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First published online May 16, 2007
doi: 10.1242/10.1242/dev.001594
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
* Author for correspondence (e-mail: lgvolk{at}weizmann.ac.il)
Accepted 20 March 2007
| SUMMARY |
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Key words: RNA, DPP, Drosophila, Wing imaginal disc, STAR proteins
| INTRODUCTION |
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Studies on the C. elegans protein GLD-1 revealed that a single
STAR protein may regulate a large number of target mRNAs, thereby
simultaneously mediating the transition between distinct differentiation
states in a given tissue (Crittenden et
al., 2003
; Lee and Schedl,
2001
). Recently, a consensus hexanucleotide sequence, UACU(C/A)A,
was reported to represent the actual GLD-1-binding site on its target RNA,
tra-2 (Ryder et al.,
2004
). It was reported that GLD-1 has the highest affinity for the
sequence UACUCA. These studies were extended to show that a similar but not
identical sequence, NA(A>C)UAA, represents the quaking response element
(QRE) in mouse (Ryder and Williamson,
2004
; Galarneau and Richard,
2005
). The partial similarity between GLD-1 and quaking response
elements suggests that the extended conserved KH domain of STAR proteins
recognizes common RNA sequences.
In this study, we characterized the nucleotide sequence of the Drosophila HOW response element (HRE) and identified secondary structure constraints that further regulate HOW binding. Based on these criteria, we identified dpp as a novel putative target for HOW regulation in the wing imaginal disc. Consistently, overexpression of the repressor isoform of HOW, HOW(L), reduced dpp mRNA levels, as well as DPP-GFP fusion-protein levels. In addition, reducing HOW levels in the wing imaginal disc led to an elevation in dpp mRNA levels. These experiments reveal a novel post-transcriptional regulation of DPP in the wing imaginal disc mediated by the RNA-binding protein HOW.
| MATERIALS AND METHODS |
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Imaginal disc labeling
The following primary antibodies were used: anti-HOW (produced in our
laboratory); anti-Spalt major (A. Salzberg, Technion, Haifa); and
anti-Engrailed (Hybridoma Stock Center). A mixture of three digoxigenin
(DIG)-DNA labeled probes for dpp mRNA were produced using PCR DIG
labeling mix (Roche).
Protein-RNA binding assay
Protein-RNA binding assays were performed essentially as previously
described (Nabel-Rosen et al.,
1999
). The biotin-labeled RNA was purified on a G-50 Sephadex
Quick Spin Column (Roche) and then mixed with equal amounts of in
vitro-translated (TNT T7 quick coupled transcription/translation system,
Promega) HOW(L) or HOW(L)m (mutated) hemagglutinin (HA)-tagged
proteins were added to the RNA (final concentration of RNA in each sample was
0.4 µM). The RNA was then precipitated with magnetic strepavidin-coupled
beads. The magnetic beads were then isolated, washed and boiled in sample
buffer, and the supernatant was analyzed by western blot analysis with anti-HA
antibodies (1:2000 dilution). HOW(L)-TAP is a fusion protein containing a
tandem affinity purification (TAP) tag at the C-terminus of HOW(L).
Transient transfection of S-2R+ cells
S-2R+ cells were grown in Schneider's medium supplemented with 10% fetal
calf serum (Hyclone) and 1% pen-strep solution. For transfection, cells were
seeded at 3.5-5x106 cells in 4.5 ml medium per 50 ml flask
(Nunc) and allowed to adhere. Transfection was performed using lipid reagent,
according to the manufacturer's protocol (Escort IV, Sigma). A total of 6
µg DNA was used for each transfection. Cells were collected for analysis 48
hours after transfection.
Primers used to construct the various RNA fragments
PCR was performed with Pwo DNA polymerase (Roche), using the cDNA of
stripe, and dpp. The following primers were used to create
the PCR fragments (all 5' primers included an additional T7 sequence):
Sr1, 5'-AGACTAGAGGAGAACTCGGCATC-3'; Sr254,
5'-AGAGCTCATCCGGAAGGCAA-3'; Sr610,
5'-TCTAATACTGTGATCTCC-3'; Sr657,
5'-TTACATAACTGCAAGTAACC-3'; Sr885,
5'-CGAACACACACACAAATCTT-3'; Sr253,
5'-ACTTCTCCTGGACGCTGACG-3'; Sr504,
5'-TTCGATTTCTTGATTCTCTT-3'; Sr533,
5'-TTGTATGGTTAGTAACTCTG-3'; Sr630,
5'-ATGGAGATCACAGTATTAGA-3'; Sr770,
5'-TTAGTGTTTGTGTGTTTCGT-3'; Sr912,
5'-CTGATATGCTAAGATTTGTG-3'; Sr1251,
5'-TGCAAGGTAAAGTAAACTAA-3'; Dpp1,
5'-ATTCGCACCACCATCGCACC-3'; Dpp1020,
5'-CTGAGCTTACGCGTTAGGTC-3'; Dppcds10,
5'-TGGCTTCTACTCCTCGCAGTG-3'; Dppcds412,
5'-TCCTTGACAGCCATTTTGTTG-3'; Dppcds766,
5'-GCTTCTTCATCGGCTCGGGGA-3'; Dpp3utr424,
5'-GCTGCTGAAGGAGAAGTTAAG-3'.
Primers for stable structures
The following primers were used: Sr_225+loop11,
5'-CCCCCGGTTTAGTATGTGCCGGGGGGTAGAAGAAGGGCTGACTGG-3'; Sr_225+
loop12, 5'-CCCCCGGTTTTAGTATGTGCCGGGGGGTAGAAGAAGGGCTGACTGG-3';
Sr_225+loop13,
5'-CCCCCGGGTTTTAGTATGTGCCGGGGGTAGAAGAAGGGCTGACTGG-3';
Sr_225+loop14,
5'-CCCCCGGGTTTTTAGTATGTGCCGGGGGGTAGAAGAAGGGCTGACTGG-3'.
Primers for mutant stripe (sr) fragments
All primers are 5' to 3', as indicated:
Sr_533_ACUGA, 5'-TTGTATGGTCAGTAACTCTGTTTTGTTTG-3';
Sr_533_ACUAC, 5'-TTGTATGGGTAGTAACTCTGTTTTGTTTG-3';
Sr_533_ACUCA, 5'-TTGTATGGTGAGTAACTCTGTTTTGTTTG-3';
Sr_770_ACUCC, 5'-GGAGTGTTTGTGTGTTTCGT-3'.
Mutagenesis of single nucleotides in stripe and dpp 3'UTR
To create point mutations in the 3'UTRs of stripe
(sr) and dpp, we used Quickchange site-directed mutagenesis
(Stratagene): Sr525mutF, 5'-CAAAACAGAGTTACTACCCATACAAAGCCTAAC-3';
Sr525mutR, 5'-GTTAGGCTTTGTATGGGTAGTAACTCTGTTTTG-3'; Sr543mutF,
5'-ACTAACCATACAAAGCCTAACTCAAGCAAATTGATTGATTAC-3'; Sr543mutR,
5'-GTAATCAATCAATTTGCTTGAGTTAGGCTTTGTATGGTTAGT-3'; Sr565mutF,
5'-AATTGATTGATTACTACCTATATTCGATGTAAT-3'; Sr565mutR,
5'-ATTACATCGAATATAGGTAGTAATCAATCAATT-3'; Sr769mutF,
5'-CACACAAACACTCATTTATTGCATT-3'; Sr769mutR,
5'-AATGCAATAAATGAGTGTTTGTGTG-3'; Dpp766mutF,
5'-CTCTCTTGTATATGTACTACACACCTATATACTTTATATGCG-3'; Dpp766mutR,
5'-CGCATATAAAGTATATAGGTGTGTAGTACATATACAAGAGAG-3'; Dpp882mutF,
5'-TTCGTTGCGCATTCAACTACACGTAACTGTATAAACAAAA-3'; Dpp882mutR,
5'-TTTTGTTTATACAGTTACGTGTAGTTGAATGCGCAACGAA-3'. The sequence of
all PCR fragments were verified before performing the transcription
reaction.
The following biotin-labeled RNA nucleotides were synthesized by IDT (IA, USA): 12 nucleotides (nt) without HRE, 5'-ACACACACACAC-3'; 12 nt with HRE, 5'-ACAUACUAACAC-3'; stem, 5'-GUUUACUAAAAUGUGGUUUUAGUAAAC-3'; loop, 5'-CCCCCGGCACATACTAACACACCGGGGG-3'; junctional UAC, 5'-CCCCUACUAACACGGACAACGUAGGGG-3'; junctional UA, 5'-CCCCUACUAACACGCACCCCUAGGGG-3'; unstructured, 5'-CUACUAACCCCAACC.
Construction of the HOW and HOW(L) double-stranded RNA (dsRNA) was in pWiz using the following primers: HL3utr572, 5'-ATCCTCTAGAAAAGTCAGATATCCTGAGCC-3'; HL3utr1179, 5'ATCCTCTAGAATAGACTTCGTGCACAATCC-3'; howcds7, 5'-ATCCTCTAGATGTCTGTGAGAGCAAAGCCG-3'; howcds519, 5'-TACCTCTAGAGCCGGTCTCCTGTTCCAATT-3'.
| RESULTS |
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To address whether the sequence ACUAA is sufficient for HOW binding, we synthesized two RNA fragments corresponding to regions a or b that contained a single pentanucleotide ACUAA sequence and tested their binding to HOW protein. Although both fragments bound HOW, point mutations altering the ACUAA motif at position 521 to either ACUCA or ACUGA abrogated HOW binding (Fig. 1A, only fragment a is shown). Mutating all of the four ACUAA sites within the context of the entire stripe 3'UTR essentially abrogated the binding of HOW (Fig. 1B). Importantly, an RNA fragment containing all three HRE sites in a single fragment showed enhanced binding to HOW (Fig. 1C), suggesting that multiple HRE sites contribute to an elevated level of binding to this protein.
We conclude that the sequence ACUAA represents the primary HRE. Importantly, one of the HRE sequences (at position 766) is conserved in the 3'UTR of stripe in Drosophila pseudoobscura. Moreover, we identified three repeats of the pentamer AAUAA (which also binds HOW, but to a lesser extent: D.I. and T.V., unpublished data) that are conserved between the two Drosophila species. Thus, we show that the HOW-binding site NA(C>A)UAA closely resembles that of STAR proteins from other species, although it is not identical. We extended our understanding of the binding of STAR proteins to their targets further by examining the binding of HOW in the context of the entire stripe 3'UTR and demonstrated that deletion of these four sites indeed abrogates the responsiveness of the stripe 3'UTR to HOW (Fig. 1B).
HOW binds to an HRE embedded within a loop secondary structure
Because a pentanucleotide sequence would be relatively abundant within the
3'UTRs of many RNAs, we suspected that additional restrictions might
exist in addition to the primary sequence ACUAA. Analysis of the distinct
HOW-binding sites in the stripe 3'UTR using the Mfold program
(Mathews et al., 1999
;
Zuker, 2003
) showed that
high-affinity binding for HOW occurs when the binding site (ACUAA) is included
within a single-stranded loop. However, secondary-structure predictions of
large RNA fragments (larger than 30-40 nucleotides) using the Mfold program
resulted in numerous alternatives. To test whether a loop secondary structure
is essential for the binding of HOW, we constructed HRE-containing loops of
distinct sizes fused to the 3' end of the stripe 3'UTR
fragment (1-225), which does not bind HOW
(Fig. 1A). We found that
single-stranded loops that are larger than 12 nucleotides and contain a single
HRE site exhibited significant binding, whereas loops smaller than 12
nucleotides did not exhibit specific binding to HOW
(Fig. 1D). Presumably, these
loops are too small to allow this binding.
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This analysis demonstrates that the secondary structure of the HRE site affects the binding specificity and that a proper secondary structure of the RNA containing the ACUAA sequence is essential for maintaining high-affinity binding of HOW to its target mRNA.
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To study further the requirements for how in the wing imaginal disc, we produced large how clones on a Minute background. In this setup, the how homozygous-mutant clones possess a growth advantage over the Minute/+ background cells, whereas the twin cells representing the homozygous Minute/Minute genotype disappear. We used the howstru null allele, which deletes HOW protein expression, allowing us to identify homozygous howstru mutant cells because they are not reactive with anti-HOW antibody. Analysis of these imaginal discs showed that large how mutant clones, covering most of the wing imaginal disc pouch, led to the formation of abnormal wing imaginal discs, in which the anterior-posterior boundaries of the centrally located Spalt domain were not sharp and the entire domain appeared enlarged (Fig. 2F). The posterior engrailed domain (detected by staining for the Engrailed protein) appeared normal (Fig. 2G). We calculated the width of the Spalt domain (relative to wing imaginal disc width) in the following manner: the values of the width of the Spalt domain at the most ventral region, most dorsal region and along the dorsoventral border were added and divided to the width of the entire wing imaginal disc. This calculated ratio was significantly larger in the wing imaginal discs carrying large how mutant clones relative to wild-type discs [1.23±0.14 (n=7) in the mutant discs versus 0.96±0.03 (n=6) in wild-type discs; Fig. 2, lower panel]; using the t-test, this difference was found to be significant (P=0.0022). Despite the abnormal shape of the wing imaginal disc, the enlargement of the Spalt domain suggested that Dpp, a major factor affecting Spalt expression in the wing imaginal disc, might represent a target for the repressive activity of HOW.
HOW binds the 3'UTR of dpp and reduces the GFP levels of a GFP-dpp 3'UTR reporter
Analysis of the primary and secondary structure of the dpp
3'UTR revealed that it contains two potential HRE sites at nucleotide
positions 762 and 878 (following the stop codon)
(Fig. 3A). Importantly, based
on the Mfold program, these HRE sites are not contained in a stem or
small-loop secondary structure, implying that they may represent active HREs.
A HOW-RNA binding assay showed that HOW binds to the entire (1092 nucleotide)
dpp 3'UTR (Fig.
3B). Point mutations in both HRE sites, changing these sites into
ACUAC (instead of ACUAA) in the context of the entire
dpp 3'UTR, essentially abrogated the binding of HOW
(Fig. 3B). Thus, HOW binds to
the dpp 3'UTR in a sequence-dependent manner.
To characterize further the activity of the HRE sites in the 3'UTR of dpp, we created a GFP reporter fused to the wild-type dpp 3'UTR or to a mutated 3'UTR, in which the two HRE sites were mutated (Fig. 3C). Transfection of S-2R+ cells with HOW(L)-TAP together with either GFP-dpp3'UTR or mutated GFP-dpp3'UTR, which lacks the HREs, was followed by western blot analysis with anti-GFP. In the presence of HOW(L), the GFP-DPP3'UTR levels were reduced threefold (after normalization to actin levels) relative to the levels of GFP-DPP3'UTR lacking the HREs. S-2R+ cells that did not overexpress HOW(L) did not show a significant difference in the GFP levels between the two constructs (Fig. 3C). For comparison, the levels of GFP-Stripe3'UTR were reduced around sixfold when combined with HOW(L) in S2R+ cells. This reduction was apparent also in the RNA levels of the GFP-dpp3'UTR construct as measured by reverse transcriptase (RT)-PCR (data not shown). These experiments demonstrate that HOW(L) exhibits repressive activity upon binding to the HRE sites in dpp 3'UTR.
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HOW(L) affects the Spalt domain non-autonomously
Consistent with the effect of HOW(L) on the production of the DPP-GFP
protein construct, we observed a significant reduction of the Spalt domain
following overexpression of HOW(L) in the wing imaginal disc pouch using the
sd-gal4 driver (Fig.
5A,H).
If HOW(L) affects the Spalt domain indirectly by repressing endogenous dpp mRNA levels, its effect should be non-autonomous, because DPP protein diffuses distally from the anteroposterior border. To differentiate between an autonomous versus non-autonomous effect of HOW on the Spalt expression domain, we overexpressed HOW(L) within the DPP domain using the dpp-gal4 driver. This resulted in a reduction of the Spalt domain beyond the HOW(L) expression domain (compare the Spalt domain in Fig. 5E with that in 5H). Importantly, in quantitative analysis of the Spalt-expressing cells in the HOW(L)-overexpressing imaginal disc, the posterior compartment (where DPP is not expressed) showed a 20% reduction of this domain (calculated as in Fig. 2), indicating a non-autonomous effect of HOW(L) (Fig. 5I). These results are consistent with HOW affecting the levels of the diffusing DPP morphogen. A control experiment driving HOW(L) with hedgehog-gal4 (expressed in the posterior compartment) did not reduce the Spalt domain, nor did it have any effect on cell viability [as measured by active Caspase 3 (also known as DECAY) staining (data not shown)].
To test directly whether HOW(L) is capable of reducing dpp mRNA levels, we performed in situ analysis with a dpp probe on the wing imaginal discs expressing ectopic HOW(L) by the sd-gal4 driver. The results indicate a significant decrease in dpp mRNA in the sd-gal4 expression domain (Fig. 5J,K). Taken together, these results demonstrate that ectopically expressed HOW(L) can repress dpp mRNA levels.
Reduction of endogenous HOW levels leads to an elevation of endogenous dpp mRNA
To test further the contribution of HOW to the reduction of endogenous
dpp mRNA levels, we reduced the levels of the HOW(L) isoform, or the
levels of all HOW isoforms, using dsRNA complementary to HOW(L), or to a part
of the HOW coding sequence shared by all isoforms, driven by the
sd-gal4 driver. We detected a significant elevation of dpp
mRNA in the wing imaginal disc pouch, where the sd-gal4 is highly
expressed in both cases (Fig.
6B,C). Accordingly, we detected a reduction in HOW protein levels
in the sd-gal4 expression domain in both cases
(Fig. 6D,G). Targeted
expression of HOW(L), or of HOW dsRNA (using sd-gal4), phenocopied
the how mutant blistered phenotype in the adult wing
(Fig. 6K,L), supporting the
relevance of these dsRNA constructs to HOW function. We also found that a
continuous expression of dsRNA corresponding to the HOW(L) isoform in the
pupal wing using the ms1096-gal4 driver led to the formation of
ectopic veins in 100% (n=60) of the wings
(Fig. 6N). This phenotype was
observed only with how(L)-specific dsRNA. Such a phenotype is
observed following the overexpression of DPP in the pupal wing
(Bangi and Wharton, 2006
).
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| DISCUSSION |
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Our structural studies helped us to identify a novel HOW target, namely dpp mRNA, in the wing imaginal disc. We suggest that, normally, the repressor isoform of HOW, HOW(L), reduces dpp mRNA levels in the wing imaginal disc and in the pupal wing, leading to reduced DPP protein levels during the establishment of the anteroposterior axis, and later during wing vein formation. Presumably, in the absence of HOW(L), higher DPP levels at the source would alter the overall shape of the DPP gradient, thus expanding the Spalt expression domain. The phenotype of ectopic veins obtained by continuous expression of HOW(L) dsRNA in the pupal wings supports an additional role for HOW(L) in repressing dpp mRNA at later stages of wing development.
The sensitivity of the embryo to DPP levels has been demonstrated by the
DPP haplo-insufficient phenotype (Podos
and Ferguson, 1999
). This sensitivity is also exhibited in the
wing imaginal disc by the observation that endogenous dpp can be
replaced by UAS-GFP-dpp driven by dpp-gal4 only at
low temperatures [16°C (Entchev et al.,
2000
) or 19°C (Teleman and
Cohen, 2000
)], at which the Gal4 protein is significantly less
active. Because the responsiveness of the cells to DPP levels is highly
sensitive, it is necessary to tightly regulate the levels of DPP protein; for
example, by constitutive reduction of its mRNA levels in DPP-secreting cells
by the HOW(L) protein.
In summary, we have elucidated the primary- and secondary-structure requirements for the binding of HOW to its target mRNA. This will facilitate the identification of novel targets for STAR proteins in other species. Importantly, our analysis uncovered a novel post-transcriptional mechanism that regulates dpp mRNA levels in the wing imaginal disc
| ACKNOWLEDGMENTS |
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