conserved in yeast. In yeast, the UAS sequences are
generally close to the promoter and there is no requirement for
long-distance interactions. This observation could support the idea
that the EHD is essential for long-distance enhancer-promoter
communication. Alternatively, yeast may just lack proteins like Chip or
Pnr.
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The DNA-binding domain and the C-terminal region are essential for the
function of Pnr during development of the DC sensory organs (Ramain et
al. 1993
). The pnrVX1 and pnrVX4
alleles (collectively pnrVX1/4) are characterized by
frameshift deletions that remove two C-terminal
-helices and result
in reduced proneural expression and loss of DC bristles.
We thus investigated the molecular interactions between Osa and
PnrD1 and between Osa and PnrVX1. We found that the
PnrD1 protein interacts with the EHD as efficiently as
wild-type Pnr (Fig. 3A,B, lanes 1,2). In
contrast, the physical interaction is disrupted when the C terminus of
Pnr encompassing the
-helices is removed (Fig. 3A,B, lanes 1,3).
Because the C terminus of Pnr is required for the Pnr-Osa interaction
in transfected cells extracts, we tested the abilities of in vitro
translated 35S-labeled Osa domains to bind to GST-CTPnr
attached to glutathione-bearing beads (Fig. 3D, lane 4). We found that
only Osa E and Osa F interact with the C terminus of Pnr (Fig. 3D; data
not shown). As expected, GST-CTPnr did not bind the
luciferase input and none of the 35S proteins bound GST
control beads (Fig. 3D, lanes 4,2). We also further investigated the
interaction between Chip and Osa and we found that Osa associates with
the N-terminal homodimerization domain of Chip (Fig. 3A,C, lane 4),
also required for the interaction between Chip and Pnr. Furthermore,
Osa E and Osa F bound also to immobilized GST-Chip (Fig. 3D, lane 3).
We found that deletion of the
helix H1 disrupts the interactions
between Pnr and Osa (data not shown). Interestingly, the same deletion
also disrupts the interaction with Chip (Ramain et al. 2000
).
Therefore, the functional antagonism between Chip and Osa during neural
development may result from a competition between these proteins for
association with Pnr. Alternatively, the deletion of H1 may affect the
overall structure of the C terminus of Pnr and disrupt the physical
interactions with Chip and Osa. To discriminate between these
hypotheses, we performed immunoprecipitations of protein extracts
containing a constant amount of Pnr, a constant amount of the tagged
Osa E domain, and increasing concentrations of Chip (Fig.
4). Pnr immunoprecipitates with
immunoprecipitated tagged Osa E and the amount of Pnr
immunoprecipitated increases in the presence of increasing
concentrations of Chip. The presence of increasing amounts of Chip does
not inhibit the Osa-Pnr interaction as would be expected if Osa and
Chip were to compete for binding to Pnr. In contrast, it suggests that
Chip and Pnr act together to recruit Osa and to target its activity and
possibly the activity of the Brm complex to the ac/sc promoter
sequences.
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Using expression vectors encoding contiguous domains of Osa, we showed that the EHD of Osa mediates interactions with Pnr and Chip. Because the EHD is lacking in the truncated Osa14060 and Osa4H, we hypothesized that the loss of interaction with Pnr and Chip are responsible for the excess of DC bristles observed in osa4H and osa14060. However, it is possible that we disrupted an additional N-terminal interaction domain in constructing the expression vectors. To exclude this possibility, we performed immunoprecipitations of protein extracts made from Cos cells cotransfected with expression vectors for a tagged Osa4H and either Pnr or a tagged Chip. We found that the truncated Osa4H does not interact either with Pnr or with Chip, indicating that there is no dimerization domain in the N terminus of Osa (Fig. 2D, lanes 13,14).
To investigate whether these interactions between Osa, Pnr, and Chip
function in vivo during DC bristle development, we have examined the
effects of both loss of function and overexpression of osa on
the activity of a LacZ reporter whose expression is driven by
a minimal promoter sequence of ac fused to the DC enhancer (transgenic line DC:ac-LacZ; Fig.
5A; Garcia-Garcia et al. 1999
; Ramain et
al. 2000
). We found that expression of the LacZ transgene is
increased in osa14060/osa4H wing discs
when compared with the wild-type control (Fig. 5A, a,b). For
overexpression experiments, we used the UAS/GAL4 system (Brand and
Perrimon 1993
) using as a driver the pnrMD237 strain
that carries a GAL4-containing transposon inserted in the pnr
locus (driver: pnr-Gal4). This insert gives an expression pattern of
Gal4 indistinguishable from that of pnr (Calleja et al. 1996
;
Heitzler et al. 1996
). We found that overexpressed Osa leads to a
strong reduction of LacZ staining in the DC area (Fig. 5A,
a,c), consistent with the lack of DC bristles (Collins et al. 1999
;
data not shown). Thus, overexpressed Osa represses activity of the
ac promoter sequences required for DC ac/sc
expression and development of the DC bristles. It has been previously
reported that wingless expression is also required for
patterning of the DC bristles (Phillips and Whittle 1993
). However, the
repressing effect of Osa on development of the DC bristles is unlikely
to be the result of an effect of Osa on wingless expression
because overexpressed Osa driven by pnrMD237 has no
effect on the expression of a LacZ reporter inserted into the
wingless locus (data not shown; Kassis et al. 1992
; Collins and Treisman 2000
). Thus, Osa acts through the DC enhancer of the
ac/sc promoter sequences to repress ac/sc and neural
development.
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ChipE disrupts the enhancer-promoter communication
and strongly affects expression of the LacZ reporter driven by
the ac promoter linked to the DC enhancer (Fig. 5A, d; Ramain
et al. 2000
). Because null alleles of osa suppress the loss of
DC bristles displayed by ChipE, we investigated the
consequences of reducing the dosage of osa in
ChipE flies. We found that the expression of the
LacZ reporter is not affected in ChipE
flies when Osa concentration is simultaneously reduced
(ChipE/ChipE;
DC:ac-LacZ/osa14060; Fig. 5A, e).
In conclusion, we have previously shown that Pnr function during
proneural patterning is regulated by interaction with several transcription factors (Fig. 5B). Pnr function is negatively regulated by Ush that interacts with its DNA-binding domain (Haenlin et al.
1997
). Chip associates with the C terminus of Pnr, bridging Pnr at the
DC enhancer with the AC/Sc-Da heterodimers bound at the proneural
promoters, thus activating proneural gene expression (Ramain et al.
2000
). Our current study reveals that Pnr function can also be
regulated by interaction with Osa. Thus, Osa activity is specifically
targeted to ac/sc promoter sequences and the binding of Osa
therefore has a negative effect on Pnr function, leading to reduced
expression of the proneural ac/sc genes. Osa belongs to Brm
complexes, which are believed to play an essential role during
chromatin remodeling necessary for gene expression. For example, in
vitro transcription experiments with nucleosome assembled human
-globin promoters have shown that the BRG1 and BAF155 subunits of
the mammalian SWI/SNF homolog are essential to target chromatin remodeling and promote transcription initiation mediated by GATA-1 (Kadam et al. 2000
). In contrast to what was observed in vitro, our
results suggest that in vivo the SWI/SNF complexes can also act to
remodel chromatin in a way that represses transcription. Alternatively,
the observed repression of proneural genes may simply define a novel
function of Osa, independent of chromatin remodeling.
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Materials and methods |
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All recombinant DNA work was performed according to standard
procedures (Sambrook et al. 1989
). Details concerning plasmid constructions are available on request.
Fly stocks and genetics
Alleles used were osa4H (Kaminker et al.
2001
), osa616 (Treisman et al. 1997
),
osa14060 (gift of M. Hoch), mor1,
and brm2 (FlyBase). The original
osa4H chromosome leads to embryonic lethality. We
found that this lethality is associated with a separable and distal
mutation. Thirty hemithoraces were examined for each of the
combinations presented in Figure 1, but for each genotype the phenotype
was found to be remarkably similar from fly to fly.
PCR analysis of the osa mutants
Genomic DNA for PCR analysis was extracted from homozygous osaE17, osa14060 embryos, and homozygous osa4H first instar larvae.
Plasmid constructions
The expression vectors pXJ Pnr+ pXJ PnrD1 and
pXJ PnrVX1, encoding truncated versions of wild-type Pnr,
PnrD1, and PnrVX1, are described in Haenlin et al.
(1997)
. The sequences encoding the domains of Osa (Osa A, Meth1/Ser581;
Osa B, Ser581/Ala903; Osa C, Thr897/Tyr1370; Osa D, Tyr1370/His1740;
Osa E, His1733/Glu2550; Osa F, Ala2339/Ala2715) and Osa4H
were amplified by PCR and inserted into the vectors pXJB, pXJF for
transient transfections in Cos cells (Ramain et al. 2000
). pXJB and
pXJF encode fusion proteins carrying at their N terminus the B epitope
of the estrogen receptor (pXJB: RPNSDNRRQGGRERL) and the Flag epitope
(pXJF: DYKDDDDK), respectively. The vectors encoding the Flag-tagged
Achaete, the B-tagged N-terminal, and the B-tagged C-terminal domain of
Chip are described in Ramain et al. (2000)
.
DNA transfections, immunoprecipitations, Western blot analysis, and GST pull-down assays
Cos cell transfections, protein extract preparations,
immunoprecipitations, and Western blot analysis were performed as
described in Haenlin et al. (1997)
. The protein extracts were
immunoprecipitated with the B10 or M2 antibodies that recognize the B
and Flag epitopes encoded by the pXJB and pXJF vectors. GST pull-down
assays were performed as in Torigoi et al. (2000)
.
Staining for
-galactosidase activity
Wing discs were stained as described in Cubadda et al. (1997)
.
A101 contains a LacZ gene insert at the neuralized
locus (Boulianne et al. 1991
) and exhibits staining in all sensory
organ precursors (Huang et al. 1991
). The transgenic strain
DC:ac-LacZ is described in Ramain et al. (2000)
.
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Acknowledgments |
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We thank Irwin Davidson and Luc Maroteaux for critical reading of the manuscript; Michael Hoch, Jim Kennisson, Tim Lebestky, Juan Modolell, Jessica Treisman, and the Bloomington stock center for reagents; Claudine Ackermann, Nadine Arbogast, and Marie-Louise Nullans for excellent technical assistance; and the sequencing, oligonucleotide synthesis, and cell culture services of the IGBMC. Inna Biryukova is supported by a fellowship from the Fondation pour la Recherche Médicale (FRM). This work was supported by grants from the CNRS, INSERM, the Hôpital Universitaire de Strasbourg, the Université Louis Pasteur, the Association pour la Recherche contre le Cancer (ARC), and the Ministère de la Recherche et de la Technologie.
The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.
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Footnotes |
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[Keywords: Transcription; enhancer-promoter communication; chromatin; Osa]
Received November 26, 2002; revised version accepted January 8, 2003.
1 E-MAIL pascal{at}igbmc.u-strasbg.fr; FAX 33-03-88-65-33-01.
2 E-MAIL phr{at}igbmc.u-strasbg.fr; FAX 33-03-88-65-33-01.
Corresponding authors.
Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/gad.255703.
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