In situ demonstration of DNA hybridizing with chromosomal and nuclear sap RNA in Chironomus tentans

Localization of nucleoli in Drosophila melanogaster polytene chromosomes

The majority of D. melanogaster salivary gland nuclei contains many nucleoli which vary in size and number. All nucleoli hybridize in situ with a cloned Drosophila DNA fragment containing 26S ribosomal gene. Autoradiographic analysis of preparations after pulse H3-uridine or H3-thymidine labelling of the salivary gland indicates an intensive transcription and replication of DNA within nucleoli. The nucleoli are bound to different sites of polytene chromosomes by chromatin fibers similar to strands of ectopic pairing and they are most often bound to regions which may be defined as intercalary heterochromatin.

Identification of the Balbiani ring 2 chromomere and determination of the content and compaction of its DNA

The giänt puff Balbiani ring 2 (BR 2) in the salivary glands of Chironomus tentants is known to contain transcriptionally active 75S RNA genes. The corresponding chromosomal superstructure, the BR 2 chromomere, has been identified and characterized in the present study. It was demonstrated by cytological methods that BR 2 originates from the broad band IV-3B10, since all the bands except the 3B10 band could be detected as intact bands in the vicinity of BR 2. In situ hybridization of BR 2 RNA to squashed Malpighian tubule chromosomes lacking BR 2, showed that all or almost all the DNA sequences complementary to BR 2 RNA are located in the 3B10 band. The DNA amount in the 3B10 band, designated the Br 2 band, was measured in relation to the DNA content of the whole chromosome set by both direct and indirect microspectrophotometry of Feulgen-stained Malpighian tubule chromosomes. From a determination of the haploid DNA content in sperm cells (0.25 pg), the amount of DNA in at BR 2 chromomere could then be calculated to be 5.1 x 10-4 pg DNA or 470 kb DNA. A minimum value of the DNA compaction within the BR 2 chromomere was estimated to 380 from the B-form length of BR 2 DNA (160 mum) and the thickness of the BR 2 band (0.42 mum). Since there are only between 1 and 4 75S RNA genes, 37 kb in size, in a BR 2 chromomere, most of the BR 2 DNA must consist of DNA not coding for 75S RNA. The nature of this DNA is discussed in relation to the high average AT-content of Chironomus DNA. The orgnization of the chromosome fiber in the BR 2 chromomere is considered in relation to the gene activation process in the salivary glands, i.e. the formation of a 75S RNA transcription loop from a protion of the tightly packed chromosome fiber in the BR 2 chromomere.

Demonstration of Balbiani ring RNA sequences in polysomes

A polysome extract from salivary glands of C. tentans was sedimented in a 15-60% sucrose gradient. Fractions from the heavy polysome region (1,000-2,000S) and fractions from the light polysome region (200-1,000S) were pooled separately, and the long-term labeled RNA was released by Sarkosyl/pronase and analysed by in situ hybridization. The results showed that BR 1 and BR 2 sequences were present in the heavy and the light polysome regions of the sucrose gradient. From control experiments with EDTA-treated extracts, it was concluded that most of the recorded BR 1 and BR 2 sequences were in fact located in polysomes. The finding that BR products enter polysomes suggests that they act as messenger RNA molecules. This study therefore strongly supports the concept that chromosome puffs represent active genes.

RNA, RIBOSOMAL/*BIOSYNon of ribosomal 5S RNA genes in Chironomus thummi by in situ hybridization of iodinated 5S RNA

5 S RNA of Chironomus thummi larvae was purified from total phenol extracted RNA by gel filtration and labelled to about 10(7) dpm/mug with carrier-free iodine-125. After hybridization in situ of 125I-5 S RNA and autoradiography only region B3c-e (containing two "normal" and two very faint bands) of chromosome II of salivary gland cells was highly labelled. In chromosomes of an animal showing pairing discontinuities a clearly "heterozygous" labelling of the 5 S RNA region was found. Region B3c-e shows no clearcut morphological signs of puffing or autoradiographically detectable 3H-uridine incorportion in spite of a continuous synthesis of 5 S RNA in salivary gland cells.

Proportionate representation of rDNA and Balbiani ring DNA in polytene chromosomes of Chironomus tentans

Attention was focussed on the question whether the most active genes of the polytene genome of Chironomus tentans, i.e. rDNA and Balbiani rings, have undergone the same number of duplications as the bulk of the genome. RNA was extracted from isolated salivary glands, enriched for messenger RNA by poly U sepharose chromatography, and labelled with 125Iodine. In situ hybridization showed that, apart from rRNA, Balbiani ring 1 and 2 transcripts are the major hybridizing RNA species present in this enriched preparation. BR1 hybridized only at the b-region. Transcripts of BR6 and puff I 17B are shown to be salivary gland specific and hybridize in situ to an extent of less than 5% of the RNA hybridized to BR1 plus BR2. Saturation hybridization levels of rRNA and Balbiani ring (BR1 plus BR2) RNA with polytene DNA from salivary glands were determined and compared with the saturation levels measured for DNA from adult flies and larvae. rRNA hybridized to the same level (0.09%) with polytene DNA as with DNA from primarily diploid cells (adult fly DNA) or from larvae. An equal hybridization level (0.04%) with each of these three types of DNA was also obtained for BR RNA. The results demonstrate that, during polytenization in C. tentans, the genes for rRNA and BR1 and 2 are duplicated to the same extent as the bulk of the genome.

A micro-method for the assay of polyadenylate-containing ribonucleic acid by gel electrophoresis

A micro-method for the determination of the electrophoretic profile of the various poly(A)-containing RNA species in a RNA sample was developed. The method is simple to carry out and allows for great reproducibility. It combines the resolving power of electrophoresis in agarose with the specificity of binding of poly(A) to poly(U)-containing glass-fibre filters. It consists of the following steps. (1) The molecules in an RNA sample are first separated according to their molecular weight by electrophoresis in agarose, at low ionic strength. 2. The molecules thus seperated are then submitted to a second electrophoresis in 'binding buffer' in a direction perpendicular to the first one. In the course of this electrophoresis the poly(A)-containing RNA species are seperated from other RNA species as they bind to a poly(U)-containing glass-fibre filter which is placed across the electrophoresis path. The method was used to determine the electrophoretic profile of Rhynchosciara salivary-gland messenger RNA. It was found that the population of messenger RNA in the gland is dominated by forms moving as 18 and 158 S peaks, but there is also polydisperse RNA with slower mobility.

Molecular characterization of an insect genome: Chironomus thummi

DNA extracted from Chironomus thummi larvae was studied by isopycnic centrifugation in CsCl, thermal denaturation and DNA-DNA reassociation techniques. The mean G+C content of the C. thummi DNA is 28-29% as indicated both by centrifugation in CsCl and thermal denaturation. According to optical reassociation analysis of total DNA and of isolated DNA fractions the C. thummi genome is composed of at least four components. About 80% of the DNA is classified as unique with a kinetic complexity of nearly 7 X 10(10) daltons. 6-8% intermediate DNA exhibits a kinetic complexity slightly above 10(8) daltons with a mean repetition frequency of 35. 11-13% fast-reassociating DNA has a kinetic complexity slightly above 10(6) daltons with a mean repetition frequency of 6000. 3-5% of the DNA cannot be properly studied by the optical reassociation technique and probably contains inverted repeats. The thermal denaturation behaviour of isolated DNA fractions indicated that most of the repetitive sequences in the C. thummi genome are tightly interspersed.

The presence of 5 S RNA genes in two consecutive chromosome bands in Chironomus tentans

It has earlier been shown by in situ hybridization that the 5 S RNA genes are located in region 2A of chromosome II in Chironomus tentans [1]. In the present study the resolution in this chromosome region could be considerably improved by using the inversion 1 A/9C of chromosome II, which carries region 2A, not in the usual position close to one end of chromosome II, but in the middle of the chromosome. It was then revealed that electrophoretically isolated 5 S RNA hybridized in situ with two adjacent bands in the region 2A. It was also observed that in heterozygotes harbouring one normal chromosome II and one with the inversion 1 A/9C, there is a close physical contact between the bands containing the 5 S RNA genes and the nucleolar organizer region.

The location of repeated DNA sequences in the chromosomes of Chironomus tentans

Polytene chromosomes of Chironomus tentans were hybridized in situ with in vivo labelled nuclear and chromosomal RNA. Nuclear RNA formed hybrids preferentially in five distinct regions considered to contain clustered, repeated DNA sequences. These are the two nucleolar organizer regions, Balbiani ring 1 and 2, and the 5 S RNA genes in region 2A of chromosome II, which together comprised almost 70% of the total number of grains over the complement. The remaining grains were diffusely distributed over the chromosomes. There was a significant difference in the distribution of grains when RNA from different chromosomes was used for hybridization. Chromosome I RNA hybridized preferentially with chromosome I, and chromosome II+III RNA preferentially with chromosome II+III. Some regions within the chromosomes hybridized significantly more chromosomal RNA than other regions. A considerable cross-hybridization of RNA from one particular type of chromosome with the other chromosomes was also found. It is concluded that repeated DNA sequences which hybridize with heterogeneous chromosomal RNA in C. tentans are widely dispersed in the genome. Some of these sequences have a delimited localization, others are dispersed, and some sequences which are transcribed in one particular chromosome are present also in the other chromosomes.

The chromosomal distribution of balbiani ring dna in chironomus tentans

RNA from Balbiani ring 2 (BR 2) of Chironomus tentans salivary gland cells was hybridized to polytene chromosomes of rectum cells, in which the Balbiani ring is not expressed. The distribution of the RNA:DNA hybrids was studied by autoradiography, using ultrathin emulsion to increase the resolution. The grains were estimated to cover 3-5 polytene chromosome bands, which indicates that information expressed by transcription in BR 2 may be present in several adjoining chromomeres. From a comparison of grain numbers over BR 2 of salivary gland chromosomes and over the BR 2 region of rectum chromosomes, it appears unlikely that selective amplification of BR DNA in the salivary glands could explain the efficient hybridization seen in this tissue. The conclusion is advanced that BR 2 DNA contains nucleotide sequences which are extensively repeated within 3-5 transcription units.

Localization of 5 S RNA genes in Chirnomus tentans

The genes for 5 S RNA in Chironomus tentans have been located to region 2A of chromosome II by cytological hybridization. RNA from individual chromosomes, nuclear sap and nucleoli of salivary gland cells hybridized with the identified 5 S RNA genes in region 2A of chromosome II. The results suggest a common origin of 5 S RNA in these different nuclear compartments.

Homology of Balbiani ring DNA in two closely related Chironomus species

Cytogenetic analysis indicates that Balbiani Ring 2 (BR 2) in the two sibling species Chironomus tentans and Chironomus pallidivittatus arises from identifically banded segments in the salivary gland polytene chromosomes, although chromosomal rearrangements have occurred. In situ hybridization of BR 2 RNA to the polytene chromosomes of each individual species, as well as their F1 hybrids, reveals that the repetitious BR 2 DNA in the two species has, within the limits of the technique, retained identity of nucleotide sequences and degree of repetition. The DNA of the naturally expressed BR 1 and BR 3 in both species and that ot the galactose induced BR 6 in C. pallidivittatus did not hybridize with BR 2 RNA, indicating that these BR's are different from BR 2 with regard to sequence content.

Multiple gene sites for 5S and 18 plus 28S RNA on chromosomes of Glyptotendipes barbipes (Staeger)

Ribosomal RNAs (28 + 18S and 5S) and 4S RNA extracted from the chironomid Glyptotendipes barbipes were iodinated in vitro with (125)I and hybridized to the salivary gland chromosomes of G. barbipes and Drosophila melanogaster. Iodinated 18 + 28 S RNA labeled three puffed sites with associated nucleoli on chromosomes IR, IIL, and IIIL of G. barbipes and the nucleolar organizer of Drosophila. Labeled 5S RNA hybridized to three sites on chromosome IIIR, two sites on chromosome IIR and one site in a Balbiani ring on chromosome IV of Glyptotendipes. Most of the label produced by this RNA was localized seven bands away from the centromere on the right arm of chromosome III, and we consider this to be the main site complementary to 5S RNA in the chironomid. This same RNA preparation specifically labeled the 56 EF region of chromosome IIR of Drosophila which has been shown previously to be the only site labeled when hybridized with homologous 5S RNA. Hybridization of G. barbipes chromosomes with iodinated 4S RNA produced no clearly localized labeled sites over the exposure periods studied.

The use of iodinated RNA for gene localization

Carrier-free iodination of 5S RNA with (125)I yields a probe suitable for use in cytological RNA-DNA hybridization studies. The genes coding for 5S ribosomal RNA in Drosophila could be localized by autoradiography after a 2-day exposure, whereas a 2-month exposure is needed when the best available [(3)H]RNA is used. The procedure introduces one covalently bound (125)I atom per 100 nucleotides, resulting in a specific activity of over 10(8) dpm/mug of RNA. The method may be readily applied to other problems involving molecular hybridization techniques.

Evidence for transport of 75S RNA from a discrete chromosome region via nuclear sap to cytoplasm in Chironomus tentans

Salivary glands of the dipteran Chironomus tentans were exposed to tritiated pyrimidines for different time periods either in vitro or in vivo. Nonribosomal, high molecular weight RNA molecules of very different sizes (15-100 S) were labeled on chromosomes I-III, while only one main species, 75S RNA, was recorded in Balbiani ring 2, a giant chromosome puff on chromosome IV. 75S RNA was present as a prominent fraction in nuclear sap, but not in cytoplasm, after 90 min of incubation in vitro. During the ensuing 90 min, 75S RNA also appeared in cytoplasm. After 1 week of labeling in vivo, radioactive 75S RNA accumulated heavily in cytoplasm. Absorbance measurements showed that 75S RNA constituted as much as 1.5% of the total salivary-gland RNA. The half-life of 75S RNA was estimated to exceed 35 hr. Available data on the intracellular distribution and metabolic stability of nonribosomal, high molecular weight RNA from Balbiani ring 2 and chromosomes I-III indicate that most of the cytoplasmic 75S RNA is transcribed in the Balbiani ring 2 region of chromosome IV. 75S RNA molecules are, therefore, likely to be transferred from Balbiani ring 2, via nuclear sap, to cytoplasm without being measurably reduced in molecular size.