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

The Balbiani Ring Story: Synthesis, Assembly, Processing, and Transport of Specific Messenger RNA-Protein Complexes

Eukaryotic gene expression is the result of the integrated action of multimolecular machineries. These machineries associate with gene transcripts, often already nascent precursor messenger RNAs (pre-mRNAs). They rebuild the transcript and convey properties allowing the processed transcript, the mRNA, to be exported to the cytoplasm, quality controlled, stored, translated, and degraded. To understand these integrated processes, one must understand the temporal and spatial aspects of the fate of the gene transcripts in relation to interacting molecular machineries. Improved methodology is necessary to study gene expression in vivo for endogenous genes. A complementary approach is to study biological systems that provide exceptional experimental possibilities. We describe such a system, the Balbiani ring (BR) genes in polytene cells in the dipteran Chironomus tentans. The BR genes, along with their pre-mRNA-protein complexes (pre-mRNPs) and mRNA-protein complexes (mRNPs), allow the visualization of intact cell nuclei and enable analyses of where and when different molecular machineries associate with and act on the BR pre-mRNAs and mRNAs.

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

BACKGROUND

The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes.

RESULTS

The genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150-250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations.

CONCLUSIONS

We show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.

Evidence for a common ancestor sequence for the Balbiani ring 1 and Balbiani ring 2 genes in Chironomus tentans

The Balbiani ring (BR) 1 and BR 2 genes in Chironomus tentans are functionally related and are only expressed in the salivary gland cells. Here we reveal the principal structure of the BR 1 gene and analyze the structural and evolutionary relationship between the BR 1 and BR 2 genes. The properties of the BR 1 gene, 37 kilobases in size, are derived from the analysis of a cloned cDNA sequence, pCt 21. A considerable part of the BR 1 gene consists of one or a few blocks of a tandemly repeated 246-base-pair (bp) major repeat unit. About half of this major repeat unit is in turn built from four tandem repeats of a 33-bp sequence. This hierarchic arrangement of repetitive sequences within the BR 1 gene suggests that the gene has evolved through two major amplification steps, starting from a short primordial sequence. A similar evolutionary model has been put forward for the BR 2 gene [Sümegi, J., Wieslander, L. & Daneholt, B. (1982) Cell 30, 579-587]. The two putative primordial genes contain a similar, 102-bp-long sequence (86% nucleotide sequence homology), indicating that the BR 1 and BR 2 genes most likely arose from the same ancestor sequence. During the course of evolution the two genes diverged, mainly due to differences in the length and sequence of the gene segments involved in the two amplification steps. Moreover, at least one of the BR genes was translocated to another chromosomal locus.

Scanning electron microscopy of polytene chromosomes (I)

The structure of polytene chromosomes has been observed by conventional scanning electron microscopy and also with a high resolution 'in lens' field emission instrument. Surface imaging with secondary electron emission has characterized condensed chromatin and regions known for their RNA synthetic potential (nucleoli, Balbiani rings and puffs). In DNA-rich bands pairing of chromatids appears so perfect that individual chromomeres cannot be visualized as discrete units. In the interbands only chromatid bundles appear as elements, but not individual chromatids. High resolution scanning electron microscopy allows resolution at the nucleosome level. Improved localization of chromosomal structures is demonstrated, as in the case of the proposed separation of the prepupal 'Balbiani ring 1'. Surface images of the RNA synthetic centres of the salivary gland cell are presented. Transcripts of the Balbiani ring template can be observed in the condensed and gradually unfolded state, allowing measurement of unit ribonucleoparticles. The surfaces of puffs have been visualized and are characterized by multiple supercoiled loop structures, which are described according to size, conformation and distribution.

Correlated changes in steady-state levels of Balbiani ring mRNAs and secretory polypeptides in salivary glands of Chironomus tentans

Balbiani rings (BRs) on polytenized chromosomes in Chironomid salivary glands contain members of a homologous multigene family that encodes a family (the sp-I family) of high Mr secretory polypeptides. Each of these BR genes is comprised largely of tandemly duplicated core repeat sequences consisting of related constant (C) regions and intergenically divergent subrepeat (SR) regions. A set of oligodeoxyribonucleotide probes were synthesized that correspond to the transcribed strand of the SR region of BR1, BR2 alpha, BR2 beta, and BR6 core repeats. Under a defined set of conditions, it was possible to show that each oligonucleotide probe hybridized exclusively to its cognate repeat type without hybridization to other repeat types in cloned DNA templates. These BR probes were then used in dot-blot hybridization experiments to simultaneously follow alterations in the steady-state level of BR mRNAs in response to prolonged exposure of larvae to galactose. The results indicated that the relative amounts of these four BR mRNAs may change in a noncoordinate manner. These BR probes were also used in experiments to compare simultaneously the salivary gland content of sp-I components and specific BR mRNAs in larvae that exhibited naturally occurring or induced alterations in BR gene expression. A correlation was found which suggested that sp-Ia is encoded in a gene comprised of BR1 repeats, sp-Ib is encoded by BR2 beta repeats, sp-Ic is encoded by BR6 repeats and sp-Id is encoded by BR2 alpha repeats.

Packing of a specific gene into higher order structures following repression of RNA synthesis

Transcription of the Balbiani ring (BR) genes of the dipteran Chironomus tentans was inhibited by teh nucleoside analogue DRB (5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole). The BR genes were emptied of RNA polymerases and the subsequent packing of the genes was monitored by transmission electron microscopy. The thin chromatin axis of the transcriptionally active genes condensed into a thick (20-25 nm) chromatin fiber, which was recorded as a linear structure, an open loop or a supercoiled loop. The compacted genes were finally packed into dense clumps of chromatin. It was proposed that upon repression of RNA synthesis the BR gene template attains the following consecutive stages with increasing compaction: transcription loop----linear thick fiber----open thick fiber loop----supercoiled thick fiber loop----dense chromatin. Within the chromatin blocks structures that resembled the supercoiled loops were discerned, suggesting that the final packing of the template might be accomplished by a close alignment of supercoiled loops.

Rapid reformation of the thick chromosome fiber upon completion of RNA synthesis at the Balbiani ring genes in Chironomus tentans

We have studied the ultrastructure of the Balbiani ring genes in Chironomus tentans during treatment with the RNA synthesis inhibitor DRB (5,6-dichloro-1-beta-D-ribofuranosyl-benzimidazole). This nucleoside analogue blocks transcription at or near the initiation site but does not interfere with the elongation and termination processes. In the ordinary active state the Balbiani ring genes display a 5 nm chromosome fiber, carrying densely distributed, growing ribonucleoprotein particles (Andersson et al., 1980). When the transcriptional activity declines, a 10 nm fiber can be observed between sparsely distributed RNA polymerases. Furthermore, after passage of the last RNA polymerase the 10 nm fiber can be seen as well as its gradual packing into a 25 nm thick fiber. Thus, the active chromosome fiber is rapidly packed into higher order structures when the fiber is not directly involved in transcription. The formation of the thick fiber does not require that the gene along its entire length is devoid of active RNA polymerases. The thick fiber can again be mobilized for transcription, since in reversion experiments the BR genes appear as ordinary active genes with an extended nucleofilament and densely packed nascent transcription products. The dynamic behaviour of the chromosome fiber during transcription is discussed as well as the packing and unpacking of a gene into higher order structures.

The fourth chromosome of Chironomus tentans Malpighian tubules: an ultrastructural study

Morphology and banding pattern of the 4th chromosome in Chironomus tentans Malpighian tubules have been investigated by electron microscopy, using the squash and selection technique. The map we composed from our observations shows a remarkable increase (75%) in band numbers as compared to the map previously presented by Beermann for the 4th chromosome from salivary glands. Extrapolation of this increase to the entire genome would result in a total band number of about 3,500. The mean DNA content of bands can thus be calculated to be about 50 kb. Many bands show a complex structure, including the BR2 band. Some bands seem to result from fusion of smaller components. "Minibands" have also been observed. Some interbands contain RNP particles. In our material the interbands appeared to be made up of fibrils with a diameter of about 120 A. On the basis of these results we estimate the DNA in the interbands as amounting to 2% of the entire genome. The results are discussed with respect to the organization of the polytene chromosomes and the functional significance of the banding pattern.

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.

Effects of DMSO on the structure and function of polytene chromosomes of Chironomus

Dimethylsulfoxide (DMSO) controlled puff induction and repression (or non-induction) in larval polytene chromosomes of Chironomus tentans were studied for the case of the Balbiani rings (BR). A characteristic reaction pattern, involving BR 1, BR 2, and BR 3, all in salivary gland chromosome IV was found. In vivo exposure of 4th instar larvae (not prepupae) to 10%n DMSO at 18 degrees C first evokes an over-stimulation of BR 3 while DMSO-stimulation of puffing at BR 1 and BR 2 always follows that of BR 3. After removal of the drug, a rapid uniform collapse of all puffs occurs, thus more or less restoring the banding pattern of all previously decondensed chromosome segments. Recovery proceeds as BR's and other puffs reappear. By observing the restoration, one can locate the site from which a BR (puff) originates. BR 2, which is normally the most active non-ribosomal gene locus in untreated larvae, here serves as an example. As the sizes of BR 3, BR 1 and BR 2 change, so do the quantities of the transcriptional products in these gene loci (and vice versa), as estimated electron-microscopically in ultrathin sections and autoradiographically in squash preparations. In autoradiograms, the DMSO-stimulated BRs exhibit the most dense concentration of silver grains and therefore the highest rate of transcriptional activity. In DMSO-repressed BRs (and other puffs) the transcription of the locus specific genes is not completely shut off. In chromosomes from nuclei with high labelling intensities the repressed BRs (and other puffs) always exhibit a low level of 3H-uridine incorporation in vivo. The absence of cytologically visible BR (puff) formation therefore does not necessarily indicate complete transcriptional inactivity. Typically, before the stage of puff formation the 3H-uridine labelling first appears in the interband-like regions.