Reverse genetics of Drosophila RNA polymerase II: identification and characterization of RpII140, the genomic locus for the second-largest subunit

Identification of genetic suppressors of the Sin3A knockdown wing phenotype

The role of the Sin3A transcriptional corepressor in regulating the cell cycle is established in various metazoans. Little is known, however, about the signaling pathways that trigger or are triggered by Sin3A function. To discover genes that work in similar or opposing pathways to Sin3A during development, we have performed an unbiased screen of deficiencies of the Drosophila third chromosome. Additionally, we have performed a targeted loss of function screen to identify cell cycle genes that genetically interact with Sin3A. We have identified genes that encode proteins involved in regulation of gene expression, signaling pathways and cell cycle that can suppress the curved wing phenotype caused by the knockdown of Sin3A. These data indicate that Sin3A function is quite diverse and impacts a wide variety of cellular processes.

Expression of a D1 dopamine receptor dDA1/DmDOP1 in the central nervous system of Drosophila melanogaster

The diverse physiological effects of dopamine are mediated by multiple receptor systems. The dDA1 represents one of the Drosophila dopamine receptors that activate the cAMP cascade. To gain insight into the role of dDA1, we generated a polyclonal antibody against the unique sequence in dDA1 and investigated dDA1 distribution in the central nervous system (CNS) of Drosophila melanogaster. In both larval and adult CNS pronounced dDA1 immunoreactivity was present in the neuropil of the mushroom bodies, a brain structure crucial for learning and memory in insects, and four unpaired neurons in each thoracic segment. In addition, the larval abdominal ganglion contained two dDA1 cells in each segment. This expression pattern appeared to be maintained in the condensed adult abdominal ganglion although the precise number and the intensity of staining were somewhat variable. The adult CNS also exhibited intense dDA1 immunoreactivity in the central complex, a structure controlling higher-order motor function, moderate expression in several neurosecretory cells, and weak staining in two unpaired neurons in the mesothoracic neuromere. The dDA1 expression in these areas was only detected in adult, but not in third instar larval CNS.

Chromosomal homologies between Drosophila melanogaster and D. funebris determined by in-situ hybridization

Seventeen biotin-labeled DNA sequences were hybridized to polytene chromosomes of Drosophila melanogaster and D. funebris in order to establish chromosomal homologies between these species. Ten probes correspond to cloned DNA sequences from D. melanogaster (RpII 215, MHC, H3-H4, Tor, hsp 68, hsp 28/23, hsp 83, PP1alpha, RpII 140, and ey), four are clones isolated from a D. subobscura genomic library (Xdh, lambdaDsubS3, lambdaDsubG3, and lambdaDsubG4), two are clones from D. funebris (F2 and Adh) and one from D. virilis (ci). The probes were chosen in order to cover all the autosomes, since X-chromosome homologies have already been studied by linkage analysis of morphological mutants. Most probes gave a unique hybridization signal; consequently, our results allow unambiguous inferences about chromosomal homologies. The results show extensive gene rearrangement within all chromosomal elements, probably due to paracentric inversions, but are consistent with Muller's proposal that chromosomal elements have conserved their genetic content during the evolution of Drosophila.

Fate of dot chromosome genes in Drosophila willistoni and Scaptodrosophila lebanonensis determined by in situ hybridization

One modification of the primitive karyotype of the Drosophilidae is the absence of dot chromosomes. The origin of this modification is diverse. In some cases, the fate of the dot chromosomes can be directly inferred from cytogenetic analysis but in other cases a genetic or a combined molecular and cytogenetic analysis is needed, as occurs in Drosophila willistoni and Scaptodrosophila lebanonensis. We determined the location of four dot chromosome sequences in D. willistoni and S. lebanonensis using in situ hybridization. Drosophila melanogaster and D. virilis, which possess dot chromosomes, were used as a control. The in situ hybridization results show that dot chromosome genes of D. melanogaster and D. virilis are closely linked in chromosome 3 of D. willistoni and in chromosome X of S. lebanonensis. These results suggest an autosome-dot fusion in D. willistoni and an X-dot fusion in S. lebanonensis, two different paths in the evolution of dot chromosomes.

Chromosomal homology and molecular organization of Muller's elements D and E in the Drosophila repleta species group

Thirty-three DNA clones containing protein-coding genes have been used for in situ hybridization to the polytene chromosomes of two Drosophila repleta group species, D. repleta and D. buzzatii. Twenty-six clones gave positive results allowing the precise localization of 26 genes and the tentative identification of another nine. The results were fully consistent with the currently accepted chromosomal homologies and in no case was evidence for reciprocal translocations or pericentric inversions found. Most of the genes mapped to chromosomes 2 and 4 that are homologous, respectively, to chromosome arms 3R and 3L of D. melanogaster (Muller's elements E and D). The comparison of the molecular organization of-these two elements between D. melanogaster and D. repleta (two species that belong to different subgenera and diverged some 62 million years ago) showed an extensive reorganization via paracentric inversions. Using a maximum likelihood procedure, we estimated that 130 paracentric inversions have become fixed in element E after the divergence of the two lineages. Therefore, the evolution rate for element E is approximately one inversion per million years. This value is comparable to previous estimates of the rate of evolution of chromosome X and yields an estimate of 4.5 inversions per million years for the whole Drosophila genome.

Drosophila TFIIE: purification, cloning, and functional reconstitution

We present a physical and molecular genetic characterization of Drosophila melanogaster TFIIE (dTFIIE), a component of the basal RNA polymerase II transcription apparatus. We have purified dTFIIE to near homogeneity from nuclear extracts of Drosophila embryos and found that it is composed of two subunits with apparent molecular weights of 55 and 38 kDa. Peptide sequence information derived from the two subunits was used to isolate the corresponding cDNA clones, revealing that dTFIIE and human TFIIE share extensive amino acid similarity. Functional conservation was demonstrated by the ability of bacterially expressed dTFIIE to substitute for human TFIIE in an in vitro transcription assay reconstituted from purified components. Cytological mapping analysis shows that both subunits are encoded by single copy genes located on chromosome III.

Drosophila TFIIA-S is up-regulated and required during Ras-mediated photoreceptor determination

Photoreceptor induction in the developing Drosophila eye is triggered by the activation of the Ras pathway. Subsequently, the Ras-mediated activation of site-specific transcription factors leads to the expression of putative "effector" genes. The coactivator function of the basal transcription factor TFIIA has been shown previously to enhance the trans-activation potential of site-specific transcription factors in vitro. Here, we show that the expression of the small subunit of TFIIA (dTFIIA-S) is specifically up-regulated in a transient manner during Ras-mediated photoreceptor induction. Furthermore, although null mutations in dTFIIA-S are cell lethal, a hypomorphic dTFIIA-S allele demonstrates an increased requirement for this factor during photoreceptor development. In addition, the cone cell to R7 photoreceptor transformation caused by ectopic activation of the Ras pathway during eye development is suppressed by the removal of one functional copy of the dTFIIA-S locus revealing the sensitivity of this process to reductions in dTFIIA-S activity. These results are the first in vivo evidence for the coactivator function in transcriptional enhancement proposed for TFIIA.

Functional studies of the carboxy-terminal repeat domain of Drosophila RNA polymerase II in vivo

To understand the in vivo function of the unique and conserved carboxy-terminal repeat domain (CTD) of RNA polymerase II largest subunit (RpII215), we have studied RNA polymerase II biosynthesis, activity and genetic function in Drosophila RpII215 mutants that possessed all (C4), half (W81) or none (IIt) of the CTD repeats. We have discovered that steady-state mRNA levels from transgenes encoding a fully truncated, CTD-less subunit (IIt) are essentially equal to wild-type levels, whereas the levels of the CTD-less subunit itself and the amount of polymerase harboring it (Pol IIT) are significantly lower than wild type. In contrast, for the half-CTD mutant (W81), steady-state mRNA levels are somewhat lower than for wild type or IIt, while W81 subunit and polymerase amounts are much less than wild type. Finally, we have tested genetically the ability of CTD mutants to complement (rescue) partially functional RpII215 alleles and have found that IIt fails to complement whereas W81 complements partially to completely. These results suggest that removal of the entire CTD renders polymerase completely defective in vivo, whereas eliminating half of the CTD results in a polymerase with significant in vivo activity.

Identifying a transcription factor interaction site on RNA polymerase II

We have generated a series of fusion proteins carrying portions of subunit IIc, the second largest subunit of Drosophila RNA polymerase I, and have used them in a domain interference assay to identify a fragment of the IIc subunit that carries the binding site for a basal transcription factor. Fusion proteins carrying a subunit IIc fragment spanning residues Ala519-Gly992 strongly inhibit promoter-driven transcription in both unfractionated nuclear extracts and in reconstituted systems. The same fusion proteins similarly inhibit dTFIIF stimulation of Pol II elongation on dC-tailed templates, suggesting that the IIc(A519-G992) fragment, which carries conserved regions D-H, interferes with transcription by binding to dTFIIF. Finally, dTFIIF can be specifically cross-linked to a GST-IIc(A519-G992) fusion protein or to subunit IIc in intact Pol II.