The Drosophila even-skipped promoter is transcribed in a stage-specific manner in vitro and contains multiple, overlapping factor-binding sites

GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

Following fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal-to-zygotic transition (MZT). However, it was unknown whether additional pioneer factors were required for this transition. We identified an additional maternally encoded factor required for development through the MZT, GAGA Factor (GAF). GAF is necessary to activate widespread zygotic transcription and to remodel the chromatin accessibility landscape. We demonstrated that Zelda preferentially controls expression of the earliest transcribed genes, while genes expressed during widespread activation are predominantly dependent on GAF. Thus, progression through the MZT requires coordination of multiple pioneer-like factors, and we propose that as development proceeds control is gradually transferred from Zelda to GAF.

New insights for Drosophila GAGA factor in larvae

GAGA factor plays important roles during Drosophila embryogenesis and its maternal contribution is essential for early development. Here, the role of GAGA factor was studied in 3rd instar larvae using depletion and overexpression conditions in wing disc and transcriptome analysis. We found that genes changing expression were different to those previously described using GAGA mutants in embryos. No apparent phenotypes on GAGA depletion could usually be observed at larval stages in imaginal discs but a strong effect on salivary gland polytene chromosomes was observed. In the adult, GAGA depletion produced many defects like abnormal cell proliferation in the wing, impaired dorsal closure and resulted in homeotic transformation of abdominal segment A5. Unexpectedly, no effects on Ultrabithorax expression were observed. Short overexpression of GAGA factor in 3rd instar larvae also resulted in activation of a set of genes not previously described to be under GAGA regulation, and in lethality at pupa. Our results suggest a little contribution of GAGA factor on gene transcription in wing discs and a change of the genes regulated in comparison with embryo. GAGA factor activity thus correlates with the global changes in gene expression that take place at the embryo-to-larva and, later, at the larva-to-pupa transitions.

Antagonistic and cooperative actions of the EGFR and Dpp pathways on the iroquois genes regulate Drosophila mesothorax specification and patterning

In Drosophila, restricted expression of the Iroquois complex (Iro-C) genes in the proximal region of the wing imaginal disc contributes to its territorial subdivision, specifying first the development of the notum versus the wing hinge, and subsequently, that of the lateral versus medial notum. Iro-C expression is under the control of the EGFR and Dpp signalling pathways. To analyze how both pathways cooperate in the regulation of Iro-C, we isolated several wing disc-specific cis-regulatory elements of the complex. One of these (IroRE(2)) integrates competing inputs of the EGFR and Dpp pathways, mediated by the transcription factors Pointed (downstream of EGFR pathway) and Pannier/U-shaped and Mothers against Dpp (Mad), in the case of Dpp. By contrast, a second element (IroRE(1)) mediates activation by both the EGFR and Dpp pathways, thus promoting expression of Iro-C in a region of elevated levels of Dpp signalling, the prospective lateral notum near the anterior-posterior compartment boundary. These results help define the molecular mechanisms of the interplay between the EGFR and Dpp pathways in the specification and patterning of the notum.

GAGA factor down-regulates its own promoter

GAGA factor is involved in many nuclear transactions, notably in transcription as an activator in Drosophila. The genomic region corresponding to the Trl promoter has been obtained, and a minimal version of a fully active Trl promoter has been defined using transient transfection assays in S2 cells. DNase I footprinting analysis has shown that this region contains multiple GAGA binding sites, suggesting a potential regulatory role of GAGA on its own promoter. The study shows that GAGA down-regulates Trl expression. The repression does not depend on the GAGA isoform, but binding to DNA is absolutely required. A fragment of the Trl promoter can mediate repression to a heterologous promoter only upon GAGA overexpression in transiently transfected S2 cells. Chromatin immunoprecipitation analysis of S2 cells confirmed that GAGA factors are bound to the Trl promoter over a region of 1.4 kbp. Using a double-stranded RNA interference approach, we show that endogenous GAGA factors limit Trl expression in S2 cells. Our results open the possibility of observing similar GAGA repressive effects on other promoters.

Tramtrack69 is required for the early repression of tailless expression

During embryogenesis, the activated Torso receptor tyrosine kinase (TOR RTK) pathway activates tailless (tll) expression by a relief-of-repression mechanism. Various lines of evidence have suggested that multiple factors are required for this repression. We show that Tramtrack69 (TTK69) binds to two sites within tll cis-regulatory DNA, TC2 and TC5, and that TTK69 is phosphorylated by mitogen activated protein kinase. In embryos lacking maternal ttk69 activity, the expression of both endogenous tll and lacZ driven by the tll minimal regulatory region (tll-MRR) are expanded. Further, in wild-type embryos, the tll-MRR mutated in TC5 drives uniform lacZ expression before late stage 4. We conclude that TTK69 is required for early (before the end of stage 4) repression of tll transcription.

Gene regulation of Wiskott-Aldrich syndrome protein and the human homolog of the Drosophila Su(var)3-9: WASP and SUV39H1, two adjacent genes at Xp11.23

The region Xp11.23 is a gene-rich, light giemsa-staining segment on the short arm of the X chromosome. In this study, we have characterized the transcriptional regulatory elements in this interval for two adjacent genes: SUV39H1, a regulator of chromatin organization, and the Wiskott-Aldrich syndrome protein (WASP). The WASP gene exhibits two alternate promoters, both of which demonstrate transcription factor binding elements specific to blood cell lineages. Reporter gene expression analyses indicate that both WASP promoters show high levels of expression in different hematopoietic cell lines. The human homolog of the Drosophila Su(var)3-9 gene was identified by sequence analysis of the region downstream from WASP. SUV39H1 is ubiquitously expressed, and the promoter sequence consists mostly of general transcription factors. The presence of putative binding sites for GAGA and Adf1 transcription factors may indicate a cross regulatory mechanism with other chromatin regulators.

Functional mapping of the GAGA factor assigns its transcriptional activity to the C-terminal glutamine-rich domain

GAGA is a nuclear protein encoded by the Trithorax-like gene in Drosophila that is expressed in at least two isoforms generated by alternative splicing. By means of its specific interaction with DNA, GAGA has been involved in several nuclear transactions including regulation of gene expression. Here we have studied the GAGA(519) isoform as a transcription factor. In vitro, the transactivation domain has been assigned to the 93 C-terminal residues that correspond to a glutamine-rich domain (Q-domain). It presents an internal modular structure and acts independently of the rest of the protein. In vivo, in Drosophila SL2 cells, Q-domain can transactivate reporter genes either in the form of GAGA or Gal4BD-Q fusions, whereas a GAGA mutant deleted of the Q-domain cannot. Our results give support to the notion that GAGA can function as a transcription activating factor.

The even-skipped locus is contained in a 16-kb chromatin domain

The even-skipped (eve) gene of Drosophila melanogaster is a crucial member of the pair-rule class of segmentation genes. We report here the characterization of a 16-kb region sufficient for all known aspects of eve expression and the rescue of an eve null mutation. We began by examining 45 kb surrounding the eve coding sequence for DNaseI hypersensitive sites and other transcription units. We find that the previously identified eve regulatory elements, those for early stripes 2, 3, and 7 and the late element, do not generate prominent hypersensitive sites. However, strong, constitutive DNaseI hypersensitive sites flank a 16-kb region, within which one developmentally regulated site is found at the eve promoter region. P-element transformation of this 16-kb domain into eve mutants rescues them to adult viability. This 16-kb domain contains regulatory elements for all known features of eve expression: the seven major blastoderm stripes, minor stripe expression during germ band extension, and later expression in the lateral mesodermal muscle precursor cells, in the central nervous system, adjacent to the invaginating proctodeum, and in a ring around the anal pad. We have begun a preliminary dissection of the 16-kb domain into its constituent regulatory elements. Other major findings include the following: (1) There is a second element for late stripe expression adjacent to the traditional late element. (2) A stripe element 3' of the gene interacts with the late element to give rise to the minor stripes seen in the even-numbered parasegments. (3) Expression in the proctodeum and anal pad is driven by sequences both 5' and 3' of the gene. (4) Expression in different sites in the central nervous system is driven by separable elements widely dispersed throughout 8 kb 3' of the gene.

The N-terminal POZ domain of GAGA mediates the formation of oligomers that bind DNA with high affinity and specificity

The Drosophila GAGA factor self-oligomerizes both in vivo and in vitro. GAGA oligomerization depends on the presence of the N-terminal POZ domain and the formation of dimers, tetramers, and oligomers of high stoichiometry is observed in vitro. GAGA oligomers bind DNA with high affinity and specificity. As a consequence of its multimeric character, the interaction of GAGA with DNA fragments carrying several GAGA binding sites is multivalent and of higher affinity than its interaction with fragments containing single short sites. A single GAGA oligomer is capable of binding adjacent GAGA binding sites spaced by as many as 20 base pairs. GAGA oligomers are functionally active, being transcriptionally competent in vitro. GAGA-dependent transcription activation depends strongly on the number of GAGA binding sites present in the promoter. The POZ domain is not necessary for in vitro transcription but, in its absence, no synergism is observed on increasing the number of binding sites contained within the promoter. These results are discussed in view of the distribution of GAGA binding sites that, most frequently, form clusters of relatively short sites spaced by small variable distances.

A double interaction screen identifies positive and negative ftz gene regulators and ftz-interacting proteins

Regulatory genes directing embryonic development are expressed in complex patterns. The Drosophila homeobox gene fushi tarazu (ftz) is expressed in a striped pattern that is controlled by several discrete and large cis- regulatory elements. One key cis-element is the ftz proximal enhancer which is required for stripe establishment and which mediates autoregulation by direct binding of Ftz protein. To identify the trans-acting factors that regulate ftz expression and autoregulation, we developed a modified yeast two hybrid screen, the Double Interaction Screen (DIS). The DIS was designed to isolate both DNA binding transcriptional regulators that interact with the proximal enhancer and proteins that interact with Ftz itself when it is bound to the enhancer. The screen identified two candidate Ftz protein cofactors as well as activators and repressors of ftz transcription that bind directly to the enhancer. One of these (Tramtrack (Ttk)) was previously shown to bind to at least five sites in the proximal enhancer; genetic studies suggested that Ttk acts as a repressor of ftz in the embryo. Here we show that, in yeast cells, Ttk protein strongly activates transcription, suggesting that yeast may be missing a necessary co-repressor which is present in Drosophila embryos. Further, we have characterized the activity of a second candidate ftz repressor isolated in the screen - the product of the pair-rule gene sloppy paired - a member of the forkhead family. We show that Slp1 is a DNA binding protein. We have identified a high affinity binding site for Slp1 in the ftz proximal enhancer. Slp1 represses transcription via this binding site in yeast cells, consistent with its role as a direct repressor of ftz stripes in interstripe regions during late stages of embryogenesis. The DIS should be a generally useful method to identify DNA binding transcriptional regulators and protein partners of previously characterized DNA binding proteins.

Identification of engrailed promoter elements essential for interactions with a stripe enhancer in Drosophila embryos

BACKGROUND

The structures and functions of promoter sequences of most genes have been analysed using in vitro transcription and/or cultured cell systems, neither possessing tissue-specific enhancers. Promoter-enhancer interactions in vivo, in particular, during ontogeny, are still poorly understood.

RESULTS

We have established a new method for the assessment of promoter activity in cells that participate in fly body formation, using the UAS/GAL4 system. A functional analysis was then conducted on the promoter sequence of the engrailed gene in Drosophila embryos. A 38-bp-long sequence, terminating with an initiator or RNA start site and a downstream promoter element, was found to be capable of receiving activation signals from the engrailed stripe enhancer. Transcriptional efficiency was improved significantly by the presence of upstream promoting elements, most functionally replaceable with synthetic GAGA factor binding sites.

CONCLUSIONS

We identified the in vivo minimum promoter of engrailed and demonstrated that the GAGA factor binding sites serve primarily as quantitative elements which augment transcriptional efficiency. Evidence was also obtained that indicated that not only enhancer but also promoter sequences were involved in the determination of the tissue-specificity of gene expression.

Patterns of conservation and divergence at the even-skipped locus of Drosophila

The even-skipped (eve) gene of Drosophila melanogaster has been intensively studied as a model for spatial and temporal control of gene expression, using in vitro and transgenic techniques. Here, the study of eve is extended, using evolutionary conservation of DNA sequences. Conservation of much of the protein, and of known regulatory elements, supports models for eve function and regulation that have previously been advanced, and extensive conservation found in noncoding sequences predicts that functional elements exist that have yet to be defined. In contrast, a part of the protein implicated in transcriptional repression has diverged extensively while preserving overall amino acid composition, highlighting potentially essential features of this domain. Also, the basal promoter has diverged extensively, indicating evolutionary flexibility of promoter function.

Chromatin. Ga-ga over GAGA factor

Recent results suggest that the Drosophila transcriptional activator known as GAGA factor functions by influencing chromatin structure.

The Trithorax-like gene encodes the Drosophila GAGA factor

Little is known about the way higher-order chromatin structure influences gene expression and chromosome topology in general. Genetic analysis in Drosophila has led to the discovery of two classes of genes, the regulators of homeotic genes and the modifiers of position-effect variegation, which seem to be good candidates for encoding some of the factors regulating chromatin functions. The Trithorax-like gene we described here is required for the normal expression of the homeotic genes and is a modifier of position-effect variegation. We found that Trithorax-like encodes the GAGA factor which is involved in the formation of an accessible chromatin structure at promoter sequences. Our genetic analysis suggests that the chromatin modelling function of the GAGA factor is not restricted to promoter regions.

Pattern formation in the limbs of Drosophila: bric a brac is expressed in both a gradient and a wave-like pattern and is required for specification and proper segmentation of the tarsus

We have identified the gene bric a brac and show that it is required for pattern formation along the proximal-distal axis of the leg and antenna of Drosophila. In bric a brac mutant legs, the bristle pattern of the three central tarsal segments is transformed towards the pattern of the most proximal tarsal segment. In addition, bric a brac mutant legs and antennae have segmentation defects. bric a brac encodes a nuclear protein that shares a highly conserved domain with two transcription factors from Drosophila. bric a brac function is dosage dependent and is required in a graded manner for the specification of tarsal segments. The graded requirement for bric a brac correlates with its graded expression pattern, suggesting that the concentration of BRIC A BRAC protein specifies segment identity in the tarsus.

Partial characterization of a novel 'GGA' factor which binds to the osteonectin promoter in bovine bone cells

Osteonectin (On)/SPARC (secreted protein, acidic and rich in cysteine) is a highly conserved extracellular matrix protein found in bone and other tissues throughout vertebrate evolution. In previous studies, approximately 500 bp of DNA 5' to the transcription start point (tsp) and a part of exon 1, including homopurine (Rn)/homopyrimidine (Yn)-rich sequences (the 'GGA box' and its complements), was demonstrated to be important in upregulation of On gene expression in a cell-specific manner. The purpose of this study was to decipher the transcriptional regulation of On through its cis- and trans-acting elements. DNase I footprinting analysis indicated protein binding which may be related to the transcriptional factors, AP2, SP1 and a novel 'GGA' factor which binds to the 3' end of the promoter (-286 to +43 to the tsp). Comparisons of footprinting between nuclear extracts of bone (On-expressing) cells and Madin and Darby bovine kidney (MDBK) (nonexpressing) cells indicate that 'GGA' factor binding to a purine GGGGA/GGA-rich sequence is cell-type specific and therefore may be involved in the cell-specific expression of this gene. From ultraviolet (UV)-crosslinking experiments, this 'GGA' factor was demonstrated to be a single 40-kDa protein.

Repression of Drosophila pair-rule segmentation genes by ectopic expression of tramtrack

The tramtrack (ttk) protein has been proposed as a maternally provided repressor of the fushi tarazu (ftz) gene in Drosophila embryos at the preblastoderm stage. Consistent with this hypothesis, we have detected by immunohistochemistry the presence of ttk protein in preblastoderm embryos. This is followed by a complete decay upon formation of the cellular blastoderm when ftz striped expression is at its peak. In addition, the highly complex pattern of zygotic ttk expression suggests specific functions for ttk late in development that are separate from the regulation of ftz. We have produced ttk protein ectopically in blastoderm-stage embryos transformed with a heat shock-ttk construct. Ectopic ttk caused complete or near-complete repression of the endogenous ftz gene, as well as significant repression of the pair-rule genes even skipped, odd skipped, hairy and runt. These findings suggest that specific repression by ttk (or by undiscovered repressors) may be more than an isolated phenomenon during the rapid cleavage divisions, a period when the need for genetic repression has not been generally anticipated.

The urate oxidase gene of Drosophila pseudoobscura and Drosophila melanogaster: evolutionary changes of sequence and regulation

The urate oxidase (UO) transcription unit of Drosophila pseudoobscura was cloned, sequenced, and compared to the UO transcription unit from Drosophila melanogaster. In both species the UO coding region is divided into two exons of approximately equal size. The deduced D. pseudoobscura and D. melanogaster UO peptides have 346 and 352 amino acid residues, respectively. The nucleotide sequences of the D. pseudoobscura and D. melanogaster UO protein-coding regions are 82.2% identical whereas the deduced amino acid sequences are 87.6% identical with 42 amino acid changes, 33 of which occur in the first exon. Although the UO gene is expressed exclusively within the cells of the Malpighian tubules in both of these species, the temporal patterns of UO gene activity during development are markedly different. UO enzyme activity, UO protein, and UO mRNA are found in the third instar larva and adult of D. melanogaster but only in the adult stage of D. pseudoobscura. The intronic sequences and the extragenic 5' and 3' flanking regions of the D. pseudoobscura and D. melanogaster UO genes are highly divergent with the exception of eight small islands of conserved sequence along 772 bp 5' of the UO protein-coding region. These islands of conserved sequence are possible UO cis-acting regulatory elements as they reside along the 5' flanking DNA of the D. melanogaster UO gene that is capable of conferring a wild-type D. melanogaster pattern of UO regulation on a UO-lacZ fusion gene.