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

DNA in the centromeric heterochromatin of polytene chromosomes is topologically open

Heterochromatin differs from euchromatin by a set of specific features. We suggested earlier that specific features of heterochromatin result from differences in DNA topology of these two chromatin types and provided explanations for the majority of them (Gruzdev 2000). We proposed that, unlike topologically closed euchromatic DNA, the DNA of heterochromatin is topologically open, i.e. it likely contains single- or doublestrand breaks. In this work, we studied the topological state of DNA in a block of centromeric heterochromatin and in a euchromatic banded region of Chironomus melanotus polytene chromosomes by microfluorimetric methods using the fluorescent intercalating dye ethidium bromide (EB). It was demonstrated that the fraction of topologically closed DNA in heterochromatin blocks is five-fold smaller than in the banded region. The data obtained support the hypothesis proposed.

Terminal long tandem repeats in chromosomes form Chironomus pallidivittatus

We provide evidence that a chromosome end in the dipteran Chironomus pallidivittatus contains 340-bp tandem repeats reaching the extreme terminus of the chromosome. After adding synthetic oligonucleotide tails to DNA extracted from the microdissected right end of the fourth chromosome, we could demonstrate that the blocks of repeats were tailed at only one end, the chromosome terminus, the interior of the arrays being unavailable for tailing. Using PCR, we furthermore showed that the added tails were connected to 340-bp repeat DNA directly, i.e., without intervening DNA of any other kind. The tailed repeats belong to a subfamily previously known to be the most peripheral one of the different types of 340-bp units. Using plasmid controls, we could also make certain that we did not amplify rare or nonrepresentative DNA termini.

Mitotic and salivary gland chromosome analyses in the Musca domestica L. (house fly) (Diptera: Muscidae)

The mitotic chromosomes in Musca domestica consist of five pairs of autosomes and an X, Y sex chromosome pair. They respond to C-banding with procentric bands on all autosomes and deep staining over most of the X and Y chromosomes. Polytene chromosomes were previously found in several larval and pupal tissue of Musca domestica. Polytene chromosome reference maps of the two sexual and the five autosomal chromosomes of Musca domestica from salivary gland cells are shown. Characteristic features of each chromosome are described identifying areas that are difficult to analyse.

3B55: a repetitious sequence family which is transcribed and proportionately replicated in germ-line polyploid nuclei of Calliphora erythrocephala

The chromosomes of dipteran polyploid nurse cell nuclei are functionally analogous to the oocyte lampbrush chromosomes of the Amphibia. In investigating the transcriptional and replicative activity of these nuclei in Calliphora erythrocephala we have identified a cloned highly repetitious DNA fragment which shows enhanced transcriptional activity in these cells and different replicative behavior in these germ-line polyploid nuclei as opposed to somatic polytene nuclei. The clone, 3B55, contains a 6.8-kb insert which consists primarily of tandemly repeated 200-bp sequences defined by RsaI sites. From Southern hybridizations to diploid (embryonic) genomic DNA, 3B55-related DNA was calculated to represent a significant fraction of the haploid genome (0.8% or 5000 kb). In situ hybridizations established that these sequences are present in the pericentric regions of four of the six chromosomes. Thus the 3B55 sequences have the properties of a satellite-type DNA family. Quantitation of the 3B55 200-bp monomer (which represents approximately 60% of the genomic 3B55 DNA sequences in all tissues examined) revealed that in somatic polytene salivary gland nuclei, 3B55 DNA is highly under-replicated to give a monomer representation of only 48 +/- 11 kb per haploid genome. However, in germ-line nurse cell nuclei, 3B55 DNA is proportionately replicated to give a monomer genomic representation (3560 +/- 344 kb) equivalent to that of diploid DNA (3011 +/- 202 kb). Transcripts complementary to 3B55 sequences are at least 25 times more abundant in total nurse cell nuclear RNA than in total embryonic nuclear RNA. These findings suggest an association of the 3B55 sequence family with some germ-line specific function.

Eukaryotic genome: model considerations

The paper presents a new model of chromosome structure based on the assumption that multiple circular subunits of DNA exist. The essential difference with previously described models is the circular DNA unit forms a central chromosome axis. Chromosome configurations during various phases of the cell cycle depend on the various conformations of this central integrating unit. The described model can be generalized for all haploid set of eukaryotic nucleus. Some aspects of the chromosome structure and their functions have been discussed.

Differential sex chromosome replication and dosage compensation in polytene trichogen cells of Lucilia cuprina (Diptera: Calliphoridae)

Non banded sex chromosome elements have been identified in polytene trichogen cells of Lucilia cuprina using Y-autosome translocations, C-banding and Quinacrine fluorescence. The X chromosome is an irregular granular structure while the much smaller Y chromosome has both a dense darkly stained and a loosely organised segment. The X and Y chromosomes are under-replicated in polytene cells but comparison of C- and Q-banding characteristics of sex chromosomes in diploid and polytene tissues indicates that selective replication of non C-banding material occurs in both the sex chromosomes. Brightly fluorescing material in the Y chromosome is replicated to such an extent that it consists of half the polytene element, while the C-banding material, which makes up most of the diploid X chromosome, is virtually unreplicated. Differential replication also occurs in autosomes. In XXY males, and in males carrying a duplication of the X euchromatic region, a short uniquely banded polytene chromosome is formed. It is suggested that in males carrying two doses of X euchromatin a dosage compensation mechanism operates in which genes in one copy are silenced by forming a banded polytene chromosome.

Interbands of polytene chromosomes: binding sites and start points for RNA polymerase B (II)

Polytene chromosomes of different chironomids, i.e., Chironomus tentans, C. melanotus and Glyptotendipes barbipes were isolated from salivary glands in a native state. These chromosomes were treated in vitro either mechanically or with different ionic strengths to modify them structurally as to yield different degrees of decondensation of the compact bands. Treated and untreated polytene chromosomes were lightly fixed with formaldehyde and stained by indirect immunofluorescence for RNA polymerase B. The distribution of this enzyme in bands, interbands, puffs and centromeric heterochromatin was scored and compared with that of histone H2B. The results indicate that failure to observe an antigen in condensed regions of chromatin does not necessarily imply its absence. Decondensation of bands, for example, leads to massive uncovering of histone H2B antigen, which appears to be masked in the bands of untreated polytene chromosomes. No evidence, however, of a corresponding unmasking of RNA polymerase B molecules was observed, indicating that few if any enzyme molecules are trapped in bands. Thus binding sites for RNA polymerase B and start points for transcriptional activity of the enzyme appear always to be the interband regions.

Underreplication during polytenization? : Recent cytophotometric DNA determinations and related biochemical results concerning polytene salivary gland nuclei of Drosophila melanogaster

Recent cytophotometric DNA determinations and results of labeling experiments are compared with results of biochemical experiments concerning larval polytene salivary gland nuclei of Drosophila melanogaster. Recent publications (Dennhöfer 1981; 1982 a, b) demonstrate that methodological errors both in hydrolysis of the DNA before Feulgen reaction and in interpretation of the cytophotometric values give raise to the hypothesis of heterochromatic underreplication during polytenization. It is concluded also that methodological difficulties cause the absence of polytene SAT-DNA in biochemical centrifugation experiments since, because of different solubilities of eu- and heterochromatic DNA, the latter is not resolved in DNA isolation procedures from polytene nuclei.

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.

Sex-linked difference in DNA content of a polytene chromosome in Prodiamesa (Chironomidae)

The chironomid Prodiamesa olivacea possesses 3 pairs of chromosomes. The underreplication of the right arm in the polytene 3rd was presented earlier and is here shown to affect in females the cell nuclei of salivary glands. Malpighian tubules and the hindgut. The same somatic nucleic in males exhibit also a polytene 3rd with specific characteristics inasmuch as it contains half the relative DNA value of the female nuclei (3% instead of 6% complemental portion). - In male meiocytes the two partners in each of the 3 diakinetic bivalents were recognized to be homomorphic. In view of this morphological criterium the polytene situation in males must be due either to an unknown elimination process or to the underreplication of both right arms and further one left arm of the 3rd chromosomes. The latter model interprets the elements of the 3rd pair as differently polytenizing heterosomes in P. olivacea.

Satellite DNA of Anopheles stephensi Liston (Diptera: Culicidae). Chromosomal location and under-replication in polytene nuclei

Four satellite DNAs in the Anopheles stephensi genome have been defined on the basis of their banding properties in Hoechst 33258-CsCl density gradients. Two of these satellites, satellites I and II, are visible on neutral CsCl density gradients as a light density peak forming approximately 15% of total cellular DNA. Hoechst-CsCl density gradient profiles of DNA extracted from polytene tissues indicates that these satellites are underreplicated in larval salivary gland cells and adult female Malpighian tubules and possibly also in ovarian nurse cells. The chromosomal location of satellite I on mitotic and polytene chromosomes has been determined by in situ hybridisation. Sequences complementary to satellite I are present in approximately equal amounts on a heterochromatic arm of the X and Y chromosomes and are also present, in smaller amounts, at the centromere of chromosome 3. A quantitative analysis of the in situ hybridisation experiments indicates that sequences complementary to satellite I at these two sites differ in their replicative behaviour during polytenisation: heterosomal satellite I sequences are under-replicated relative to chromosome 3 sequences in polytene larval salivary gland and ovarian nurse cell nuclei.

In situ binding of AT-rich repetitive DNA to the centromeric heterochromatin in polytene chromosomes of chironomids

Native highly repetitive DNA sequences have been allowed to react in situ with DNA-depleted polytene chromosomes of chironomids in cytological preparations. The double-stranded DNA can bind specifically to the centromeric heterochromatin, where these sequences have been localized previously by in situ hybridization. Various control experiments support the conception that heterochromatin-specific DNA-binding proteins are involved in the in situ binding.

Chromosomal replication in Drosophila virilis. III. Organization of active origins in the highly polytene salivary gland cells

Using DNA fiber autoradiography, the rate of fork movement in D. virilis salivary glands was determined to be 0.1 micron/ml (25 degrees C). This value is 3.5 times slower than the replication rate determined in the diploid brain cells using the same experimental conditions (Steinemann, 1981). Replicon lengths in the polytene cells span from 5 to 203 micron, with a mean of approximately x = 46.7 micron and a median of approximately x = 39.5 micron. The polytene replicon length is about the same as that for diploid brain cells (31.0 micron). Dividing the haploid genome of D. virilis by the estimated number of 5,000 bands and taking the resulting 13.6 micron as average DNA length per chromomere, the average replicon length covers 3.4 chromomere units. This result does not support the concept that "one-band-plus interband" behaves as a replicating unit (Pelling, 1966). From the positive skew of the replicon length distributions, combined with the results derived from the chromosomal labelling patterns, the following schedule of chromosomal euchromatin doubling is infered: A short initiation period (discontinuous phase I), asynchronous with respect to individual origins, is followed by a phase of common replication activity at all inducible origins (continuous phase). The discontinuous II pattern is formed by few, long replicons which are still replicating while the shorter ones have already finished (weak points are not considered). Replicons, distributed in the main peak of the histogram and smaller than about 100 micron, are then responsible for the replication of the bulk of chromosomal euchromatin, the continuous phase. the interpretation is in conflict with the hypothesis assuming a clustered organization of the replicons to explain spot labelling (reviewed in Hand 1978). The diploid karyotype of D. virilis contains 45% satellite sequences, located in the alpha-heterochromatin (Gall et al., 1971). They do not replicate in the highly polytene salivary gland cells of 3rd instar larvae. Comparison of DNA fiber autoradiograph patterns from salivary glands and brains suggests that these satellite sequences replicate in short (less than 10 micron), to some extent irregularly spaced replicons.

Two AT-rich satellite DNAs in the chironomid Glyptotendipes barbipes (Staeger): isolation and localization in polytene chromosomes of G. barbipes and Chironomus thummi

Two AT-rich satellite DNAs are present in the genome of Glyptotendipes barbipes. The two satellites have densities of 1,680 g/cm3 (=21% GC) and of 1.673 g/cm3 (=13% GC) in neutral CsCl-density gradients. The main band DNA has a density of 1.691 g/cm# (= 32% GC). This value is in agreement with the 33% GC=content of G. barbipes DNA calculated from thermal denaturation (TM=83 degrees C). - In brain DNA as well as in salivary gland DNA the two satellite sequences together comprise 12-15% of the total G. barbipes DNA. Comparisons of the density profiles of DNA extracted from polytene and non-polytene larval tissue gave no hints for under-replication of the satellite DNAs during polytenization. - The two satellite DNAs have been isolated from total DNA by Hoechst 33258-CsCl density centrifugation and then localized in the polytene salivary gland chromosomes by in situ hybridization. Both satellite sequences hybridize to all heterochromatic centromer bands of all four chromosomes of G. barbipes. Satellite I (1.673 g/cm3) hybridizes mainly with the middle of the heterochromatin, satellite II (1.680 g/cm3) hybridizes with two bands at the margin of the heterochromatin. In situ hybridization with polytene chromosomes of Chironomus thummi revealed the presence of G. barbipes satellite sequences also in the Ch. thummi genome at varios locations, mainly the centromere regions.

The organization of DNA in the mitotic and polytene chromosomes of Sciara corprophila

The organization of DNA in the mitotic metaphase and polytene chromosomes of the fungus gnat, Sciara coprophila, has been studied using base-specific DNA ligands, including anti-nucleoside antibodies. The DNA of metaphase and polytene chromosomes reacts with AT-specific probes (quinacrine, DAPI, Hoechst 33258 and anti-adenosine) and to a somewhat lesser extent with GC-specific probes (mithramycin, chromomycin A3 and anti-cytidine). In virtually every band of the polytene chromosomes chromomycin A3 fluorescence is almost totally quenched by counterstaining with the AT-specific ligand methyl green. This indicates that GC base pairs in most bands are closely interspersed with AT base pairs. The only exceptions are band IV-8A3 and the nucleolus organizer on the X. In contrast, quinacrine and DAPI fluorescence in every band is only slightly quenched by counterstaining with the GC-specific ligand actinomycin D. Thus, each band contains a moderate proportion of AT-rich DNA sequences with few interspersed GC base pairs. - The C-bands in mitotic and polytene chromosomes can be visualized by Giemsa staining after differential extraction of DNA and those in polytene chromosomes by the use of base-specific fluorochromes or antibodies without prior extraction of DNA. C-bands are located in the centromeric region of every chromosome, and the telomeric region of some. The C-bands in the polytene chromosomes contain AT-rich DNA sequences without closely interspered GC base pairs and lack relatively GC-rich sequences. However, one C-band in the centromeric region of chromosome IV contains relatively GC-rich sequences with closely interspersed AT base pairs. - C-bands make up less than 1% of polytene chromosomes compared to nearly 20% of mitotic metaphase chromosomes. The C-bands in polytene chromosomes are detectable with AT-specific or GC-specific probes while those in metaphase chromosomes are not. Thus, during polytenization there is selective replication of highly At-rich and relatively GC-rich sequences and underreplication of the remainder of the DNA sequences in the constitutive heterochromatin.

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.

Nucleolar relationships in some Australian chironomus species

Members of a group of Australian Chironomus species in the pseudothummi complex show wide variation in number and location of nucleolar organizing regions (NORs). The structure of these regions has been examined by phase contrast microscopy and silver banding of salivary gland polytene chromosomes. Presence of nucleoli was also checked on other types of chromosomes in some species. The contribution of the silver banding technique to nucleolar studies in these chironomid chromosomes is discussed. Nucleoli often seem to emerge from groups of (up to 9) bands. Further studies are necessary to confirm the presence of rRNA cistrons in all of these bands. Banding differences, in particular absence of bands from homologous regions of some species which have smaller nucleoli or lack particular nucleoli, have been found. In the case of Ch. tepperi, however, little banding difference is apparent in the 16B region between the N(IV)+ and N(IV)- chromosomes, although in situ hybridization (Eigenbrod 1978) shows a deletion of rRNA cistrons in the N(IV)- stock. Differences in heterochromatin amount have also been observed at different NORs. A scheme for the evolution of nucleolar-producing regions in this Chironomus group in terms of these and other known chromosomal changes is presented and discussed.