Distribution of RNA polymerase on Drosophila polytene chromosomes as studied by indirect immunofluorescence

greenCUT&RUN: Efficient Genomic Profiling of GFP-Tagged Transcription Factors and Chromatin Regulators

Genome-wide mapping of transcription factors and chromatin regulators is important to distinguish their direct from indirect effects on gene transcription or chromatin function. Novel approaches for studying their genomic localization under native conditions, such us cleavage under target and release using nuclease (CUT&RUN), offer higher resolution and lower sequencing costs than classical chromatin immunoprecipitation (ChIP) assays, and require fewer cells but they still depend on the availability of high-quality antibodies. Here, we describe detailed and robust protocols for greenCUT&RUN, which is a generic CUT&RUN-based approach for mapping the genome-wide localization of green fluorescent protein (GFP)-tagged factors in intact mammalian cells. The greenCUT&RUN method makes use of a micrococcal nuclease (MNase) coupled to a high affinity nanobody against GFP, which exploits the accessibility of multiple surfaces of the GFP tag, thus eliminating issues of antibody variability and availability. We also provide efficient protocols for the expression and purification of two different GFP nanobodies, which recognize non-overlapping GFP epitopes and can be combined for a further gain in sensitivity and accuracy. Compared to traditional CUT&RUN, genomic localization by greenCUT&RUN reduces handling time and experimental variability. GreenCUT&RUN is a versatile, robust, and universal procedure for surveying the genome-wide localization of GFP-tagged versions of proteins that drive key transcriptional programs and regulate chromatin function. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Standard greenCUT&RUN for GFP-tagged proteins in mammalian cells Alternate Protocol: High-Ca⁺⁺ /low-salt greenCUT&RUN for GFP-tagged histone proteins in mammalian cells Support Protocol: Expression and purification of GFP nanobody-MNase fusion proteins for greenCUT&RUN.

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.

Chriz, a chromodomain protein specific for the interbands of Drosophila melanogaster polytene chromosomes

Polytene interphase chromosomes are compacted into a series of bands and interbands reflecting their organization into independent chromosomal domains. In order to understand chromosomal organization, we set out to study the role of proteins that are selective for interbands. Here we describe the Drosophila melanogaster chromodomain protein Chriz that is coimmunoprecipitated with the zinc finger protein Z4. Both proteins colocalize exclusively to the interbands on Drosophila polytene chromosomes. Like Z4, Chriz is ubiquitously expressed throughout development and is associated with chromatin in all interphase nuclei. Following dissociation from chromatin, early in mitosis Chriz binds to the centrosomes and to the mitotic spindle. Newly induced amorphic Chriz alleles are early lethal, and ubiquitous overexpression of Chriz is lethal as well. Available Chriz hypomorphs which survive until pupal stage have a normal chromosomal phenotype. Reducing Z4 protein does not affect Chriz binding to polytene chromosomes and vice versa. Z4 is still chromosomally bound when Chriz protein is depleted by RNA interference.

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.

The Drosophila gene stand still encodes a germline chromatin-associated protein that controls the transcription of the ovarian tumor gene

The Drosophila gene stand still (stil) encodes a novel protein required for survival, sexual identity and differentiation of female germ cells. Using specific antibodies, we show that the Stil protein accumulates in the nucleus of all female germ cells throughout development, and is transiently expressed during early stages of male germline differentiation. Changes of Stil subnuclear localization during oogenesis suggest an association with chromatin. Several mutant alleles, which are point mutations in the Stil N-terminal domain, encode proteins that no longer co-localized with chromatin. We find that Stil binds to many sites on polytene chromosomes with strong preference for decondensed chromatin. This localization is very similar to that of RNA polymerase II. We show that Stil is required for high levels of transcription of the ovarian tumor gene in germ cells. Expression of ovarian tumor in somatic cells can be induced by ectopic expression of Stil. Finally, we find that transient ubiquitous somatic expression of Stil results in lethality of the fly at all stages of development.

Association of individual hnRNP proteins and snRNPs with nascent transcripts

As they are transcribed, RNA polymerase II transcripts (hnRNAs or pre-mRNAs) associate with hnRNP proteins and snRNP particles, and the processing of pre-mRNA occurs within these ribonucleoprotein complexes. To better understand the relationship between hnRNP proteins and snRNP particles and their roles in mRNA formation, we have visualized them as they associate with nascent transcripts on the polytene chromosomes of Drosophila melanogaster salivary glands. Simultaneous pairwise detection of the abundant hnRNP proteins hrp36, hrp40, and hrp48 by direct double-label immunofluorescence microscopy reveals all of these proteins are bound to most transcripts, but their relative amounts on different transcripts are not fixed. Numerous differences in the relative amounts of snRNP particles and hnRNP proteins on nascent transcripts are also observed. These observations directly demonstrate that individual hnRNP proteins and snRNP particles are differentially associated with nascent transcripts and suggest that different pre-mRNAs bind different combinations of these factors to form transcript-specific, rather than a single type of, hnRNA-hnRNP-snRNP complexes. The distinct and specific constellation of hnRNP proteins and snRNP particles that assembles on different pre-mRNAs is likely to affect the fate and pathway of processing of these transcripts.

The presence of an antigen reactive with a human autoantibody in Trichosia pubescens (Diptera: Sciaridae) and its association with certain transcriptionally active regions of the genome

The antigens in HeLa and Trichosia pubescens cells, recognized by sera from patients with rheumatic diseases containing anti-Ku antibodies, were compared by means of immunoprecipitation of labeled cell extracts. The autoantibodies present in the tested sera precipitate at least two polypeptides of approximately Mr = 70,000 and Mr = 80,000 in HeLa cell extracts and a polypeptide of approximately Mr = 72,000 in Trichosia salivary gland cell extracts. The distribution of the insect antigen in chromatin was studied in salivary gland polytene chromosomes by indirect immunofluorescent staining with sera from two different patients. Both sera react with certain transcriptionally active chromosomal sites. The presence of the antigen in polytene chromosomes is strictly dependent on transcription, as no reaction is observed in the same sites before or after gene activation. Other sites, such as the nucleolar organizing region, are very active in transcription but never reacted with the anti-Ku positive sera. These results show that the insect antigen is associated with transcription-related processes of a subset of the chromosomal loci of T. pubescens. The anti-Ku positive sera react with a highly conserved antigen, which may serve a very important and similar role in the cellular metabolism of both insect and mammalian cells.

Two puff-specific proteins bind within the 2.5 kb upstream region of the Drosophila melanogaster Sgs-4 gene

The Drosophila nuclear proteins Bj6 and Bx42 characterized previously are detected in a series of developmentally active puffs on salivary gland chromosomes. Here the binding of both proteins at puff 3C11-12 containing the glue protein gene Sgs-4 is described in more detail. By deletion analysis we show that both proteins bind within a chromosomal segment containing 17-19 kb of DNA surrounding the Sgs-4 gene. They are detectable at this site during the intermoult stages, before the puff regresses in response to the moulting hormone ecdysone. If the Sgs-4 gene together with flanking DNA sequences is brought into a different chromosomal position by P element transfer, both proteins are detected at this new location. Both proteins are bound to the chromosome within the range of 2.5 kb DNA upstream of the Sgs-4 gene. A strain containing a 52 bp deletion within this region fails to bind Bx42 protein suggesting that the missing DNA, which overlaps a hypersensitive region, may be required for the binding of the Bx42 protein.

Isolation and distribution of a Drosophila protein preferentially associated with active regions of the genome

A non-histone chromosomal protein of Mr = 75,000 was isolated from Drosophila embryos. The distribution pattern of this protein was determined by indirect immunofluorescence on salivary gland chromosomes of Drosophila melanogaster third instar larvae and compared with the distribution pattern of RNA polymerase II. Despite its preferential association with transcriptionally active regions of the chromosomes there was in many cases an almost inverse correlation with the RNA polymerase II content of a given locus. We postulate a function of the Mr = 75,000 protein in posttranscriptional regulation of gene expression by storing the newly synthesized RNA.

Two proteins from Drosophila nuclei are bound to chromatin and are detected in a series of puffs on polytene chromosomes

Immunizing chromatin protein fractions from Drosophila melanogaster embryos, monoclonal antibodies have been generated against two nuclear proteins of different molecular weight. These proteins are present in a chromatin fraction of Drosophila Kc-cell nuclei and both proteins could be shown to cosediment with nucleosomes following separation on sucrose gradients. Early in development both proteins are located in the embryo cytoplasm. Later, at times when transcription starts at blastoderm, they become redistributed into the nuclei. On salivary gland chromosomes both proteins are detected in a series of developmentally active puffs. The number of sites where these antigens can be detected, as well as the qualitative properties of the antigens at these sites differ between both proteins.

A cytological and molecular analysis of Adh gene expression in Drosophila melanogaster polytene chromosomes

Analysis of puffing patterns in Drosophila melanogaster salivary gland chromosomes indicates the existence of a developmentally specific puff in the 35B region. This puff seems to originate from bands 35B2 or 35B3, where Adh is located, and it is expanded in more than 60% of the nuclei examined. The presence of RNA polymerase II in this puff as well as its ability to incorporate tritiated uridine shows that it corresponds to a transcriptionally active site. RNA blotting and in situ hybridization experiments indicate that Adh is transcribed, although not very actively, in salivary glands during the third larval instar. However, this tissue does not display detectable levels of ADH activity. By contrast, we have found that in midgut polytene chromosomes the 35B region is not visibly puffed in spite of the high levels of Adh transcripts detected. These results seem to suggest that puffing at the 35B region could be mainly promoted by genes closely linked to Adh, possibly with a minor contribution of this gene.

Isolation and distribution of a Drosophila protein preferentially associated with inactive regions of the genome

The distribution patterns of chromosomal proteins from Drosophila can be observed by immunofluorescent staining of the polytene chromosomes from larval salivary glands. We have purified a non-histone chromosomal protein of Mr = 69,000 molecular weight which has a high affinity for DNA with little sequence specificity. Immunofluorescent staining indicates that this protein is preferentially associated with the inactive portions of the genome, including the centric heterochromatin and the condensed bands within the euchromatic arms of the chromosomes. Observation of both the heat shock loci 87A and 87C and the developmentally regulated loci 74EF and 75B shows an inverse correlation between immunofluorescent staining for the Mr = 69,000 protein and for RNA polymerase. The presence of this protein appears to be correlated with the packaging of the chromatin in an inactive form.

Studies on a possible relationship between alterations in the cytoskeleton and induction of heat shock protein synthesis in mammalian cells

Heat shock-induced alterations in protein synthesis and the cytoskeleton of two mammalian cell types have been investigated. A hyperthermic treatment of 30 min at 43 degrees C causes an accumulation of heat shock proteins (HSPs). The apparent molecular weights of HSPs of Reuber H35 hepatoma cells and of N2A neuroblastoma cells are 28 000, 65 000, 68 000, 70 000, 84 000, 100 000 D and 68 000, 70 000, 84 000 and 100 000 D respectively. Hyperthermia induces the disruption of microfilaments in hepatoma cells. Microtubules and intermediate filaments (vimentin and cytokeratin) remain intact. In neuroblastoma cells microfilaments remain intact whereas microtubules become disorganized after heat shock. As a result vimentin is found as a perinuclear aggregate. These cells were still able to synthesize heat shock proteins after pretreatment with cytoskeleton disrupting drugs such as dihydroxycytochalasin B and colchicine. Therefore it is concluded that the alterations in the cytoskeleton observed after the heat treatment are unlikely to be the cause of heat shock protein synthesis. Our results suggest that these heat shock-induced alterations in the cytoskeleton can be considered as a part of the heat shock response.

Drosophila DNA topoisomerase I is associated with transcriptionally active regions of the genome

The distribution of DNA topoisomerase I within Drosophila polytene chromosomes was observed by immunofluorescent staining with affinity-purified antibodies. The enzyme is preferentially associated with active loci, as shown by prominent staining of puffs. The heat shock loci 87A-87C are stained after, but not before, heat shock induction. A detailed comparison of the distribution of topoisomerase I with that of RNA polymerase II reveals a similar, although not identical, pattern of association. Topoisomerase I is also found in association with the nucleolus, the site of transcription by RNA polymerase I.

A cytological approach to the ordering of events in gene activation using the Sgs-4 locus of Drosophila melanogaster

The polytene chromosomes of Drosophila strains that differ in the synthesis of the major salivary gland glue protein sgs-4 were examined by indirect immunofluorescence using antisera to several nonhistone chromosomal proteins. The Oregon-R X chromosome, which produces sgs-4 messenger RNA, showed a strong fluorescent band at locus 3C11-12 when stained with anti-RNA polymerase II, whereas the null mutant Berkeley 1 failed to exhibit fluorescence at that locus. The presence of another antigen (Band 2), normally associated with developmentally active loci, was clearly evident at locus 3C11-12 of both transcriptionally competent and null strains, indicating that the association of Band 2 antigen with the chromatin is an event independent of RNA polymerase II binding. Antibodies directed against Drosophila topoisomerase I stained 3C11-12 in the Sgs-4+ (wild-type) strain brightly, but gave significantly less staining in the null strain. This indicates that the high concentrations of topoisomerase I seen at active loci are closely associated with the transcriptional event. In some of these analyses, we have made use of flies heterozygous for the wild-type and null alleles in order to make internally controlled comparisons. The results suggest that this type of analysis will enable conclusions to be drawn concerning the interdependence and order of action of chromosomal proteins involved in developmental gene activation.

Selective exposure of antigenic determinants in chromosomal proteins upon gene activation in polytene chromosomes

The immunological accessibility of the nucleosomal core protein H3 and non-histone protein, HMG-1, was studied in transcriptionally active regions of Chironomus thummi polytene chromosomes. Chromosomal loci were decondensed by incubating isolated salivary glands in various salt solutions or hemolymph. Indirect immunofluorescence studies on these chromosomes using anti-sera to histone H3 revealed that the puffed regions were depleted of fluorescence. The lack of fluorescence could be correlated with the degree of puffing and the level of transcriptional activity. The puffed regions fluoresce after anti-H3 addition if the chromosomes are not cross-linked with formaldehyde, and if prior to the addition of antibodies the chromosomes are treated with 45% acetic acid. We conclude that, whereas histone H3 is present in the puffed regions, its antigenic determinants are sterically hindered by components which are extractable by 45% acetic acid. On the other hand, the antigenic determinants of protein HMG-1 are always available to antibody binding in puffed regions, as well as other chromosomal areas.

Immunofluorescent characterization of DNA . RNA hybrids on polytene chromosomes of Trichosia pubescens (Diptera, sciaridae)

We have studied the distribution of DNA X RNA hybrids on polytene chromosomes with the aid of a goat antibody against DNA X RNA hybrids using the immunofluorescence technique. Fixed polytene chromosomes of the sciarid Trichosia pubescens (Diptera) show distinct, stage-specific labelling patterns throughout larval development. Controls for the staining procedure - including preincubation with hybrid-specific endoribonuclease H - prove that DNA X RNA hybrids are present on fixed chromosomes. They are revealed only under mild fixation conditions which do not efficiently immobilize all chromosomal proteins, indicating that some proteins have to be removed to make the antigens accessible to antibody. Certain fixation conditions may also cause local denaturation of chromosomal DNA, and some hybrids may possibly form during specimen preparation. After incorporation of radioactive uridine, a combination of phase contrast, fluorescent, and autoradiographic images of one and the same chromosomal preparation demonstrates that hybrid fluorescence is confined to transcriptionally active regions. Two puff classes can be distinguished. The first binds antibody and includes most RNA puffs and all DNA puffs so far studied; the second, comprising some RNA puffs, does not show bright fluorescence in spite of the fact that RNA synthesis is high as revealed by 3H-uridine incorporation. DNA X RNA hybrids are not found at DNA puff sites during the DNA amplification period; these sites contain detectable hybrids only when transcription is taking place. - Combination of the fluorescent technique with its excellent resolution and autoradiography should be helpful in studying detailed topological aspects of transcriptionally active chromosomal regions.

In situ immunofluorescent visualization of chromosomal transcripts in polytene chromosomes

The induction and distribution of chromosomal transcripts in the polytene chromosomes of D. melanogaster and D. hydei has been investigated by indirect immunofluorescence using an antiserum directed against DNA/RNA hybrids. The fluorescence was intense and occurred in most of the chromosomal subdivisions when the chromosomes were exposed to denaturing conditions and then allowed to reanneal. The extent of hybrid formation depended both on the extent of DNA denaturation and on the maintenance of RNA integrity. Fluorescence was absent from chromosomes treated with pancreatic RNase before denaturation. The velocity of the chromosomal DNA/RNA hybridization reaction and the effects of the initiation inhibitor of RNA synthesis, DRB, suggest that in order to hybridize the RNA has to be located in its transcriptional compartment. Even though overall patterns of fluorescence seem to be similar during a developmental stage, variations were observed, particularly some correlated with puff induction after ecdysone stimulation.

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.

RNA polymerase II transcribes all of the heat shock induced genes of Drosophila melanogaster

Heat shock of Drosophila melanogaster induces the transcription of a small number of RNAs. Some of these encode protein products, but not all. We have investigated whether the several induced RNAs are transcribed by RNA polymerase II or by some other RNA polymerase. Immunochemical staining of polytene chromosomes indicates that, on heat shock, RNA polymerase II is relocalized; it "migrates" from previously-active transcription sites to the heat shock induced loci. All heat shock induced puffs show immunochemical staining. Such staining correlates with RNA polymerase II activity as judged by the sensitivity of RNA synthesis at these sites to low concentrations of alpha-amanitin. Thus the protein-coding and non-protein-coding heat shock-induced RNAs are transcribed by this polymerase specifically. We have also identified several non-puffed chromosomal sites at which RNA synthesis is induced by heat shock.

Isolation of DNA from single microsurgically excised bands of polytene chromosomes of Chironomus

A method is described for excising by a glass knife single bands of isolated polytene chromosomes of the salivary glands of Chironomus tentans larvae. DNA strands were isolated from cut-out bands and their contour lengths were determined on electron micrographs. The mean contour length of DNA strands isolated from the double band I-8A was about twice that of the single band I-11B, namely 63 versus 34 micrometers. The described method may be applicable for molecular studies on single bands (e.g., by DNA cloning).

RNA polymerase B in polytene chromosomes: immunofluorescent and autoradiographic analysis during stimulated and repressed RNA synthesis

The distribution of RNA polymerase B (or II) in native and fixed polytene chromosomes isolated from salivary glands of Chironomus tentans and C. pallidivittatus was investigated by both indirect immunofluorescence and autoradiography. The chromosomes, especially the Balbiani rings (BR2, BR1 and BR3), were examined during periods of stimulated and repressed RNA synthesis. In repressed BR2a and, after the salivary gland chromosomes had been stretched, in various chromosomal segments, it was possible to establish unequivocally that RNA polymerase B is not confined to puffs, but also occurs in interbands. The enzyme was absent from the bands, or at least there was not enough of it to be detected with indirect immunofluorescence. It was shown that the distribution of the indirect immunofluorescence in the chromosomes concurs with that of the 3H-uridine or 3H-UTP labeling. However, RNA polymerase B molecules remain associated with the chromosomal template even after an in vivo alpha-amanitin or actinomycin D treatment to inhibit RNA synthesis. Following heat shocks (37 degrees C to 39 degrees C), transcriptively active RNA polymerase B is still found in interbands, in the BRs and in other puffs that have collapsed as a result of the heat treatment; the greatest enzyme concentrations, however, are in the stimulated heat-shock puffs.

Distribution studies on polytene chromosomes using antibodies directed against hnRNP

The distribution of nuclear ribonucleoprotein (hnRNP) particles in Drosophila polytene chromosomes has been investigated using anti-B-36 serum as a probe. The use of polytene chromosomes allows resolution at the level of the chromomere, and provides the opportunity to look for both positive and negative correlations with transcriptional activity. The antiserum was obtained using the nuclear protein B-36 from Physarum polycephalum as the immunogen. It has been shown to precipitate hnRNP particles from HeLa cells through a cross-reaction with the major 32,000- and 34,000-dalton hnRNP particle proteins. The antiserum cross-reacts with a Drosophila nuclear protein of approximately 34,000 daltons. By indirect immunofluorescence, we observed that the antiserum reacts preferentially with transcriptionally active loci of the polytene chromosomes, whereas loci previously or subsequently active do not show significant fluorescence. The overall pattern of fluorescence is very similar to that generated with anti-RNA polymerase B serum. The correlation of fluorescence and transcriptional activity observed suggests that the anti-B-36 serum is recognizing hnRNP proteins which have combined with nascent RNA molecules at the sites 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.

Heat shock induced alterations in polyadenylate metabolism in Drosophila melanogaster

We have studied the effect of heat shock on poly(adenylic acid) [poly(A)] metabolism in Drosophila melanogaster cells by using hybridization of ribonucleic acid (RNA) samples to [3H]poly(uridylic acid). Shortly after heat shock begins, cytoplasmic poly(A) decays rapidly. Two components were detected. Component I constitutes 46% of the total cytoplasmic poly(A) and decays with a half-life of 10 min. Component II (54% of total) is more stable. A half-life was not estimated for component II because new synthesis was not blocked. Studies on the size of cytoplasmic poly(A) indicate component I is completely degraded while component II remains essentially unchanged. Nuclear poly(A) increases rapidly, peaking at 2 or 3 times the normal level after 90 min of heat shock. Studies on the size of nuclear poly(A) indicate the increase is not due to addition of poly(A) to existing poly(A) segments nor appreciably to newly synthesized RNA unless transit time is markedly increased. We conclude that nuclear poly(A) is added in large part to already existing nonadenylated primers. Studies with RNA and protein synthesis inhibitors show RNA and protein synthesis are not required for the changes in poly(A). As the temperature is raised above 34--35 degrees C, the effect on poly(A) metabolism becomes more severe. Changes in external pH, without increased temperature, also alter poly(A) levels. Poly(A) changes may therefore be a rapid response to a variety of physiological factors.

Monoclonal antibody directed against RNA polymerase II of Drosophila melanogaster

Monoclonal antibodies were raised against purified RNA polymerase II ( or B) from Drosophila melanogaster. The antibody produced by one hybridoma cell clone was found to be directed against the two large subunits of the enzyme. The absence of antibodies directed against proteins possibly contaminating the antigens used for immunization allowed us to identify RNA polymerase unequivocally in interbands and puffs of polytene chromosomes. Within a single heat shock puff (87C1) RNA polymerase was found to be clustered in two separate areas suggesting two distinct regions of RNA polymerase activity in this puff.

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.

Features of in vitro puffing and RNA synthesis in polytene chromosomes of Chironomus

In order to elucidate the causal relation between RNA synthesis and puffing in polytene chromosomes, salivary gland nuclei and chromosomes from Chironomus tentans and C. pallidivittatus (Diptera, Chironomidae) were isolated in the native state under controlled and optimized conditions. The behavior of the polytene chromatin in vitro as compared to that in vivo was studied morphologically and autoradiographically. It was shown that the absence of cytologically visible puffing does not necessarily indicate transcriptional quiescence. Under suitable conditions all potential puff sites incorporate the radioactive precursor simultaneously. This can be seen in vivo and even more clearly in chromosomes decondensed by 340-400 mM NaCl in vitro. Potential puff sites therefore appear to be permanently equipped with RNA-polymerases, and there is always a basic low level of transcriptive activity. Experimental shrinking of Balbiani rings and other puffs by dimethylsulfoxide (DMSO) or heat shock in vivo, leaves the genes in the collapsed puffs still transcriptionally active, although to a reduced extent. Light optically visible puffing is therefore not a necessary prerequisite for RNA synthesis, while, conversely, RNA synthesis is required for puff formation.

Cell-specific antigens in chicken erythroid nuclei: species specificity

Antisera raised to dehistonized chicken reticulocyte chromatin were tested for their cell and species specificity. Quantitative microcomplement fixation and immunohistochemical localization revealed the presence in chromatin of erythroid cell-specific nonhistone protein antigen(s). The antigenic specificity was shown to depend on the association of the antigenic protein(s) with deoxyribonucleic acid (DNA). Although the antisera were exceptionally cell specific, they cross-reacted with erythroid cells of other avian species. The extent of cross-reactivity was found to approximate the phylogenetic distances of the tested avian species. Erythroid cells from fish and amphibians were not reactive. Reconstitution experiments of partially purified chicken reticulocyte chromosomal nonhistone protein antigens with DNAs isolated from several vertebrate species showed that the species specificity of the antigenic complexes is determined principally by the species origin of the nonhistone proteins. Our results show that a cell-specific chromosomal nonhistone protein(s) has undergone evolutionary change and the relative immunological differences are consistent with the accepted phylogenetic distances of the species examined.

Genetic and molecular analysis of the 87A7 and 87C1 heat-inducible loci of D. melanogaster

Two different types of heat-inducible sequences are found at the cytogenetic loci 87A7 and 87C1 of D. melanogaster. One of these codes for the 70,000 dalton heat shock protein (hsp 70) and is found at both loci. The other type of sequence (alpha beta) codes for an RNA of unknown function and is found only at 87C1. We have completed a study of the organization of the two loci, using deficiencies that delete one or other locus, and have estimated the number of the hsp 70 genes at each locus. Thus in at least three strains of files there are a total of five coding sequences, three at 87C1 and two at 87A7. Restriction mapping of the coding regions at the two loci reveals that each of the two cytogenetic loci has its own characteristic coding sequence. The overall organization of the two loci appears to differ considerably. The alpha beta and hsp 70 heat-induced sequences at 87C1 are closely linked and are contained within two Eco RI restriction fragments.

Physical map of two D. melanogaster DNA segments containing sequences coding for the 70,000 dalton heat shock protein

The isolation of the two hybrid plasmids 56H8 and 132E3, which contain D. melanogaster (Dm) DNA sequences complementary to the mRNA coding for the 70,000 dalton heat shock protein, has been reported (Schedl et al., 1978). Here we compare the sequence arrangement in the two cloned Dm DNA segments by restriction, cross-hybridization and heteroduplex analysis. The results show that the two cloned DNA segments derive from nonoverlapping regions of the Dm genome; that they contain homologous regions present once in 56H8 and twice in 132E3; and that each homologous region is composed of three distinct contiguous sequence elements, x, y and z, which together define a 3 kb common unit. While the 2.5 kb z elements show a high degree of sequence homology in all three common units, the three x and y elements display an intriguing relationship. The localization of the mRNA coding sequences within each of these common units is presented in the accompanying paper (Artavanis-Tsakonas et al., 1979).

Production and characterization of antisera against three individual NHC proteins; a case of a generally distributed NHC protein

In order to assess the selectivity of the distribution patterns of individual nonhistone chromosomal proteins (NHC proteins), immunofluorescent staining experiments were performed on Drosophila polytene chromosomes. Antisera have been prepared against three individual NHC proteins which were isolated by sequential preparative slab gel isoelectric focusing and SDS polyacrylamide gel electrophoresis. In two cases, immunofluorescent staining of the chromosomes indicated a specific limited distribution pattern; apparently the antigen in each case is present at a reproducible and distinct subset of chromomeres. This type of pattern has also been obtained with antisera prepared against molecular weight subfractions of NHC proteins (Silver and Elgin, 1977). Each selective fluorescence distribution pattern obtained so far is reproducible and unique to the antiserum under study. In a third case, an antiserum caused prominant staining at dense chromomeres and the chromocenter in a pattern mimicking DNA (and presumably histone) distribution. Indirect radioimmunostaining of SDS and isoelectric focusing gels on which total NHC proteins had been separated confirmed that this antiserum reacted specifically with a protein(s) of molecular weight 21,000 D and pI 5.2. The data in conjunction with absorption experiments indicates that the chromosomal staining is due to an interaction of antibodies with NHC protein(s) and not with histones. This finding suggests that at least one major acidic NHC protein plays a very general role (comparable to that of the histones) in maintaining chromatin structure.

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.

Two hybrid plasmids with D. melanogaster DNA sequences complementary to mRNA coding for the major heat shock protein

The isolation and partial characterization of two cloned segments of Drosophila melanogaster DNA containing "heat shock" gene sequences is described. We have inserted sheared embryonic D. melanogaster DNA by the poly(dA-dt) connector method (Lobban and Kaiser, 1973) into the R1 restriction site of the ampicillin-resistant plasmid pSF2124 (So, Gill and Falkow, 1975). A collection of independent hybrid plasmids was screened by colony hybridization (Grunstein and Hogness, 1975) for sequences complementary to in vitro labeled polysomal poly(A)+ heat shock RNA. Two clones were identified which contain sequences complementary to a heat shock mRNA species that directs the in vitro synthesis of the 70,000 dalton heat-induced polypeptide. Both cloned segments hybridize in situ to the heat-induced puff sites located at 87A and 87C of the salivary gland polytene chromosomes.