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First published online 22 April 2008
doi: 10.1242/jcs.025320
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Research Article |
1 Department of Genetics and Molecular Biology – "Sapienza" Università di Roma, 00185 Rome, Italy
2 Department of Evolutionary Biology, University of Siena, I-53100 Siena, Italy
* Author for correspondence (e-mail: roberto.piergentili{at}uniroma1.it)
Accepted 20 February 2008
| Summary |
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Key words: Lampbrush-like loops, Triplex, Heterochromatin, Y chromosome, Drosophila hydei
| Introduction |
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12% of the male genome (Pimpinelli et al., 1976
70% of the Y chromosome DNA is highly repetitive (Fig. 1). In particular, the h3 region, responsible for the formation of the kl-5 loop, contains the AAGAG, AAGAGAG and AAGAC satellites; the h21 region, responsible for the formation of the ks-1 loop, contains the AAGAG and AAGAC satellites; and the h8-h9 region, responsible for the formation of the kl-3 loop, contains the AATAT satellite. At least the AAGAC satellite is abundantly and specifically transcribed inside the kl-5 and ks-1 loops, but these transcripts do not migrate to the cytoplasm and are degraded together with the loops at the beginning of meiosis (Bonaccorsi et al., 1990
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In the present paper we used these two antibodies to test the presence of triple stranded nucleic acids inside the lampbrush-like loops formed by the Y chromosome of D. melanogaster. We found that two Y-loops, kl-3 and kl-5, are intensely and specifically decorated by Jel318 and Jel466 respectively, indicating that these two structures harbor triple-stranded nucleic acids. Our results suggest that the differential immunostaining exerted by Jel318 and Jel466 is related to the specific molecular organization of each loop. Moreover, we demonstrated the presence of triplexes inside the pseudonucleolus and the clubs Y-loops of Drosophila hydei, a species that diverged from D. melanogaster at least 58 million years ago. These results suggest that triplexes are a conserved feature of Y-loops in drosophilids. Finally, we have found that heat-stress-induced male sterility is coupled to an alteration of triplex immunostaining and, at the same time, to the absence of the high molecular weight polypeptides encoded by the kl-5 and kl-3 fertility factors of D. melanogaster (Goldstein et al., 1982
).
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| Results |
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Jel318 specifically recognizes AT-rich triplexes but, using the standard fixing procedure, no staining of primary spermatocyte nuclei was detectable with this antibody. However, a weak trypsin pre-treatment of fixed slides before incubation with Jel318 allowed an intense and specific immunostaining of the kl-3 loop (Fig. 2). No staining was ever detected on the other two loops, or the double-stranded DNA of the chromatin clumps that correspond to the premeiotic bivalents. To check the specificity of kl-3 loop immunostaining, X0 males were also analyzed. These males were obtained by crossing C(1)RM females with wild-type Oregon-R males. In X0 spermatocyte nuclei no triad signal is detectable by immunostaining with either Jel466 or Jel318 under the same experimental conditions described above.
Analysis of DNA fibers reveals that the kl-3 and kl-5 loops have a different organization
To better understand the molecular and cytological organization of the two triplex-forming loops, fibers of DNA were prepared according to Piergentili (Piergentili, 2006
). Results are shown in Fig. 3, and it can be seen that the two loops exhibit a different organization. Jel318 specifically stains a thin filament that is barely visible after staining with the DNA dye Hoechst 33258. In some cases, this filament appears quite long and shows no interruptions (Fig. 3A'). In those nuclei with a less squashed chromatin it is possible to detect a more compact kl-3 loop, and the Jel318 antibody decorates a lampbrush-like structure similar to that observed in non-squashed preparations (Fig. 3B'). It is noteworthy that, during fiber preparation, the pre-treatment with trypsin can be omitted without significant differences in the immunostaining (data not shown).
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Triplexes are a conserved feature of Y-loops in drosophilids
It is known that lampbrush-like loops are a conserved feature of primary spermatocytes among drosophilids (Pisano et al., 1993
; Piergentili, 2007
). Thus, we decided to check whether the presence of triplexes on these structures was also evolutionary conserved. For this purpose, the same antibodies were tested on the male germ line of D. hydei, a species that diverged from D. melanogaster 58 million years ago. Primary spermatocytes of D. hydei contain five well-characterized Y-loops, formed by five fertility factors (for a review, see Hackstein and Hochstenbach, 1995
). Similarly to D. melanogaster, D. hydei Y-loops also have huge physical dimensions, but they mainly transcribe middle-repetitive DNA sequences whose nucleotide content is different from that of D. melanogaster satellite DNA. Notwithstanding these differences, both Jel318 and Jel466 antibodies are able to intensely decorate at least two D. hydei Y-loops, namely the pseudonucleolus and the clubs (Fig. 5). Remarkably, in this case the two antibodies do not show different staining patterns and, in fixed preparations, the trypsin pre-treatment before Jel318 staining can be omitted. Also in this species, the Jel318 and Jel466 immunostaining seems to be specifically restricted to the loops, and no other signal is detected on other intranuclear structures (even with trypsin pre-treatment) or on the chromatin.
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Heat stress influences the formation of triplexes and alters the biochemical profile of testis extracts in D. melanogaster
To artificially induce an alteration in the triplex structure of the Y-loops, wild-type Oregon-R flies were reared at 31±0.5°C for one generation. Under these conditions, male flies become sterile (Young and Plough, 1926
) and data from the literature demonstrate that sterility is indeed generated in primary spermatocytes (Ayles et al., 1973
). Testes prepared from these males and analyzed by phase-contrast microscopy show apparently normal Y-loops. Accordingly, the immunostaining pattern observed with either the S5 or the T53-1 antibody does not seem to be affected (data not shown). However, the immunostaining with both Jel318 and Jel466 failed, even after trypsin pre-treatment, and no signal was ever found in three different sets of experiments (data not shown).
We then evaluated whether heat stress can affect the biochemical profile of the Y-related axonemal dynein heavy chains described by Goldstein and co-workers (Goldstein et al., 1982
), by analyzing testis extracts by SDS-PAGE. As shown in Fig. 6A, at least two high-molecular weight bands are missing in the profile, namely those associated with the presence of the kl-3 and kl-5 loci (Goldstein et al., 1982
) that are responsible for the formation of the loops decorated by the anti-triplex antibodies. To rule out the possibility that their absence is due to an intrinsic instability of these proteins at high temperature, testes of wild-type males reared at 24±1°C were dissected in physiological solution, quickly transferred to physiological solution at 32±0.5°C for 1 or 2 hours, and then analyzed in the same way. At both timings the electrophoretic profile is indistinguishable from the control (Fig. 6B), indicating that these proteins are stable under these testing conditions.
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| Discussion |
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It is known that at least the AAGAC satellite DNA associated to the kl-5 locus is abundantly transcribed, and that the resulting RNA does not migrate to the cytoplasm, being degraded prior to meiotic prophase I (Bonaccorsi et al., 1990
). However, no evidence has been provided to date about the transcription of the kl-3-associated AATAT satellite, although some open reading frames have been mapped inside this Y chromosome region (Fig. 1). It is known that the best prerequisite for triplex formation is the presence of a homopurine stretch of nucleotides on one filament and a corresponding homopyrimidine stretch on the complementary strand, but this does not occur in this case. Nevertheless, it should be taken into account that an AATAT-associated triplex has been already described by Dayn and collaborators (Dayn et al., 1992
), and that the AATAT- and AATATAT-rich region 81F of polytene chromosomes of D. melanogaster is intensely stained by Jel318 (Burkholder et al., 1991
), indicating that this satellite DNA may indeed form triple-stranded nucleic acids. We believe that, although not `perfect', the organization and nucleotide content of the kl-3 locus is sufficient to force the formation of triplex structures, even inside the kl-3 loop. It is possible to hypothesize that the torsional stress induced by the presence of an open chromatin conformation and the contemporary absence of free loop ends (Bonaccorsi et al., 1988
) supplies the necessary energy to establish such structure. The mechanism could be similar to that used by other non B-DNA structures such as Z-DNA, even in the absence of a homopurine sequence. RNase-treated slides did not show significant differences with respect to non-treated slides in the immunostaining pattern produced by either Jel318 or Jel466. Although we cannot completely rule out the possibility that RNase treatment is inefficient under our experimental conditions, these data suggest that, in Y-loops RNA is not part of the triplex structure, and both kl-3 and kl-5 harbor intramolecular DNA triplexes.
Since the AT content and the GC content of the AAGAG and AAGAGAG satellites are comparable (Fig. 1), it is rather surprising that the kl-5 loop is not stained by either of the anti-triplex antibodies. However, it is known that, at the molecular level, the two antibodies recognize the Hoogsteen triads differently (Agazie et al., 1994
). We believe that the T*AT triads inside the kl-5 loop triplex, because of the simultaneous presence of the C+*GC triads recognized by Jel466, have a geometry that is incompatible with the Jel318 antibody recognition. A difference between the kl-5- and kl-3-associated triplexes is suggested also by the pattern of the immunostaining signals produced by the antibodies inside primary spermatocyte nuclei. Jel318 decorates a long, continuous filament resembling the appearance of the kl-3 loop immunostained by T53-1 (Pisano et al., 1993
). This suggests that probably the entire DNA axis of this loop is involved in the formation of the triplex structure. However, immunostaining obtained with the Jel466 antibody on the kl-5 loop consists of a set of discrete dots that, in fiber preparations, appear aligned along a DNA filament. This suggests that the triplex-forming regions inside the kl-5 loop are either discontinuous, or that only a part of the triplex structure is accessible to Jel466. The former possibility might be supported by the evidence that in D. melanogaster only the AAGAGAG satellite has been tested for triplex formation (Horn et al., 2004
; Paris et al., 2007
); no data are available to date for the other two sequences. It is interesting to note that this satellite is not present inside the ks-1 locus (Fig. 1) and, under our experimental conditions, the corresponding Y-loop did not stain using Jel466. The latter possibility is indirectly supported by the fact that Jel318 staining can be obtained only after pre-treating the slides with trypsin or after the strong squashing that allows fiber visualization. These data suggest that Y-loop-associated triplexes are associated to proteins, probably triplex-binding units that can be removed either by a weak proteolytic digestion or by a mechanical shock, as it happens during fiber preparation.
In both D. melanogaster and C. tentans polytene chromosomes there is no triplex immunostaining associated to intensely transcribed puffs, suggesting that triplexes are present in transcriptionally inactive regions of the genome (Burkholder et al., 1991
). This association is also supported by a large number of studies on various systems indicating that triplex formation inside the promoter region usually downregulates gene expression (reviewed by Faria and Giovannangeli, 2001
). However, it is unlikely that this is the function of the triplexes associated to the lampbrush-like loops of primary spermatocytes, because both the kl-5 and D. hydei Y-loops are transcriptionally active (Bonaccorsi et al., 1990
; Hackstein and Hochstenbach, 1995
). We hypothesize that these triplexes are able to mediate the interaction between DNA-specific regions and some proteins that might recognize triplex structure as a specific binding site. Indeed, at least one triplex-binding protein has been already identified in D. melanogaster (Jimenez-Garcia et al., 1998
).
It has long been known that primary spermatocytes are sensitive to both cold and hot stresses (Young and Plough, 1926
; Sanders and Ayles, 1970
; David et al., 1971
; Cohet, 1973
; Ayles et al., 1973
; Suchowersky et al., 1974
). Since the most typical feature of these cells is the presence of lampbrush-like loops, we checked whether heat stress can affect these intranuclear structures. Although apparently normal, Y-loops of flies that have been reared at 31±0.5°C showed no reaction using either the Jel318 or the Jel466 antibody. Biochemical analysis of testis extracts from flies reared at 31±0.5°C showed that at least two of the putative dynein heavy chains described by Goldstein and co-workers (Goldstein et al., 1982
) were missing. Remarkably, these polypeptides correspond to those encoded by the triplex-containing kl-3 and kl-5 loops. This biochemical phenotype resembles that exhibited by some autosomal mutants (Piergentili et al., 2004
), in which the kl-3 loop is absent or strongly reduced. However, after heat stress, both the kl-3 and the kl-5 loops are present and still able to bind at least the proteins recognized by the S5 and T53-1 antibodies. The easiest explanation for these observations is that, analogous to what has been observed with autosomal mutations, the two proteins are produced but they are unstable and possibly rapidly degraded. Taken together, these data suggest that triplexes have a role in protein stabilization. They might serve as a docking, storing and/or modification site of proteins synthesized before meiosis, but exerting their function in post-meiotic stages. If this hypothesis will be further supported, Y-loops of drosophilids will be the first example of triplexes whose role is not only functional but also structural, i.e. protein docking. Another possibility, although restricted to the kl-5 loop, is that triplexes are involved in the splicing of the extremely long introns among which the coding sequences of some genes are interspersed (Fig. 1). Indeed, it has been demonstrated that a polypurine stretch with alternating A and G can stimulate (Tanaka et al., 1994
) or inhibit (Carstens et al., 2000
) the splicing of the surrounding intron(s). Moreover, a triplex structure has been described inside an intron splicing intermediate (Adams et al., 2004
). Of course, it is still possible that triplexes have both roles in the D. melanogaster male germ line, further supporting the differences between the two loops in both content and structure (Bonaccorsi and Lohe, 1991
; Lohe et al., 1993
) (our data): a protein-docking role on the kl-3 loop (where no RNA transcription has been demonstrated to date) and an intron-splicing role on the kl-5 loop.
| Materials and Methods |
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Testis immunofluorescence
Larval, pupal or adult testes were dissected and fixed according to Bonaccorsi et al. (Bonaccorsi et al., 1988
) and Pisano et al. (Pisano et al., 1993
). After fixation, slides were rinsed twice in Dulbecco's PBS modified formula for 5 minutes and incubated for 1 hour in a humid chamber at room temperature with one of the following: 20 µl of the T53-1 antiserum (Pisano et al., 1993
) diluted 1:10 in PBS, 20 µl of the S5 monoclonal antibody (Saumweber et al., 1980
) diluted 1:20 in PBS, 10 µl of Jel466 monoclonal antibody (Agazie et al., 1994
) diluted 1:10 in PBS or 10 µl of Jel318 monoclonal antibody (Lee et al., 1987
) diluted 1:10 in PBS. As for the last antibody, when preparing intact loops for Drosophila melanogaster, a pre-treatment of each slide with trypsin (10 µl at 25%) for 60-90 seconds was necessary before antibody incubation; after the pre-treatment, slides were rapidly washed in PBS and subsequently transferred for 3 minutes in clean PBS, to avoid excessive trypsin contact. Then all slides were washed twice in PBS for 5 minutes and incubated 1 hour with the secondary antibody, a sheep anti-mouse IgG conjugated with fluorescein (FLUOS, Boehringer), diluted 1:20 in PBS. Slides were finally air dried and mounted in PBS containing 0.5 µg/ml Hoechst 33258 dye. Analysis of DNA fibers was performed using a standard protocol (Piergentili, 2006
). The entire preparation was performed the same day, without interruptions. In another set of experiments, all slides prepared according to the above methods were also been treated with RNase to test the presence of RNA inside triplexes. According to published protocols (Bonaccorsi and Lohe, 1991
), 20 µl of a DNase-free RNase mixture (Roche) (2 µg/ml or 10 µg/ml in 2xSSC) were put onto the preparations and incubated for 30 minutes at room temperature in a humid chamber. Subsequently, slides were washed twice in 2xSSC and immunostaining was performed. The RNase treatment was performed either before or after the trypsin digestion in both Jel318 and Jel466 immunostained slides, for both standard and fiber preparations. Cell stages were identified as described by Cenci and co-workers (Cenci et al., 1994
).
Light mcroscopy
Microscope analysis and pictures were made using a Zeiss III RS photomicroscope equipped with an HBO fluorescent light (100 Watts), or with a Zeiss Axioplan photomicroscope equipped with an HBO fluorescent light (50 Watts). The Zeiss filter combination 09 was used for immunostained preparations with FLUOS-conjugated secondary antibodies, and Zeiss filter combination 01 for staining using Hoechst dye 33258. Pictures at the Zeiss Axioplan microscope were taken using a CCD camera from Photometrics and saved using IP Lab Spectrum software. Pseudocoloration of micrographs was performed using the Adobe Photoshop® software.
Electrophoretic analysis of testis protein from heat-induced sterile males
Testes from males reared at 31±0.5°C were dissected and immediately denatured; their high molecular weight protein complement was then analyzed by electrophoresis on 3-5% SDS-polyacrylamide gels, according to Laemmli (Laemmli, 1970
), using a constant amperage of 7 mA in the stacking gel and of 15 mA in the separation gel. After electrophoresis, gels were silver stained by the method of Wray et al. (Wray et al., 1981
).
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