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Genetics, Vol. 178, 749-759, February 2008, Copyright © 2008
doi:10.1534/genetics.107.083105
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Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
2 Corresponding author: University of Washington, Department of Biology, 24 Kincaid Hall, Box 351800, Seattle, WA 98195-1800.
E-mail: csink{at}u.washington.edu
| ABSTRACT |
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While these studies addressed cis-acting PEV, there is a similar, related phenomenon in flies of silencing by heterochromatin in trans. In trans-acting PEV, or "trans-inactivation," the block of heterochromatin and the silenced gene are not necessarily on the same DNA molecule, but are brought close to each other within the space of the interphase nucleus. It is probable that this type of PEV is similar to downregulation of a number of normal genes in higher eukaryotes, as increasing evidence finds developmentally silenced loci that move into association with large blocks of heterochromatin (for example, see SU et al. 2004). A well-studied example of trans-inactivation is the brownDominant (bwD) allele of the Drosophila melanogaster brown (bw) eye-color gene. The bwD allele contains an insertion of
1.6 Mbp of heterochromatin into the brown coding sequence (PLATERO et al. 1998). Except for a few small distinct spots, eyes of bwD /bw+ flies totally lack red eye pigment. The trans-inactivation of the bw+ gene on the homologous chromosome is a consequence of the repositioning of bwD into the pericentric heterochromatic compartment (CSINK and HENIKOFF 1996; HARMON and SEDAT 2005; THAKAR et al. 2006) through interactions of heterochromatic binding proteins (SAGE and CSINK 2003). In bwD/bw+ heterozygotes somatic pairing of the homologs causes the bw+ chromosomal region to associate with pericentric heterochromatin along with the bwD heterochromatic insertion. Hence, the wild-type bw gene is silenced due to its localization in a neighborhood of the nucleus inhibitory to its transcription.
In parallel to the work on cis PEV, studies have found that some genes are resistant to trans-inactivation. MARTIN-MORRIS et al. (1997) have demonstrated that some mini-white transgenes can be trans-inactivated while full-length white cannot. Additionally, earlier work of ours demonstrated that transgenes with different promoters have different susceptibilities to silencing by heterochromatin in trans (CSINK et al. 2002). One factor that differed between these promoters was the developmental time of expression. This is intriguing, as studies on cis-acting PEV have shown that development plays a role in silencing (LU et al. 1996; WEILER and WAKIMOTO 1998; AHMAD and HENIKOFF 2001). The studies on cis-acting PEV and trans-inactivation have provided intriguing results and suggest additional questions to be addressed. For example, does gene expression play the same role in the ability of a gene to be silenced in cis and in trans? In the circumstance of cis silencing the silenced gene is always located near heterochromatin, while in trans-inactivation the heterochromatic association required for silencing changes during development (THAKAR and CSINK 2005). Because of this, one may predict that a gene with the same pattern of expression could have different susceptibilities to cis and trans silencing.
Here we study the role that temporal, spatial, and quantitative differences in gene expression play in the susceptibility of a gene to trans-inactivation. We use an upstream activating sequence (UAS)–GFP transgene near the brown locus in combination with lines activating GAL4 in specific patterns of expression (BRAND and PERRIMON 1993). This allows an examination of trans-inactivation when the reporter is expressed in different times of development and in different tissues and cell types. We find that transgenes whose expression is delayed until differentiation are more likely to be silenced, while those with earlier expression are more resistant to silencing. Additionally, we found no general trend toward increased or decreased silencing of transgenes as adult flies aged, except that there was a bit less silencing in freshly emerged adults. We also did not find a tendency for silencing established in earlier developmental stages to be lost upon differentiation. Examining the level of silencing in different tissues showed that even the same gene with the same driver was differentially susceptible to trans-inactivation in the various tissues. Finally, we were unable to find a consistent correlation between ability to be trans-inactivated and level of wild-type expression. Combined, these results demonstrate the diversity of outcomes of heterochromatin in trans and the strong influence of developmental expression pattern in determining the sensitivity of a gene to chromatin-mediated gene silencing.
| MATERIALS AND METHODS |
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Microscopic examination and measurement of GFP expression:
Eye imaginal discs, salivary glands, and the central nervous system were examined for GFP expression and trans-inactivation. Wandering third-instar male larvae were used and 3–13 tissues of each genotype were examined. Tissues were from at least three different larvae. Occasionally one of a pair of discs or glands was unusable due to damage during dissection; hence odd numbers of these tissues were sometimes used (Table 2). Two bwD and two bw+ larvae were dissected in tandem in PBS for 5 min. Tissues were placed in fix mix (made immediately before use: 100 µl 37% paraformaldehyde, 900 µl PBS, 1 µl of 1 mg/ml DAPI) for 10 min. Tissues were further dissected during this 10 min, rinsed once with PBS, and then placed in permeabilization mix (made immediately before use: 665 µl PBS, 2 µl Triton-X, 0.67 µl of 1 mg/ml DAPI) for 3 min. Tissues were rinsed twice with PBS. Tissues were attached to a polylysine-coated printed-well slide in a drop of PBS. All tissues from the four larvae were placed on the same slide, with bwD and bw+ tissues juxtaposed, and covered by a 18 x 18-mm coverslip. Tissues were examined immediately after the slide was made. Images were taken using a 4x objective so that multiple tissues could be visualized in one image. Microscopy used a Deltavision system (Applied Precision) built around an Olympus IX70 microscope. The images were gathered with a cooled CCD camera (Micromax 350; Photometrics, Tucson, AZ). Quantification utilized SoftWorx software (Applied Precision) and was performed by measuring the total GFP fluorescence in the tissue and standardized by dividing by total DAPI staining in the tissue. This was performed for bwD and bw+ tissues from each of the lines, as well as a negative control for each cross (see Figure 1) lacking UAS–EFGP. Background fluorescence was removed by subtracting the lowest value obtained from the negative control line from each of the driver lines. These corrected values were averaged and are shown with their 95% confidence intervals in Figures 3–5
. All statistical analysis and graphing were done using the Statview program (Abacus Concepts, Berkeley, CA). In all statistical analysis significance was tested by a two-tailed, unpaired Student's t-test. P-values <0.05 are marked as significant in Table 2.
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| RESULTS |
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5 Kbp from where the heterochromatic insertion is found on the bwD chromosome. P{UAS-EGFP} also contains a mini-white reporter gene that gives the eye an orange color. As with other transgenes we have studied containing the mini-white reporter gene in this same location (CSINK et al. 2002; SAGE et al. 2005), the expression from this reporter is very strongly repressed when heterozygous with a bwD chromosome. We selected seven driver lines to use in this study on the basis of two criteria: pattern of expression as reported in FlyBase and the previous examination of silencing by heterochromatin in cis (AHMAD and HENIKOFF 2001). To confirm their pattern of expression, we reexamined the expression of these drivers lines throughout development using our P{UAS–GFP}59E reporter heterozygous to a wild-type chromosome. The embryos, larvae, pupae, adults, and some dissected tissues were examined under a fluorescent dissecting scope and/or a standard compound fluorescent microscope. Our findings are summarized in Table 1 and generally confirmed the previous descriptions of these various driver lines in FlyBase (CROSBY et al. 2007).
Lines were initially selected to test a number of specific hypotheses concerning trans-inactivation. For instance, lines c355 and 167Y were chosen to test the possibility that lack of expression in the embryo promoted silencing. arm and act were used to test both the importance of very early transcription and the strength of the expression. Lines GMR, elav, and 179Y were used to test for the role of differentiation in trans-inactivation.
Trans-inactivation in differentiated and undifferentiated cells of the eye imaginal disc:
The eye imaginal discs of third-instar larvae are bisected by the morphogenetic furrow with cells posterior to the furrow undergoing differentiation and cells anterior being undifferentiated. Previous results from our lab have shown that there are profound changes in both nuclear organization and chromatin dynamics that accompany this differentiation event in the eye imaginal disc (THAKAR and CSINK 2005; THAKAR et al. 2006). To determine if these changes were correlated with changes in specific aspects of gene expression, we examined the eye discs of wandering third-instar larvae for trans-inactivation of UAS–GFP. Our selection of driver lines allowed us to compare trans-inactivation in differentiated and undifferentiated cells. Three of the lines (act, arm, and c355) expressed throughout the disc, while three others (elav, 179Y, and GMR) expressed GFP only in the differentiated cells posterior to the morphogenetic furrow. The trans-inactivation of the lines expressing in the eye discs is shown in Figure 3A and quantification is shown in Figure 3B and Table 2.
The lines that show trans-inactivation are only those where expression is not activated until after differentiation. In none of the lines with GAL4-driven GFP expression in undifferentiated cells do we see silencing by bwD heterochromatin in trans, including the weakly expressing arm and moderately expressing c355 drivers. While this resistance to silencing appears uninfluenced by the strength of expression of the transgene in the undifferentiated cells, careful examination of the later-expressing lines (three rightmost bar graph sets in Figure 3B) reveals that the level of silencing (decrease in the bwD bars in Figure 3B) is slightly weaker in the more strongly expressed lines. It should also be noted that expression during embryogenesis does not seem to be necessary to confer resistance to silencing. Line c355 does not show expression in eye discs until the second instar, but is still not trans-inactivated.
Tissue-specific differences in trans-inactivation:
In our study, the amount and timing of GAL4 expression in some of the driver lines are different in different tissues. To determine if silencing would vary depending on the tissue examined we examined trans-inactivation in two additional third-instar larval tissues: the central nervous system (CNS) (Figure 4) and the salivary glands (Figure 5). The only line to display significant trans-inactivation in the CNS was line 179Y. The only line to display trans-inactivation in the salivary glands was line arm. Therefore, a single driver is differentially susceptible to trans-inactivation in different tissues (Table 2). For instance, arm is silenced in salivary glands, but not in the eye disc. The elav expression is silenced in differentiated eye disc cells, but not in the CNS. This tissue specificity may result from differences in the state of the nucleus as we are comparing diploid, polytene, and differentiated cells and is further discussed below.
Silencing in adults:
We examined whole adult flies for trans-inactivation of UAS–GFP activated by five of the driver lines. Adult flies contain more differentiated tissue than larvae, so one may expect a bit more trans-inactivation. Additionally, we were interested in finding out if the level of silencing changed in a general direction as the adults aged. Therefore, we examined flies at five different times after eclosion. Figure 6 shows the levels of expression in the bw+ male flies in the top graph and the level of trans-inactivation in the bottom graph. In general, there is a modest level of silencing in all lines at least at some age. This silencing seems mostly unaffected by the age of the adult and there is no obvious correlation between overall expression and silencing. However, there does seem to be a bit less silencing in the newly emerged flies (1 day, 0–24 hr after eclosion) using the 179Y (females), elav, and arm drivers and in no lines is the strongest trans-inactivation seen in this earliest sample (Table 3).
Strong trans-inactivation is seen for GFP driven by the elav promoter in all but the youngest adults. The elav regulatory region would drive GAL4 expression mostly in differentiating or differentiated neurons, not in their neuroblast precursors (ROBINOW and WHITE 1991). Additionally, very strong silencing is found for the ubiquitous, but weakly expressed arm driver. Silencing is not seen for elav in the larval CNS and is seen only for arm in the larval salivary gland. These two lines highlight the fact that we often see different levels of trans-inactivation in different tissues and stages of development.
Fluorescence was measured separately in adult males and females. With one exception the trend was the same in both sexes (data not shown). The one line that had a difference was 179Y, where there was substantial silencing in females, but less in males (Figure 6 and Table 3). This line drives expression in the ovary and the testis (Table 1), so it is probable that this difference arises from a different degree of silencing in the gonads. Alternatively it could be due to the large number of eggs within the female, which have a different developmental state from the rest of the adult fly.
| DISCUSSION |
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The commonality between these studies is the demonstration that the expression pattern of a gene affects its ability to be silenced. While these studies addressed cis-acting PEV, we wanted to address the role of expression pattern in trans-inactivation. Previous results from our lab have demonstrated that different transgenes have different abilities to be trans-inactivated. Additionally, we have shown that enhancer trap transgenes located near the brown locus are unable to be trans-inactivated. This implies that the expression pattern of the enhancers near the brown locus renders them resistant to trans-inactivation (CSINK et al. 2002; SAGE et al. 2005).
In this study, we determined that transgenes not expressed until differentiation are more likely to be trans-inactivated than those expressed earlier. This result concurs with the cis-acting PEV results. In the study of AHMAD and HENIKOFF (2001), when the transgene was turned on earlier in development it was less likely to be silenced than when it was turned on later in development. As we see a similar trend in cis and trans silencing, this may be a fundamental feature of silencing and not particular to cis or trans mechanisms. Additionally, we determined that the level of trans-inactivation varies depending on the stage of development in which it is examined (Table 1). This result further supports the hypothesis that when a gene is expressed in development affects the ability of this gene to be silenced.
We examined the overall amount of trans-inactivation in adults to determine if there was a general relaxation of silencing with differentiation. Such relaxation would predict that lines whose expression was inhibited by bwD in an earlier developmental stage (larvae or undifferentiated cells in the eye disc) would become active later in development (adult or differentiated cells in the eye disc). Indeed, it would predict little silencing in adult tissue, as the bulk of the adult is terminally differentiated. This is not what we find. Indeed, we find the exact opposite in the eye imaginal discs, with silencing seen only in differentiated tissue and no silencing in undifferentiated tissue. We also find that the 179Y-driven expression is silenced in eye imaginal discs and CNS in larvae and is still mostly trans-inactivated in older adults. Additionally, the highest level of silencing in this study is seen for the GFP expression driven by arm in adults, even though it is not seen at all in some larval tissues. We also find that GFP expression driven by the elav, arm, and 179Y (females) regulatory regions (Figure 6) shows an overall increase in silencing in the older flies compared to the day-1 flies. This may indicate that heterochromatin formation is stable during aging and that the ability of genes to escape from silencing decreases as an organism matures. Alternatively, it is possible that in newly eclosed adults there is perdurance of GFP from the undifferentiated state that is degraded as the fly ages.
It is not surprising that there are changes in silencing with development, as there are large-scale changes in heterochromatin during development (ARNEY and FISHER 2004). In Drosophila, heterochromatin is first visible (MAHOWALD and HARDY 1985; VLASSOVA et al. 1991), and heterochromatin protein 1 (HP1) first begins to be concentrated in heterochromatin (JAMES et al. 1989), in syncytial blastoderm. Heterochromatin stays in a condensed state and replicates late in the cell cycle, beginning with the 14th cell cycle (FOE et al. 1993; HIRAOKA et al. 1993). Additionally, recent results from our group have found that bwD associations are stabilized and promoted during differentiation. This is correlated with a general decrease in the movement of euchromatic loci within the nuclei of the differentiated cells of the eye imaginal disc (THAKAR et al. 2006).
The experiments we present in this article find very different levels of trans-inactivation in different tissues (Table 1). Among other things, this could be due to the different organization of the nucleus in these different tissues. The CNS, eye discs, and salivary glands were examined in a third-instar larva, which allowed us to examine trans-inactivation in diploid tissue, tissue pre- and postdifferentiation, and polytene tissues, respectively. The differences seen pre- and postdifferentiation relate to time of developmental expression and are discussed above. An unanticipated result was to find trans-inactivation in salivary glands. This was unexpected as salivary glands contain polytene chromosomes, which mostly lack the heterochromatic association between bwD and pericentric heterochromatin that promotes bwD trans-inactivation (TALBERT et al. 1994; CSINK and HENIKOFF 1996). In this special circumstance, however, inactivation by bwD may not require heterochromatic association for the transgene to be located near a large concentration of heterochromatin. Silencing could be due to the juxtaposition of the transgene and heterochromatin found in the bwD allele. In polytene tissues the DNA strands are copied thousands of times; however, the pericentric heterochromatin does not have a correspondingly high copy number. Interestingly, bwD heterochromatin does appear to have this high copy number. In these polytene tissues bwD represents a large fraction of heterochromatin and strongly concentrates HP1 (PLATERO et al. 1998). This results in a large concentration of heterochromatic proteins, which could silence the euchromatic transgene located nearby. In this special circumstance, bwD may be acting as a heterochromatic compartment to silence the transgene. Therefore, although the transgene is in trans to the bwD allele, in this circumstance heterochromatic association may not be required and may be more similar to cis-PEV. Correspondingly, the only driver silenced in the polytene tissues was a very weak driver line, arm.
In contrast to the results on cis silencing (AHMAD and HENIKOFF 2001), we were unable to find a consistent correlation between ability to be trans-inactivated and level of expression. On the one hand, there are certain aspects of our study that fit this trend. For instance, in the three lines where GPF is driven and silenced only in the differentiated cells of the eye disc (GMR, elav, and 179Y) we find that the degree of silencing is inversely related to the level of wild-type expression. Additionally, arm, the most strongly silenced line in the adult is also one of the normally weakly expressing lines. However, there are clear data in this study that are inconsistent with the level of expression being of primary importance to susceptibility to trans-inactivation. Neither arm-driven expression in eye discs, nor 167Y-driven expression in CNS, nor GMR expression in the salivary glands is silenced, despite their very weak expression in those tissues. Second, 179Y is nicely silenced in the CNS despite having more expression than 167Y and a similar level to elav, neither of which are trans-inactivated. We believe that our data do not support a primary role for level of expression in susceptibility to trans-inactivation. However, it is possible that level of expression plays a role in silencing once the locus comes close to the heterochromatic compartment and this could account for the inconsistencies. That is, if the locus is unassociated with centric heterochromatin and being expressed, the level of expression is irrelevant because silencing cannot occur when the UAS–GFP is not close enough to the heterochromatic compartment. However, once it resides in this compartment the level of silencing may be subject to similar influences that modify cis heterochromatic silencing, such as the overall concentration of the GAL4 transcription factor (AHMAD and HENIKOFF 2001).
The above results indicate that there may be fundamental differences between cis and trans silencing. Other results that may also be due to such differences involve the behavior of two lines used both in this study and in the work by AHMAD and HENIKOFF (2001). Those authors found variegated silencing in cis of arm- and act-driven expression both before and after the morphogenetic furrow, while we find no silencing by bwD in those same two lines in the eye disc either before or after the morphogenetic furrow. These contrasting results may be due to differences in how silencing is brought about and maintained in the different types of PEV (Figure 7). In the circumstance of cis silencing the silenced gene is always located near heterochromatin, while in trans-inactivation the heterochromatic association required should change during development. Close association of the gene in cis with a large block of heterochromatin early in development would allow the effect of heterochromatic proteins to modify the early organization of the regulatory region and may limit the influence of early-acting transcription factors.
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Combined, our results demonstrate that the pattern of expression of a gene affects its ability to be trans-inactivated and emphasize the importance of the interaction of nuclear organization, chromatin structure, and temporal and quantitative variation in transcription factor abundance in determining the final expression state of a locus.
| ACKNOWLEDGEMENTS |
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| FOOTNOTES |
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