RNA polymerase B (or II) in heat induced puffs of Drosophila polytene chromosomes

Widespread colocalization of the Drosophila histone acetyltransferase homolog MYST5 with DREF and insulator proteins at active genes

MYST family histone acetyltransferases play important roles in gene regulation. Here, we have characterized the Drosophila MYST histone acetyltransferase (HAT) encoded by cg1894, whose closest homolog is Drosophila MOF, and which we have termed MYST5. We found it localized to a large number of interbands as well as to the telomeres of polytene chromosomes, and it showed strong colocalization with the interband protein Z4/Putzig and RNA polymerase II. Accordingly, genome-wide location analysis by ChIP-seq showed co-occurrence of MYST5 with the Z4-interacting partner Chriz/Chromator. Interestingly, MYST5 bound to the promoter of actively transcribed genes, and about half of MYST5 sites colocalized with the transcription factor DNA replication-related element-binding factor (DREF), indicating a role for MYST5 in gene expression. Moreover, we observed substantial overlap of MYST5 binding with that of the insulator proteins CP190, dCTCF, and BEAF-32, which mediate the organization of the genome into functionally distinct topological domains. Altogether, our data suggest a broad role for MYST5 both in gene-specific transcriptional regulation and in the organization of the genome into chromatin domains, with the two roles possibly being functionally interconnected.

Whole-genome analysis reveals that active heat shock factor binding sites are mostly associated with non-heat shock genes in Drosophila melanogaster

During heat shock (HS) and other stresses, HS gene transcription in eukaryotes is up-regulated by the transcription factor heat shock factor (HSF). While the identities of the major HS genes have been known for more than 30 years, it has been suspected that HSF binds to numerous other genes and potentially regulates their transcription. In this study, we have used a chromatin immunoprecipitation and microarray (ChIP-chip) approach to identify 434 regions in the Drosophila genome that are bound by HSF. We have also performed a transcript analysis of heat shocked Kc167 cells and third instar larvae and compared them to HSF binding sites. The heat-induced transcription profiles were quite different between cells and larvae and surprisingly only about 10% of the genes associated with HSF binding sites show changed transcription. There were also genes that showed changes in transcript levels that did not appear to correlate with HSF binding sites. Analysis of the locations of the HSF binding sites revealed that 57% were contained within genes with approximately 2/3rds of these sites being in introns. We also found that the insulator protein, BEAF, has enriched binding prior to HS to promoters of genes that are bound by HSF upon HS but that are not transcriptionally induced during HS. When the genes associated with HSF binding sites in promoters were analyzed for gene ontology terms, categories such as stress response and transferase activity were enriched whereas analysis of genes having HSF binding sites in introns identified those categories plus ones related to developmental processes and reproduction. These results suggest that Drosophila HSF may be regulating many genes besides the known HS genes and that some of these genes may be regulated during non-stress conditions.

Polytene chromosome squash methods for studying transcription and epigenetic chromatin modification in Drosophila using antibodies

The giant polytene chromosomes from Drosophila third instar larval salivary glands provide an important model system for studying the architectural changes in chromatin morphology associated with the process of transcription initiation and elongation. Especially, analysis of the heat shock response has proved useful in correlating chromatin structure remodeling with transcriptional activity. An important tool for such studies is the labeling of polytene chromosome squash preparations with antibodies to the enzymes, transcription factors, or histone modifications of interest. However, in any immunohistochemical experiment there will be advantages and disadvantages to different methods of fixation and sample preparation, the relative merits of which must be balanced. Here we provide detailed protocols for polytene chromosome squash preparation and discuss their relative pros and cons in terms of suitability for reliable antibody labeling and preservation of high resolution chromatin structure.

Human SRCAP and Drosophila melanogaster DOM are homologs that function in the notch signaling pathway

The putative ATPase chromatin-remodeling machine SRCAP was identified in a yeast two-hybrid protein screen by interaction with the histone acetylase CBP. SRCAP is implicated in the transcriptional coactivation of cyclic AMP- and steroid-dependent promoters, but no natural chromosomal targets for SRCAP regulation have been identified. DOM is the unique SRCAP homolog in Drosophila melanogaster. The goal of this study was to test whether SRCAP is a functional homolog of DOM and to identify potential activities and targets of SRCAP in vivo. We show that human SRCAP complements recessive domino mutant phenotypes. This rescue depends on an intact ATPase homology domain. SRCAP colocalizes extensively with DOM on Drosophila polytene chromosomes and is recruited to sites of active transcription, such as steroid-regulated loci, but not to activated heat shock loci. We show that SRCAP recruits Drosophila CBP to ectopic chromosomal sites, providing the first evidence to suggest that SRCAP and CBP interact directly or indirectly on chromosomes. We show that DOM is a Notch pathway activator in Drosophila and that wild-type SRCAP-but not an ATPase domain mutant-can substitute for DOM in Notch-dependent wing development. We show that SRCAP potentiates Notch-dependent gene activation in HeLa cells. Taken together, these data implicate SRCAP and DOM in developmental gene activation.

Regulation of Heat Shock Gene Expression by RNA Polymerase II Elongation Factor, Elongin A

The elongation stage of transcription by RNA polymerase II (Pol II) has emerged as an essential regulated step. Elongin A (EloA) is the largest subunit of the Elongin complex that can increase the catalytic rate of mRNA synthesis by Pol II. We recently demonstrated that the Elongin A homologue in Drosophila, dEloA, is essential and has properties consistent with those of a Pol II elongation factor in vivo. The goal of this study was to test whether dEloA is required for heat shock gene transcription, since heat shock gene expression is thought to be controlled at the level of Pol II elongation. Here, we demonstrate that dEloA is rapidly recruited to heat shock loci with Pol II in response to heat shock. Furthermore, through the use of RNA interference in vivo, we show that dEloA is required for the proper expression of one of these genes, HSP70, and that its requirement for heat shock gene expression is exerted after the initiation of transcription at heat shock loci. Our data represent the first demonstration of an essential role for an RNA polymerase II elongation factor in the regulation of heat shock gene expression in an animal model.

Drosophila ELL is associated with actively elongating RNA polymerase II on transcriptionally active sites in vivo

Several factors have been biochemically characterized based on their ability to increase the overall rate of transcription elongation catalyzed by the multiprotein complex RNA polymerase II (Pol II). Among these, the ELL family of elongation factors has been shown to increase the catalytic rate of transcription elongation in vitro by suppressing transient pausing. Several fundamental biological aspects of this class of elongation factors are not known. We have cloned the Drosophila homolog (dELL) in order to test whether ELL family proteins are actually associated with the elongating Pol II in vivo. Here we report that dELL is a nuclear protein, which, like its mammalian homologs, can increase the catalytic rate of transcription elongation by Pol II in vitro. Interestingly, we find that dELL co-localizes extensively with the phosphorylated, actively elongating form of Pol II at transcriptionally active sites on Drosophila polytene chromosomes. Furthermore, dELL is relocalized from a widespread distribution pattern on polytenes under normal conditions to very few transcriptionally active puff sites upon heat shock. This observation indicates a dynamic pattern of localization of dELL in cells, which is a predicted characteristic of a Pol II general elongation factor. We also demonstrate that dELL physically interacts with Pol II. Our results strongly suggest that dELL functions with elongating RNA polymerase II in vivo.

P-TEFb kinase recruitment and function at heat shock loci

P-TEFb, a heterodimer of the kinase Cdk9 and cyclin T, was isolated as a factor that stimulates formation of productive transcription elongation complexes in vitro. Here, we show that P-TEFb is located at >200 distinct sites on Drosophila polytene chromosomes. Upon heat shock, P-TEFb, like the regulatory factor HSF, is rapidly recruited to heat shock loci, and this recruitment is blocked in an HSF mutant. Yet, HSF binding to DNA is not sufficient to recruit P-TEFb in vivo, and HSF and P-TEFb immunostainings within a heat shock locus are not coincident. Insight to the function of P-TEFb is offered by experiments showing that the direct recruitment of a Gal4-binding domain P-TEFb hybrid to an hsp70 promoter in Drosophilacells is sufficient to activate transcription in the absence of heat shock. Analyses of point mutants show this P-TEFb stimulation is dependent on Cdk9 kinase activity and on Cdk9's interaction with cyclin T. These results, coupled with the frequent colocalization of P-TEFb and the hypophosphorylated form of RNA polymerase II (Pol II) found at promoter-pause sites, support a model in which P-TEFb acts to stimulate promoter-paused Pol II to enter into productive elongation.

Targeting to transcriptionally active loci by the hydrophilic N-terminal domain of Drosophila DNA topoisomerase I

DNA topoisomerase I (topo I) from Drosophila melanogaster contains a nonconserved, hydrophilic N-terminal domain of about 430 residues upstream of the conserved core domains. Deletion of this N terminus did not affect the catalytic activity of topo I, while further removal of sequences into the conserved regions inactivated its enzymatic activity. We have investigated the cellular function of the Drosophila topo I N-terminal domain with top1-lacZ transgenes. There was at least one putative nuclear localization signal within the first 315 residues of the N-terminal domain that allows efficient import of the large chimeric proteins into Drosophila nuclei. The top1-lacZ fusion proteins colocalized with RNA polymerase II (pol II) at developmental puffs on the polytene chromosomes. Either topo I or the top1-lacZ fusion protein was colocalized with RNA pol II in some but not all of the nonpuff, interband loci. However, the fusion proteins as well as RNA pol II were recruited to heat shock puffs during heat treatment, and they returned to the developmental puffs after recovery from heat shock. By immunoprecipitation, we showed that two of the largest subunits of RNA pol II coprecipitated with the N-terminal 315-residue fusion protein by using antibodies against beta-galactosidase. These data suggest that the topo I fusion protein can be localized to the transcriptional complex on chromatin and that the N-terminal 315 residues were sufficient to respond to cellular processes, especially during the reprogramming of gene expression.

Identification of a nonhistone chromosomal protein associated with heterochromatin in Drosophila melanogaster and its gene

Monoclonal antibodies were prepared against a fraction of nuclear proteins of Drosophila melanogaster identified as tightly binding to DNA. Four of these antibodies were directed against a 19-kilodalton nuclear protein; immunofluorescence staining of the polytene chromosomes localized the antigen to the alpha, beta, and intercalary heterochromatic regions. Screening of a lambda gt11 cDNA expression library with one of the monoclonal antibodies identified a recombinant DNA phage clone that produced a fusion protein immunologically similar to the heterochromatin-associated protein. Polyclonal sera directed against the bacterial lacZ fusion protein recognized the same nuclear protein on Western blots. A full-length cDNA clone was isolated from a lambda gt10 library, and its DNA sequence was obtained. Analysis of the open reading frame revealed an 18,101-dalton protein encoded by this cDNA. Two overlapping genomic DNA clones were isolated from a Charon 4 library of D. melanogaster with the cDNA clone, and a restriction map was obtained. In situ hybridization with these probes indicated that the gene maps to a single chromosome location at 29A on the 2L chromosome. This general strategy should be effective for cloning the genes and identifying the genetic loci of chromosomal proteins which cannot be readily assayed by other means.

Identification of a nonhistone chromosomal protein associated with heterochromatin in Drosophila melanogaster and its gene

Monoclonal antibodies were prepared against a fraction of nuclear proteins of Drosophila melanogaster identified as tightly binding to DNA. Four of these antibodies were directed against a 19-kilodalton nuclear protein; immunofluorescence staining of the polytene chromosomes localized the antigen to the alpha, beta, and intercalary heterochromatic regions. Screening of a lambda gt11 cDNA expression library with one of the monoclonal antibodies identified a recombinant DNA phage clone that produced a fusion protein immunologically similar to the heterochromatin-associated protein. Polyclonal sera directed against the bacterial lacZ fusion protein recognized the same nuclear protein on Western blots. A full-length cDNA clone was isolated from a lambda gt10 library, and its DNA sequence was obtained. Analysis of the open reading frame revealed an 18,101-dalton protein encoded by this cDNA. Two overlapping genomic DNA clones were isolated from a Charon 4 library of D. melanogaster with the cDNA clone, and a restriction map was obtained. In situ hybridization with these probes indicated that the gene maps to a single chromosome location at 29A on the 2L chromosome. This general strategy should be effective for cloning the genes and identifying the genetic loci of chromosomal proteins which cannot be readily assayed by other means.

The association of transcribed genes with the nuclear matrix of Drosophila cells during heat shock

Using the transcriptional modulation afforded by heat shock, we found that the association of active genes with the nuclear matrix was not dependent on their level of transcription. Heat shock genes were matrix associated both before heat shock (when transcription was relatively low), and during heat shock (when transcription was greatly increased). Conversely, the cytoplasmic actin gene was matrix associated during normal growth conditions (when transcription was high) and during heat shock (when transcription was greatly decreased). Removal of greater than 99.7% of nascent RNA during preparation of the matrices did not affect these findings. Detailed examination of the cytoplasmic actin gene revealed that its matrix association was apparently mediated by multiple interactions near the 5' end of the gene.

Differential distribution of nonhistone proteins from polytene chromosomes of Drosophila melanogaster after heat shock

Nine monoclonal antibodies directed against chromosomal proteins of D. melanogaster were used to study, by indirect immunofluorescence, the distribution of their respective antigens on polytene chromosomes following heat shock. This treatment is known to induce a specific set of transcriptionally active puffs with concomitant reduction of transcriptional activity in previously active loci. Our studies revealed wide differences in the distribution of the individual chromosomal proteins under heat shock conditions with regard to pattern and rate of both elimination from the inactivated loci and accumulation in the activated loci.

Immunoelectron microscopic localization of RNA polymerase B on isolated polytene chromosomes of Chironomus tentans

RNA polymerase B (or II) was localized by immunoelectron microscopy in ultrathin sections of polytene chromosomes isolated from larval salivary glands of Chironomus tentans. The enzyme was found at decondensed sites (puffs and interbands), whereas no detectable RNA polymerase B was present in condensed loci (bands). Within each of the large puffs the highest enzyme concentration was observed wherever the chromatin was in the most decondensed state. Otherwise the enzyme appeared homogeneously distributed within puffs and interbands. This immunoelectron microscopic study, along with the recently published immunofluorescent and autoradiographic analysis of isolated Chironomus chromosomes (Sass, 1982) unequivocally demonstrates that RNA polymerase B is present in most, if not all interbands.

Kinetics and models of the Drosophila heat-shock system

The puffing of Drosophila heat-shock genes after (1) a step-wise temperature increase ("heat-shock"); (2) recovery from anaerobiosis; and (3) incubation with uncoupling reagents was expressed as percent of the maximal size and normalized to the time scale. Data were taken from the literature and new measurements. In addition, puffing was measured after a 30-min temperature pulse and after two 30-min pulses. The latter experiment revealed a second, smaller increase in puff-size. Data on RNA and protein synthesis in Drosophila cells were collected from the literature and also normalized. From the available data, a feed-back control system is derived that consists of a controlled variable x, possibly a metabolic function of the mitochondria, interacting with an activator molecule which exists in an active (A+) and an inactive (A-) configuration. A+ activates the heat-shock genes which in turn produce their mRNA (y) and proteins (z) which then change the controlled variable x into a new steady state. A modified version of this model assumes a feed-back control of the heat-shock proteins on the activator molecule. A mathematical model of this system (Goodwin, 1965) was simulated by computer and compared with the experimental results.

Primary sequence of the 5' flanking regions of the Drosophila heat shock genes in chromosome subdivision 67B

The 5' flanking regions of the four small heat shock genes of Drosophila melanogaster from cytological locus 67B have been characterized. Approximately 500 bp of the primary sequence upstream from the proposed site of initiation of translation has been determined and the 5' end of the messenger RNAs have been localized for each gene. Each of the four genes contains an A-T rich sequence, either TATAAATA or TATAAAAG, which is flanked by a G-C rich region. This A-T rich sequence, which ends about 23 bp upstream from the proposed site of initiation of transcription, is similar to those found in most eukaryotic genes. Novel features of these four genes include a region of homology beginning near the proposed site of initiation of transcription and extending about 20 bp into the 5' noncoding region of the genes. This sequence is also found in the gene for the major heat shock protein, hsp 70. The leaders of these five heat shock genes are long, from 111 to 253 bases in length, as well as unusually A rich, from 46% to 51% A. In addition, each of the four small genes contains the sequence ACTTTNA, 195 +/- 12 bp from the proposed site of initiation of transcription.

Localization of RNA polymerase B and histones in the nucleus of primary spermatocytes of Drosophila hydei, studied by immunofluorescence microscopy

By means of indirect immunofluorescence microscopy, we have studied the distribution of RNA polymerase B, of the nucleosomal histones H2b, H3, and H4 and of histone H1, in nuclei of primary spermatocytes of Drosophila hydei. RNA polymerase B and histones, including H1, are found to be present on the loop structures of the Y chromosome. The nucleolus stains only for the histones, but not for RNA polymerase B. Various mutants deficient for some of the loops or altering their morphology, were used to identify the individual chromosomal segments. In growing spermatocytes of the genetic constitution X/0, autosomes and the chromosome X react strongly with antibodies against RNA polymerase B, but not with antibodies against histones. The results suggest that the autosomes, the chromosome X and the Y chromosomal loop structures, with the exception of the nucleolus, are transcribed mostly by RNA polymerase B.

A DNA segment isolated from chromosomal site 67B in D. melanogaster contains four closely linked heat-shock genes

cDNA clones coding for two different small heat-shock polypeptides were isolated. Both clones hybridize exclusively to the heat-shock puff site 67B, and restriction mapping of embryonic Drosophila melanogaster DNA showed that the two genes probably occur as single copies and are closely linked. The analysis was extended by isolating genomic clones, which contain these genes and two additional ones. The four different genes code for heat-induced poly(A)+ RNAs. These genes are clustered within an 11 kb segment and are separated by spacers of 1.0-4.7 kb. Three of the genes were found to exhibit alternating polarities. Thus in spite of their close linkage, the four heat-induced genes are most likely organized in individual transcription units.

Monoclonal antibodies against chromosomal proteins of Drosophila melanogaster: establishment of antibody producing cell lines and partial characterization of corresponding antigens

Total nuclear protein from the embryonic D. melanogaster cell line Kc and crude hydroxyapatite fractions thereof were used for immunization of mice. From the spleen cells of these mice we established 755 permanent lymphoid cell lines using the hybridoma technique originally developed by Köhler and Milstein (1975). Radioimmunoassay showed 455 of these cell lines secreted antibodies which bound to component(s) contained in the antigen mixtures used for immunization. Screening of 311 cell lines using indirect immunofluorescence revealed 58 lines whose antibodies showed a highly selective staining pattern on polytene chromosomes from the salivary glands of D. melanogaster third instar larvae. Eight of these cell lines were cloned and further characterized. We were able to order the staining patterns into three distinct classes based on the staining behaviour of the monoclonal antibodies: staining of active regions, staining of phase dark bands or staining of most interbands. The molecular weight of those antigens against which the monoclonal antibodies were directed was determined in SDS polyacrylamide gels.

Nuclear proteins in Drosophila melanogaster cells after heat shock and their binding to homologous DNA

After 5 minutes heat shock at 37 degrees C Drosophila melanogaster Kc-cell nuclear proteins were extracted wit 0.4M NaCl and compared by SDS gel electrophoresis with extracts from cells grown at 25 degrees C. Two proteins (39 000 and 46 000) were only found in heat shock nuclei. Reconstitution with total Drosophila DNA or a DNA fragment from the heat inducible locus 87A/C covalently coupled to sepharose was performed. In the presence of calf thymus competitor DNA these proteins and also others of lower molecular weight showed preferential binding to the homologous DNA.

Effect of salt-treatment on manually isolated polytene chromosomes from Chironomus tentans

A method for the rapid manual isolation of polytene chromosomes and nuclear membranes from salivary glands of Chironomus tentans is presented and the analysis of some of their RNA and protein components before and after treatment with 2 M salt solutions is summarized.--After salt-incubation the chromosomes still display a considerable number of bands which stain with ethidium bromide and which are sensitive to treatment with DNase, RNase, trypsin, and proteinase K, to a lesser extent with pronase and papain. Analysis of the iodinated residual proteins on SDS gels yield three major and two minor bands (MW between 50,000 and 70,000 dalton) which were also shown to be present in interphase chromosomes of Ehrlich ascites cells which had been treated similarly and are also tightly bound constituents of DNA prepared according to Gross-Bellard et al. (1973). This result indicates the existence of a general class of non-histone proteins involved in keeping the DNA in a supercoiled state. Furthermore their presence in salt-treated nuclear membranes of Chironomus salivary gland cells (and Xenopus oocytes, unpubl.) will be of interest with respect to functional aspects of the nuclear matrix.