The replicative organization of DNA in polytene chromosomes of Drosophila hydei

Replication timing in Drosophila and its peculiarities in polytene chromosomes

Drosophila melanogaster is one of the popular model organisms in DNA replication studies. Since the 1960s, DNA replication of polytene chromosomes has been extensively studied by cytological methods. In the recent two decades, the progress in our understanding of DNA replication was associated with new techniques. Use of fluorescent dyes increased the resolution of cytological methods significantly. High-throughput methods allowed analysis of DNA replication on a genome scale, as well as its correlation with chromatin structure and gene activi ty. Precise mapping of the cytological structures of polytene chromosomes to the genome assembly allowed comparison of replication between polytene chromosomes and chromosomes of diploid cells. New features of replication characteristic for D. melanogaster were described for both diploid and polytene chromosomes. Comparison of genomic replication profiles revealed a significant similarity between Drosophila and other well-studi ed eukaryotic species, such as human. Early replication is often confined to intensely transcribed gene-dense regions characterized by multiple replication initiation sites. Features of DNA replication in Drosophila might be explained by a compact genome. The organization of replication in polytene chromosomes has much in common with the organization of replication in chromosomes in diploid cells. The most important feature of replication in polytene chromosomes is its low rate and the dependence of S-phase duration on many factors: external and internal, local and global. The speed of replication forks in D. melanogaster polytene chromosomes is affected by SUUR and Rif1 proteins. It is not known yet how universal the mechanisms associated with these factors are, but their study is very promising.

Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species

The size of eukaryotic genomes can vary by several orders of magnitude, yet genome size does not correlate with the number of genes nor with the size or complexity of the organism. Although "whole"-genome sequences, such as those now available for 12 Drosophila species, provide information about euchromatic DNA content, they cannot give an accurate estimate of genome sizes that include heterochromatin or repetitive DNA content. Moreover, genome sequences typically represent only one strain or isolate of a single species that does not reflect intraspecies variation. To more accurately estimate whole-genome DNA content and compare these estimates to newly assembled genomes, we used flow cytometry to measure the 2C genome values, relative to Drosophila melanogaster. We estimated genome sizes for the 12 sequenced Drosophila species as well as 91 different strains of 38 species of Drosophilidae. Significant differences in intra- and interspecific 2C genome values exist within the Drosophilidae. Furthermore, by measuring polyploid 16C ovarian follicle cell underreplication we estimated the amount of satellite DNA in each of these species. We found a strong correlation between genome size and amount of satellite underreplication. Addition and loss of heterochromatin satellite repeat elements appear to have made major contributions to the large differences in genome size observed in the Drosophilidae.

Polytene Chromosomes: 70 Years of Genetic Research

Polytene chromosomes were described in 1881 and since 1934 they have served as an outstanding model for a variety of genetic experiments. Using the polytene chromosomes, numerous biological phenomena were discovered. First the polytene chromosomes served as a model of the interphase chromosomes in general. In polytene chromosomes, condensed (bands), decondensed (interbands), genetically active (puffs), and silent (pericentric and intercalary heterochromatin as well as regions subject to position effect variegation) regions were found and their features were described in detail. Analysis of the general organization of replication and transcription at the cytological level has become possible using polytene chromosomes. In studies of sequential puff formation it was found for the first time that the steroid hormone (ecdysone) exerts its action through gene activation, and that the process of gene activation upon ecdysone proceeds as a cascade. Namely on the polytene chromosomes a new phenomenon of cellular stress response (heat shock) was discovered. Subsequently chromatin boundaries (insulators) were discovered to flank the heat shock puffs. Major progress in solving the problems of dosage compensation and position effect variegation phenomena was mainly related to studies on polytene chromosomes. This review summarizes the current status of studies of polytene chromosomes and of various phenomena described using this successful model.

Abnormal tissue-dependent polytenization of a block of chromosome 3 pericentric heterochromatin in Drosophila melanogaster

Heterochromatic DNA sequences in the polytene chromosomes of Drosophila melanogaster salivary glands are under-replicated in wild-type strains. In salivary glands of SuUR and in the nurse cells of otu mutants, under-replication is partly suppressed and a banded structure appears within the centric heterochromatin of chromosome 3. This novel banded structure in salivary gland chromosomes was called Plato Atlantis. In order to characterize the heterochromatic component of Plato Atlantis, we constructed a fine-scale cytogenetic map of deletions with break points within centric heterochromatin (Df(3L)1-16, Df(3L)2-66, Df(3R)10-65, Df(3R)4-75 and Df(3L)6B-29 + Df(3R)6B-29). Salivary gland chromosomes show that Df(3L)1-16 removes the complete Plato Atlantis, while Df(3L)2-66 deletes the most proximal 3L regions. These deletions therefore show a substantial cytological overlap. However, in the chromosomes of nurse cells, the same deficiencies remove distinct heterochromatic blocks, with the region of overlap being almost invisible. Satellite (AATAACATAG, AAGAG) and dodecasatellite DNAs mapped in a narrow interval in salivary glands but were found in three clearly distinguishable blocks in nurse cells. The 1.688 satellite was found at a single site in salivary glands but at two sites in nurse cells. We show that newly polytenized heterochromatic structures include blocks h47-h50d of mitotic heterochromatin in salivary glands, but the additional blocks h50p, h53 and h57 are also included in nurse cell chromosomes. Tissue specificity of the patterns of abnormal heterochromatic polytenization implies differential control of DNA replication in somatic and germline cells.

Alpha and beta heterochromatin in polytene chromosome 2 of Drosophila melanogaster

The formation of alpha and beta heterochromatin in chromosomes of Drosophila melanogaster was studied in salivary glands (SGs) and pseudonurse cells (PNCs). In SGs of X0, XY, XYY, XX and XXY individuals the amounts of alpha heterochromatin were similar, suggesting that the Y chromosome does not substantially contribute to alpha heterochromatin formation. Pericentric heterochromatin developed a linear sequence of blocks in PNCs, showing morphology of both alpha and beta heterochromatin. In situ hybridization with Rsp sequences (Ho clone) revealed that the most proximal heterochromatic segment of the mitotic map (region h39) formed a polytenized block in PNCs. Dot analysis showed that the clone had a hybridization rate with PNC-DNA very close to that with DNA from mainly diploid head cells, whereas the homologous SG-DNA was dramatically underrepresented. A similar increase of DNA representation in PNC was found for AAGAC satellite DNA. The mitotic region h44 was found not to polytenize in the SG chromosome, whereas in PNC chromosome 2 this region was partly polytenized and presented as an array of several blocks of alpha and beta heterochromatin. The mapping of deficiencies with proximal breakpoints in the most distal heterochromatin segments h35 in arm 2L and h46 in 2R showed that the mitotic eu-heterochromatin transitions were located in SG chromosomes distally to the polytene 40E and 41C regions, respectively. Thus, the transition zones between mitotic hetero- and euchromatin are located in banded polytene euchromatin. A scheme for dynamic organization of pericentric heterochromatin in nuclei with polytene chromosomes is proposed.

Polytene chromosomes in mammalian cells

This article deals with the structural and functional organization of polytene chromosomes in mammals. Based on cytophotometric, autoradiographic, and electron microscopic data, the authors put forward a concept of nonclassic polytene chromosomes, with special reference to polytene chromosomes in the mammalian placenta. In cells with nonclassic polytene chromosomes, two phases of the polytene nucleus cycle are described, such as the endointerphase (S phase) and endoprophase (G phase). The authors generalize that the main feature of nonclassic polytene chromosomes is that forces binding the sister chromatids are much weaker than in the Diptera classic polytene chromosomes. This concept is confirmed by comparative studies of human, mink, and fox polytene chromosomes. The final step of the trophoblast giant cell differentiation is characterized by a transition from polyteny to polyploidy, with subsequent fragmentation of the highly polyploid nucleus into fragments of low ploidy. Similarities and dissimilarities of pathways of formation and rearrangement of nonclassic polytene chromosomes in mammals, insects, plants, and protozoans are compared. The authors discuss the significance of polyteny as one of the intrinsic conditions for performance of the fixed genetic program of trophoblast giant cell development, a program that provides for the possibility of a long coexistence between maternal and fetal allogenic organisms during pregnancy.

The salivary gland chromosomes of Drosophila virilis: a cytological map, pattern of transcription and aspects of chromosome evolution

By combining information from microscopical observation and photography a graphical map of Drosophila virilis salivary gland chromosomes was constructed. About 1,560 individual bands are shown and patterns of transcription at about 360 sites are indicated. The application of the map is demonstrated by using genetic, morphological and in situ hybridization data to identify the white-Notch regions of D. virilis and Drosophila melanogaster as homologous chromosome segments with constant and variable features.

Increase of DNA content in tissue stages of Entamoeba histolytica strain SFL 3

The DNA content of culture forms and tissue stages of pathogenic E. histolytica strain SFL 3 were measured photometrically after the nuclei had been stained with the fluorochrome BAO. As a control, the DNA guartity of E. histolytica strain HK 9 and E. invadens were determined by the same method and compared with reference values. Tissue stages were obtained from hamsters experimentally infected by intrahepatic injection of SFL 3 amoebae. Further studies concerning possible changes in the DNA content of tissue stages involved the following methods: (a) isolation of tissue stages from the liver, followed by distinct suspension periods. (b) Infected liver pieces were directly transferred into culture medium; amoebae emigrating therefrom were cultivated. The study demonstrated that tissue stages contained up to 4 times more DNA than did culture forms. After 3 h cultivation, the DNA content of tissue stages decreased to the level of culture forms. Possible reasons for this change are discussed.

Position-effect variegation and intercalary heterochromatin: a comparative study

The behaviour of IH (intercalary heterochromatin) regions of Drosophila melanogaster polytene chromosomes was compared with that of euchromatin condensed as a result of position-effect variegation. Normally replicating regions, when subject to such an effect, were found to become among the last regions in the genome to replicate. It is shown that the factors which enhance position effect (low temperature, the removal of the Y chromosome, genetic enhancers of position effect) increase the weak point frequency in the IH, i.e. enhance DNA underreplication in these regions. We suggest that the similarity in the properties of IH, CH (centromeric heterochromatin) and the dense blocks induced by position effect is due to strong genetic inactivation and supercondensation caused by specific proteins in early development. The primary DNA structure is not likely to play a key role in this process.

Matrix models. Essential tools for microscopic cytochemical research

An overview is given of the preparation and use of model systems for cytochemistry, dealing with quantitative as well as qualitative aspects. Descriptions are given of the various possibilities to prepare cytochemical matrix models, ranging from macroscopic and microscopic films, to models with more cell-like dimensions as agarose beads, artificial cells and erythrocyte ghosts. Such models allow the study of a large variety of cytochemical processes. Their potentialities are demonstrated in a number of specific applications, comprising: the study of the influence of fixation on cellular processes, reaction specificity and reaction kinetics, quality of reagents and biochemical calibration in cytochemical staining; factors influencing localization of the specific endproduct in enzyme cytochemistry; immunocytochemistry and hybridocytochemistry.

DNA sequence comparison among closely related Drosophila species in the mulleri complex

DNA hybridization was used to establish DNA sequence relationships among seven Drosophila species. Single-copy DNA was isolated from four species within the Drosophila mulleri complex, D. mojavensis, D. arizonensis, D. ritae and D. starmeri. These single-copy DNAs were used as tracers to be hybridized with each other and one additional member of the mulleri complex, D. aldrichi, a member of a closely related complex, D. hydei, and a distantly related species, D. melanogaster. Two methods have been used to determine the relatedness between these species: (1) the extent of duplex formed as measured by binding to hydroxyapatite and (2) the thermal stability of the duplexed DNA. Moderately repetitive DNA was purified from these species and used similarly to determine the divergence of this family of sequences. The rate of nucleotide substitution was estimated to be 0.2 +/-, 0.1% base pair change per million years for both single-copy and middle-repetitive DNAs. The size of the D. arizonensis genome, a representative of the mulleri complex, was calculated to be 2.2 X 10(8) base pairs from its kinetic complexity similar to that of D. hydei. The relative amounts (18%) and average reiteration frequency (100 copies) of the middle-repetitive DNA are similar for all Drosophila species studied. Finally, the data are presented in a phylogenetic tree.

Mapping of the pattern of DNA replication in polytene chromosome from Chironomus thummi using monoclonal anti-bromodeoxyuridine antibodies

We present results from a nonautoradiographic study of DNA replication in polytene chromosomes from dipteran larvae. Monoclonal antibodies with specificity for 5-bromodeoxyuridine (BrdUrd) were used to localize by indirect immunofluorescence the sites of BrdUrd incorporation and to follow the dynamics of DNA synthesis in salivary gland cells of 4th instar Chironomus thummi larvae. This technique presents numerous advantages over autoradiographic procedures and allows mapping of DNA synthesis patterns at the level of resolution of one chromosomal band. Several replication patterns were observed, classified according to characteristic features, and tentatively assigned to specific periods of the S-phase. In early S-phase, DNA synthesis is first detectable in puffs and interbands, later in bands. Most chromosomal bands appear to initiate DNA synthesis synchronously; however, in bands within centromeric and heterochromatic regions the start of synthesis is delayed. At mid S-phase, all the bands show uniform staining. Subsequent staining patterns are increasingly differential with the bands displaying characteristic fluorescence intensities. As replication progresses through the late S-phase period, the chromosomes show a decreasing number of fluorescent bands. The last bands to terminate replication are located in centromeric and heterochromatic DNA-rich regions and a few bands of low DNA content in region IIAa-c.

Control of DNA replication and spatial distribution of defined DNA sequences in salivary gland cells of Drosophila melanogaster

In dividing cells, each sequence replicates exactly once in each S-phase, but in cells with polytene chromosomes, some sequences may replicate more than once or fail to replicate during S-phase. Because of this differential replication, the control of replication in polytene cells must have some unusual features. Dennhöfer (1982a) has recently concluded that the total DNA content of the polytene cells of Drosophila salivary glands exactly doubles in each S-phase. This observation, along with previous studies demonstrating satellite underreplication in salivary gland cells, led us to consider the hypothesis that there is a "doubling of DNA" mechanism for the control of DNA replication in polytene cells. With this mechanism, a doubling of DNA content, rather than the replication of each sequence, would signal the end of a cycle of DNA replication. To test this hypothesis, we have reinvestigated the replication of several sequences (satellite, ribosomal, histone and telomere) in salivary gland cells using quantitative in situ hybridization. We find that underreplication of some sequences does occur. In addition we have repeated Dennhöfer's cytophotometric and labeling studies. In contrast to Dennhöfer, we find that the total DNA contents of nonreplicating nuclei do reflect this partial replication, in accord with Rudkin's (1969) result. We conclude that DNA replication in polytene cells is controlled by modifications of the mechanism operating in dividing cells, where control is sequence autonomous, and not by a "doubling of DNA" mechanism. In situ hybridization to unbroken salivary gland nuclei reveals the distribution of specific sequences. As expected, satellite, histone and 5S sequences are usually in a single cluster.(ABSTRACT TRUNCATED AT 250 WORDS)

Replication in Drosophila chromosomes. X. Two kinds of active replicons in salivary gland polytene nuclei and their relation to chromosomal replication patterns

DNA fibre autoradiography of highly polytenized nuclei in salivary glands of Drosophila nasuta larvae reveals two distinct types of active replicons. Type I replicons are longer (mean size = 64 micrometers), have a very high rate of fork migration (average rate = 0.95 micrometer/min) and generally occur in large arrays often extending over several thousand micrometers. In contrast, the type II replicons are smaller (mean size = 20 micrometers), slow replicating (average rate = 0.07 micrometer/min) and occur in short arrays containing only a few closely spaced active replicons. Evidence is presented that type I replicons are active in the early S and type II in the late S. Observations on autoradiographic labelling of partially lysed polytene chromosomes provide evidence for a lack of temporal and spatial agreement in the activation of origin points in homologous regions of the lateral polytene strands; these observations also suggest local variations in levels of polyteny within a chromosome. On the basis of this and other available information on replication in polytene chromosomes the possible roles of the two replicon types in the generation of the different 3H-thymidine labelling patterns of polytene chromosomes are discussed.

Determination of the region of rDNA involved in polytenization in salivary glands of Drosophila hydei

During the formation of polytene chromosomes in salivary glands of Drosophila hydei, the genes for ribosomal RNA (rDNA) are underreplicated relative to the rest of the genome. We have measured the number of rRNA genes with and without intervening sequences (ivs+ and ivs- genes) in polytene chromosomes of different genotypes. In the group of genotypes having a large number of ivs- rRNA genes polytenization only occurs within the cluster of ivs- genes. In each of these genotypes rDNA polytenization reaches a constant level of 150 ivs- genes per two chromatid sets (2C); X/X constitutions having two nucleolus organizers (NOs) in the diploid set polytenize the same amount of rDNA as X/O constitutions. In the group of genotypes with small ivs- gene numbers, the rDNA region involved in polytenization is longer and has an average length of 1,700 kb per NO, which is constant in these genotypes. Polytenization of rDNA is extended into the cluster of ivs+ genes, in spite of the fact that these genes appear to be nonfunctional. The smaller the number of ivs- genes, the greater the number of ivs+ genes that are polytenized in the NO. In these genotypes, X/X females replicate twice as much rDNA as X/O males, suggesting that both NOs of the diploid set are polytenized. A comparison of the pattern of spacer length heterogeneity in hybrids between different stocks also demonstrates that both NOs are replicated during polytenization.

Cytophotometric DNA determinations and autoradiographic studies in salivary gland nuclei from larvae with different karyotypes in Drosophila melanogaster

Cytophotometric DNA determinations in Feulgen stained mitotic diploid chromosome sets of neuroblasts from larvae of Drosophila melanogaster stocks, which possess different karyotypes, show significant differences between the 4C values, caused by an additional or deficient X- and Y-chromosome depending on the karyotype. The ranges of polytenic DNA size classes are theoretically expected to be doublings of the corresponding 4C mean value of each karyotype. The extinction integral data of nuclei with completely duplicated 4C quantities exclusively fall into the range of the expected size classes. Not all data falling into the range of a size class necessarily originate from duplicated nuclei, because the limits of the DNA size classes cannot be determined by measurements, but must be estimated from the confidence limits of the corresponding 4C mean value. The validity of the mitotic 4C values of the karyotypes X/X and X/Y is tested using data from non-labeled interphase nuclei, where extinction integral data accumulate in two groups. The larger values (= G2-nuclei) confirm the 4C values of mitotic chromosome sets, and the lower values (= G1-nuclei) are just half of these. Extinction integrals from individual, 3H-thymidine non-incorporating polytene salivary gland nuclei accumulate in distinct, non-overlapping groups which are always complete doublings of the preceding smaller group. In each karyotype, the most frequent data of each group are in accord with the 4C doublings. The data from labeled nuclei alternate with those from unlabeled nuclei. The measured DNA values of individual polytene nuclei that did not incorporate any 3H-thymidine, demonstrate that all chromosomal DNA replicates completely during polytenization of the chromosomes in the larval salivary gland nuclei of Drosophila melanogaster. Specifically, this would mean that the heterochromatic Y-chromosome replicates as well as the partially heterochromatic X-chromosome along with the autosomes. There is no indication of underreplicating heterochromatin.

The DNA content of polytene nuclei in midgut and Malpighian tubule cells of adultDrosophila melanogaster

The amounts of DNA in midgut and Malpighian tubule cells of adult maleDrosophila melanogaster have been determined by Feulgen-DNA cytophotometry. The DNA values fall into discrete classes reflecting different levels of polyteny. The maximum level is 64C in the midgut, 256C in Malpighian tubules, and the modal values are 32C and 128C respectively. The data provide no evidence for extensive underreplication of heterochromatin. It is suggested that the reduced amount of satellite DNA found in the tissues of young adult flies may be a consequence of the fact that cycles of DNA replication started in the pre-adult stages are not completed until some hours after eclosion.

Intervening sequences in ribosomal RNA genes and bobbed phenotype in Drosophila hydei

The "bobbed' (bb) mutation in Drosophila is represented phenotypically by shortened and abnormally thin scutellar bristles and by delayed development. There is a direct correlation between bristle size and ribosomal RNA (rRNA) synthesis, and the bb mutation was at first explained as a deficiency of rRNA genes (rDNA). However, the bb phenotype can occur in Drosophila melanogaster and Drosophila hydei with high rDNA content, while phenotypically wild-type flies are known with few rRNA genes, suggesting that what matters is not the number of rRNA genes but their transcriptional activity. In D. melanogaster, it has recently emerged that rRNA genes interrupted by an intervening sequence are not transcribed. We now report that in D. hydei, the length of the scutellar bristle is directly proportional to the number of rRNA genes without this intervening sequence.

Structural paradox of polytene chromosomes

The observation of thick chromatin fibers in interbands of Dipteran polytene chromosomes suggests that there should be 5 to 10 times more mass and DNA in interbands than is commonly thought to be present. To resolve this paradox, the chromatin content of interbands was estimated, using whole-mounted polytene chromosomes from Drosophila melanogster. Densitometry of high voltage electron microscopic negatives provides an estimate of less than 4:1 for the average ratio of cross-sectional dry mass (or mass per unit chromosome length) of bands relative to interbands. This ratio, combined with an estimate of the length of chromosome composed of interbands, indicates that at least 26% of chromosome mass is contributed by interband chromatin. Since DNA comprises a similar proportion of chromatin mass in bands and interbands (Laird et al., 1980b), these data imply that DNA sequences in interbands represent at least 26% of the euchromatic genome of D. melanogaster. This result calls for reinterpretation of some of the genetic and molecular data from Diptera. The discrepancy between this higher estimate of interband mass and DNA, and previous estimates of 3-5%, is discussed. One possibility is that previous measurements were made on prominent interbands, which are proposed here to be in regions that are delayed in DNA replication. Such interbands would be reduced in polyteny and DNA content compared with the average interband region. The concept of local variations in polyteny is also used here to explain major differences in the cross-sectional mass of bands. This leads to a revised model of polytene chromosomes in which at least three levels of polyteny, rather than one or two levels, can be present within one euchromatic region.

Disproportionate rDNA replication does occur in diploid tissue in Drosophila hydei

The rDNA content in Drosophila hydei has been compared in wild-type and in two translocation genotypes possessing only one nucleolus organizer. In highly polyploid salivary glands where rDNA is underreplicated, an 'independent polytenization' of the rDNA occurs resulting in about the same rDNA level in each genotype independently of the number of nucleolous organizers present in the genome. Thus, the situation in the salivary glands of D. hydei is similar to that in D. melanogaster (Spear and Gall 1973). In tetraploid thoracic muscle where rDNA is not underreplicated, the rDNA percentage in the two translocation genotypes is also considerably increased, although the wild-type level is not completely attained. This result shows that rDNA replication is independently controlled even in a non-underreplicating tissue. In larval diploid brain the situation in the two translocation stocks is dissimilar: in one genotype the rDNA content remains unaltered whereas in the other it is increased. This demonstrates for the first time that a gene compensation does occur in a diploid tissue.

Characterization of extrachromosomal DNA in the flesh fly Sarcophaga bullata

The polytene pupal foot pad cells of the flesh fly Sarcophaga bullata contain numerous extrachromosomal DNA containing granules. We have determined both the origin and the nature of the DNA sequences present in these granules. Studies done with quinacrine staining of seven day old pupal foot-pad polytene nuclei showed that the granules fluoresced very brightly while the chromosomal bands to which the granules were attached did not. The only other highly fluorescent regions of the polytene karyotype were the centromeric heterochromatin of chromosomes C and E and several bands associated with the nucleolus of Chromsome A. When polytene nuclei were hybridized in situ with cRNA made from highly repetitive DNA, many of the granules positively labeled. Most of the label on these slides was concentrated on the centromeric heterochromatin of chromosomes C and E. Quinacrine staining of the foot-pad cells at very early stages of pupal development showed that when granules were present, they were always closely associated with the same two centromeric regions, those of chromosomes C and E. Since the highly repetitive DNA located in these centromeric regions is underreplicated, we conclude that the granules result from an extrusion process which takes place early during the polytenization of these cells. The chromosomal integrity of the centromeric heterochromatin of chromosomes C and E is apparently disrupted and repetitive sequences are dissociated from the chromosomes as DNA granules which then secondarily become associated with chromosomal bands throughout the nucleus.

Underreplication of a polytene chromosome arm in the chironomid Prodiamesa olivacea

The genome of Prodiamesa olivacea (Diptera, Chironomidae) has a 2 CDNA content of 0.25 pg. Mitotic metaphases reveal 3 pairs of chromosomes: 2 metacentric ones and one submetacentric. The latter comprises 20.8% of total Feulgen DNA. During larval polytenization the complemental portion of the 3rd falls to 6.5%. Concomitantly the polytene 3rd chromosome is much shorter than expected. It has no constriction and is shaped like a ball sector. -- Underreplication is understood as suppression of DNA syntheses mainly in the long arm of the 3rd chromosome at the first to third endoreplicative cycle. Most of the dense heterochromatin seen in the apex of the 3rd polytene element is not itself underreplicated; it conceals the underreplicated long arm of this chromosome. -- In ovarian nurse cells which are closely connected with the germ line the longer heterochromatic arm of the 3rd polyneme chromosome is fully replicated. -- Underreplication is discussed in the context of "dna silencing".

Co-replication of satellite DNA of Chironomus melanotus with mainband DNA during polytenization

The DNAs of five Chironomus species, C. plumosus, C. nuditarsis, C. thummi thummi, C. melanotus, and Camptochironomus pallidivittatus, were investigated in analytical neutral isopycnic CsCl density gradients. DNA was isolated both from larval brains ("diploid-DNA") and salivary glands ("polytene-DNA"). The buoyant densities of mainband DNAs were 1.692 g/cm3, with the exception of C. melanotus whose mainband had a density of 1.693 g/cm3. The densities correspond to a calculated GC content of 33% and 34% respectively. Only in C. melanotus was the DNA clearly resolved into mainband DNA and two distinct satellite shoulders: Satellite I, with a buoyant density of 1.684 g/cm3 (25% GC, calculated) and satellite II of 1.679 g/cm3 (19% GC, calculated). The two satellites comprise 15% of the total DNA in the "diploid-DNA"' and they also occur in the "polytene-DNA", where they make up 11%. The results are discussed in the general context of under- and overreplication in polyploid and polytene cells.

Chemical and conformational changes in chromosome regions being actively transcribed

U.V. microspectrophotometry has been used to calculate quantities of nucleic acids and proteins of complete polytene chromosomal sets and specific regions of these chromosomes. It has been found that in chromosomes the ratio of DNA to proteins is approximately 1:4. This ratio however changes when specific regions are compared. The average ratio of DNA to proteins in a puffed region (2-48B4C5) increases to 1:16 in contrast to 1:6 from the same region but in non puffed state. At the same time the RNA quantity increases by a factor of 2. thermal denaturation profiles of formaldehyde fixed chromosomes show that the Tm of this region in puffed and non puffed state differ by 10 degrees C. Moreover these profiles suggest that a large fraction of histone-bound DNA is destabilized during puffing.

Chromosomal rearrangements which affect the chromosomal integration of the ribosomal genes in Drosophila melanogaster

Sucrose gradient analysis of DNA from detergent-pronase lysates of whole adult flies has been used to examine a variety of genotypes for the presence of ribosomal genes not integrated into the DNA of the chromosome. Such genes were found in females in which one X chromosome carries an inversion, having one of its breakpoints between the nucleolus organizer and the centromere. These inversions move the nucleolus organizer to the distal end of the X chromosome. Other inversions which do not move the nucleolus organizer, as well as a series of bobbed deficiencies, did not induce unintegrated genes. The same inversions which induce unintegrated genes in adults also produce them in the diploid brain and imaginal discs of larvae. On the other hand, in the polytene salivary glands, unintegrated genes were found in every genotype examined.

Gene control in eukaryotes and the c-value paradox "excess" DNA as an impediment to transcription of coding sequences

Ways in which control of gene activity may lead to the observed high DNA content per haploid eukaryote genome are examined. It is proposed that deoxyribonucleoprotein (DNP) acts as a barrier to transcription at two distinct structural levels. At the lower level, melting of the nucleosome supercoil (quaternary structure) and of the nucleosomes (tertiary structure) might be brought about by the process of transcription itself. After unwinding the barrier section, the polymerase would eventually reach the structural gene. The transcripts of noncoding sequences, at least as far as their "unique" sequence components are concerned, may thus have filled their main function through the very process of transcription. The possibility of an inverse relationship between the length of the DNP barrier and the rates of transcription of the coding sequences is to some extent supported by available data. Different modes of coordination between the transcription of mRNA and of hnRNA from a single functional unit of gene action (funga) are considered. An analysis of gene control at high structural levels of DNP is made on the basis of other data, in relation to the concepts of eurygenic and stenogenic control. The concept of a euryon is introduced, namely of a set of linked fugas under common eurygenic control. Structure of order higher than quaternary can be inferred to exist in larger chromomeres of polytene chromosomes and in corresponding sections of ordinary chromosomes. Only moderate amounts of highest order interphase euchromatic structure are likely to be able to be accomodated in average chromomeres and none in very thin chromomeres. Puffs are interpreted as the melting of highest order interphase structure, and the absence of puffs during transcription as the absence of this highest order structure in the resting state of the chromomeres. Genes that are constantly active in all tissues may dispense with highest order interphase structure and with the corresponding control mechanism, and the fugas involved thus may not puff. Puffs, large chromomeres and highest order interphase euchromatic DNP structure seem to be correlated with genes that need to be transcribed only under certain developmental conditions. It is proposed that the function of high order structure is to sequester genetic material, namely mainly controller sequences. Since such high order structure, in most cases, would be built up to house the controller dependencies of just one structural gene, the amount of DNA per structural gene needed for gene control would be considerable, and the concept, if correct, would go a long way towards explaining the c-value paradox ("excess" DNA in eukaryotes). In eurygenic determination, the high order structure is thought to be conditioned for melting or to actually melt to an intermediate level of structure. From there, stenogenic control, leading to transcription, is considered to carry the melting process further to yet lower structural levels...

Unintegrated ribosomal genes in diploid and polytene tissues of Drosophila melanogaster

We have examined DNA from polytene salivary glands and diploid brains and imaginal discs of male and female larvae having one or two nucleolus organizers. DNA having an estimated molecular weight of 5 X 10(9) or greater was obtained by sucrose gradient sedimentation of gently prepared lysates. Hybridization of the gradient fractions with 3H-ribosomal RNA REVEALS THAT 42% OF THE RIBOSOMAL GENES ARE FOUND IN DNA of lower molecular weight (approximately 3 X 10(8) daltons) in the salivary glands of every genotype examined. In the brains and imaginal discs, by contrast, all of the ribosomal genes are found in the high molecular weight peak except in females with one nucleolus organizer where 42% are found in lower molecular weight DNA, as in the salivary gland. Thus unintegrated genes are not an exclusive feature of polytene tissue, but can occur in diploid tissue as well in at least one genotype.

Interchromosomal asynchrony of DNA replication in polytene chromosomes of Drosophila pseudoobscura

Analysis of 3H-thymidine autoradiograms of late third instar larval salivary glands of Drosophila pseudoobscura revealed a unique example of asynchrony of replication in the autosome complement. The two autosomal arms, 2 and 3, show similar labeling pattern during the initial phases, DD to 3C, and thereafter, the chromosome 3 has fewer labeled sites than chromosome 2 until the most terminal pattern, 1D. Detailed sitewise analysis of 3H-thymidine labeling shows that while nearly 54% of the sites examined in chromosome 2 have a labeling frequency greater than 50%, only 13% of all sites in chromosome 3 have labeling frequency at that range. The number of labeled sites on chromosome 3 plotted against that on chromosome 2 shows a hyperbolic profile rather than a linear relationship. The silver grain ratio of the 2nd to 3rd increases from 1.5 to 3.1 through different stages of the cycle. These results suggest that both chromosomes start replication simultaneously but the third chromosome appears to complete the replication earlier than the second. These data open up the possibility of separate control mechanisms for the initiation and termination of DNA replication in polytene chromosomes.

The proteins of polytene chromosomes of Drosophila hydei

It is reported that chromatin can be prepared from highly purified polytene nuclei from the salivary glands of third instar larvae of Drosophila hydei; such chromatin differs from that of diploid nuclei mainly by deficiencies in certain nonhistone chromosomal proteins. It is suggested that these proteins are important components of constitutive heterochromatin, which is severely underrepresented in polytene chromosomes. Chromosome morphology, including the pattern of induced puffs, is maintained throughout the mass isolation of glands and sucrose gradient purification of nuclei, as indicated by studies on temperature-shocked and control larvae. No significant alteration in the chromosomal proteins following puff induction by heat shock could be detected on analysis of the isolated protein fractions by disc gel electrophoresis. More sensitive techniques must be developed to study the apparent rearrangement or accumulation of protein at puff sites, and to elucidate the role of this protein in gene activation.

Differential replication of satellite DNA in polyploid tissues of Drosophila virilis

Satellite DNA amounts were examined in adult tissues of Drosophila virilis, a species whose DNA contains three prominent satellites. Satellite amounts in DNA from six of the seven tissues were lower than in DNA from diploid (adult brain) tissue. Satellite amounts in adult ovary DNA, however, were equivalent to or greater than diploid levels. When DNA from pupal ovaries was examined, a 30% increase in satellite amounts over diploid levels was found. An RNA-DNA hybridization experiment showed that the ribosomal RNA genes in pupal ovary DNA were under-replicated relative to diploid DNA levels.

Under-replication of ribosomal cistrons in polytene chromosomes of Rhynchosciara

DNA preparations obtained from several tissues of Rhynchosciara americana and two related species, R. milleri and R. papaveroi, were hybridized to R. americana rRNA. The percentage of hybridization was found to be higher in tissues with low polyteny than in tissues with high polyteny, suggesting a relationship between the amount of rDNA and the tissue polyteny. This could be explained by under-replication of ribosomal cistrons in polytene cells, such as those from the salivary gland. Only slight tissue-dependent changes in the percentages of hybridization can be observed in heterologous hybridization using Xenopus laevis rRNA. The possibility that these experiments could not detect differences in the amount of ribosomal cistrons among tissues is discussed. The female:male ratio for the percentages of hybridization in the salivary gland of R. americana agrees with the results obtained by in situ hybridization experiments (16, 17) which have shown that the rRNA cistrons are distributed among chromosomes other than chromosome X.