Giant poly(A)-rich RNP aggregates form at terminal regions of avian lampbrush chromosomes.

The cell nucleus comprises a number of chromatin-associated domains. Certain chromatin-associated domains are nucleated by nascent RNA and accumulate non-nascent transcripts in the form of ribonucleoprotein (RNP) aggregates. In the transcriptionally active nucleus of the growing avian oocyte, RNP-rich structures, here termed giant terminal RNP aggregates (GITERA), form at the termini of lampbrush chromosomes. Using GITERA as an example, we aimed to explore mechanisms of RNP aggregate formation at certain chromosomal loci to establish whether they accumulate non-nascent RNA and to analyze protein composition in RNP aggregates. We found that GITERA on chicken and pigeon lampbrush chromosomes do not contain nascent transcripts. At the same time, RNA fluorescent in situ hybridization (FISH) and in situ reverse transcription demonstrated that GITERA accumulate poly(A)-rich RNA. Moreover, subtelomere chromosome regions adjacent to GITERA are transcriptionally active as shown by detection of incorporated BrUTP and the elongating form of RNA polymerase II. GITERA on both chicken and pigeon lampbrush chromosomes are enriched in splicing factors but not in heterogeneous nuclear RNP (hnRNP) L and K. A subtype of GITERA concentrates hnRNP I/PTB and p54nrb/NonO. Interestingly, hnRNP I/PTB and p54nrb/NonO in such subtype of GITERA were revealed in long threads. The resemblance of these threads to amyloid-like fibers is discussed. Our data suggest that transcription of subtelomeric sequences serves as a seeding event for accumulation of non-nascent RNA and associated RNP proteins. Such accumulation leads to GITERA formation in terminal chromosomal regions in avian oocyte nucleus. 3'-processed transcripts derived from other chromosomal loci may be attracted to GITERA by binding to the same RNP proteins or to their interaction partners.

HE ROLE OF REPETITIVE SEQUENCES IN THE EVOLUTION OF SEX CHROMOSOMES IN BIRDS.

In this paper, we analyzed the distribution and the transcriptional activity of different repetitive elements in the sex chromosomes of chicken at the lampbrush stage. Based on these results, we suggest participation of interspersed repeats in the maintenance evolutionarily significant level of variability of heteromorphic sex chromosomes in birds. Analysis of the organization peculiarities of chicken sex chromosome W specific repeats allowed us to hypothesize that the accumulation of tandem repeats enriched with homopurine tracks is significant for the evolution of sex chromosomes.

Precise centromere positioning on chicken chromosome 3.

Despite the progress of the chicken (Gallus gallus) genome sequencing project, the centromeric sequences of most macrochromosomes remain unknown. This makes it difficult to determine centromere positions in the genome sequence assembly. Using giant lampbrush chromosomes from growing oocytes, we analyzed in detail the pericentromeric region of chicken chromosome 3. Without knowing the DNA sequence, the centromeres at the lampbrush stage are detectable by immunostaining with antibodies against cohesin subunits. Immunostaining for cohesin followed by FISH with 23 BAC clones, covering the region from 0 to 23 Mb on chicken chromosome 3 (GGA3), allowed us to map the GGA3 centromere between BAC clones WAG38P15 and WAG54M22 located at position 2.3 and 2.5 Mb, respectively. This corresponds to the gap between 2 supercontigs at the 2.4-Mb position in the current GGA3 sequence assembly (build 2.1). Furthermore, we have determined that the current putative centromeric gap at position 11.6-13.1 Mb corresponds in fact to a long cluster of tandem chicken erythrocyte nuclear membrane repeats (CNM).

Polymorphic heterochromatic segments in Japanese quail microchromosomes.

Using highly extended lampbrush chromosomes from diplotene oocytes, we have examined the distribution of heterochromatin protein 1 beta (HP1 beta) and histone H3 modifications on chicken (Gallus gallus) and Japanese quail (Coturnix japonica) (2n = 78) microchromosomes. Acrocentric microchromosomes of chicken and submetacentric microchromosomes of quail differ in several morphological features. In addition to pericentromeric and subtelomeric blocks of constitutive heterochromatin, which are enriched in HP1 beta protein and repressive histone modifications, not completely condensed but heterochromatic segments were found to be an attribute of the short arms of submetacentric microchromosomes in Japanese quail. These heterochromatic regions are variable in length and do not form chiasmata in female germ cells. Dissimilarity in the centromere positions in chicken and Japanese quail microchromosomes is proposed to be due to the accumulation of repetitive sequences on the short arms of quail microchromosomes. Transcriptional activation of polymorphic heterochromatic segments of quail microchromosomes during the lampbrush stage is demonstrated.

Avian lampbrush chromosomes: a powerful tool for exploration of genome expression.

Lampbrush chromosomes (LBCs) are highly extended bivalents that function in the growing oocytes of many animals. Due to their distinctive chromomere-loop organization and intense transcriptional activity of lateral loops the LBCs, mainly amphibian ones, have served as a powerful system for exploring the general principles of chromosome organization and function. The exploitation of avian LBCs has considerably broadened the opportunities for comparative genome research and for cytogenetic analysis of domestic species. In this review we highlight the advantages of avian LBCs for research in different areas including integration of genome organization studies with studies on gene activity in vivo, analysis of co-transcriptional events occurring on nascent transcripts and investigation of chromosome-associated intranuclear domains. Recent findings concerning the organization of transcriptionally active and silent chromatin together with involvement of cohesin and condensin complexes into maintenance of structural integrity of LBCs are presented. The biological significance of the LBC phenomenon is discussed. The intensive transcription on LBCs shows some specific features: very long transcription units, deregulated termination, and transcription of non-coding satellite repeats. Here, based on the modern view on a role of RNA interference machinery in regulation of genome expression, we suggest a mechanism of initiation of satellite DNA transcription and offer a novel interpretation of the 'classical' hypothesis that sought to explain the significance of widespread transcription during oocyte growth.

Centromeric tandem repeat from the chaffinch genome: isolation and molecular characterization.

A new family of avian centromeric satellites is described. The highly repeated sequence, designated FCP (Fringilla coelebs PstI element), was cloned from the 500-bp PstI digest fraction of the chaffinch (Fringilla coelebs L.) genomic DNA, sequenced, and characterized. The FCP repeat was found to have 505-506 bp length of monomer, 57% content of GC, to compose about 0.9% of the chaffinch genome, and to be highly methylated. Results of Southern-blot hybridization of cloned FCP element onto genomic DNA digested with different restriction enzymes, and sequencing directly from total genomic DNA using FCP-specific primers and ThermoFidelase enzyme (Fidelity Systems Inc.) were in agreement with a tandem arrangement of this repeat in the chaffinch genome. Five positions of single-nucleotide polymorphism (SNP) were found in the FCP monomers using direct genomic sequencing. Fluorescence in situ hybridization (FISH) with FCP probe and primed in situ labelling (PRINS) with FCP specific primers showed that the FCP elements occupy pericentric regions of all chaffinch chromosomes. On chromosome spreads, the fluorescent signals were also observed in the intercentromeric connectives between nonhomologous chromosomes. The results suggest that the centromeric FCP repeat is responsible for chromosome ordering during mitosis in chaffinch.

A highly repeated FCP centromeric sequence from chaffinch (Fringilla coelebs: Aves) genome is revealed within interchromosomal connectives during mitosis.

A highly repeated FCP (Fringilla coelebs PstI element) sequence was localized by FISH in centromeric regions of all chromosomes of the chaffinch. Besides, FISH signal was found also in interchromosomal connectives linking centromeres of non-homologous chromosomes in mitotic cells. The presence of DNA in the connectives was confirmed by immunostaining with anti-dsDNA antibodies as well as in experiments on nick-translation and random primed labeling in situ. Non-denaturing FISH with FCP probe and random primed labeling of non-denatured chromosomes resulted in fluorescence signal on both centromeres and intercentromeric connectives, thus providing evidence for the availability of single-strand DNA tracts in FCP sequence. It is suggested that the highly repeated FCP centromeric sequence may be respondible for interconnection of mitotic chromosomes and may by involved in nuclear architecture maintenance in the chaffinch.

Transcription of lampbrush chromosomes of a centromerically localized highly repeated DNA in pigeon (Columba) relates to sequence arrangement.

A highly repetitive, centromerically localized DNA sequence (PR1) has been isolated from the genomic DNA of two species of pigeon (Columba livia and C. palumbus). PR1 is approximately 900 bp long. It includes a sequence that is similar to the CENP-B box of mammals. It represents about 5% of the genome in C. livia and 2% in C. palumbus. In both species, tandem arrays of PR1 form part of larger repeating units. The organization of PR1 repeats and the larger repeating units is strikingly different in the two species. The large repeating units in C. livia include long (at least 14 units) tandem arrays of PR1 interspersed with relatively short intervening sequences. The large repeats of C. palumbus have much shorter (4 units or fewer) PR1 arrays interspersed with longer sections of non-PR1 DNA. PR1 is transcribed on short lampbrush loops in the centromeric regions of all lampbrush bivalents of C. palumbus. In C. livia, it is not transcribed at any of the major pericentromeric sites at which it is known to be present, although it is transcribed at one minor centromeric site on chromosome 2. It is proposed that transcription of the noncoding PR1 sequence on lampbrush chromosomes of pigeons relates to its genomic organization. The proposal is discussed with regard to the 'read-through' hypothesis for transcription on lampbrush loops.

Single stranded nucleic acid binding structures on chicken lampbrush chromosomes.

In chicken oocytes, proteins of the K/J family or their analogs, such as are known to be involved in mRNA processing in humans, are closely associated with nascent C-rich RNA transcripts on the loops of lampbrush chromosomes. Using labelled single stranded nucleotide probes and an antibody to protein K, these C-rich transcripts have been mapped to six different pairs of lampbrush loops situated on 3 macrochromosomes, the sex bivalent (ZW) and certain microchromosomes. Each of these loop pairs has a distinctive morphology. The observations represent cytological evidence of the connection between K-proteins and C-rich RNA transcripts. Another structure, the spaghetti marker of macrochromosome II, also preferentially binds C-rich homonucleotides. This spaghetti marker has a highly distinctive fine structural organization that is quite unlike that of lampbrush loops. Its proteins are not recognised by antibodies to protein K. Homonucleotide binding loops are recommended as potentially extremely valuable as markers on physical maps of chicken chromosomes.

The arrangement and transcription of telomere DNA sequences at the ends of lampbrush chromosomes of birds.

The arrangement of loops and chromomeres at the ends of lampbrush chromosomes in four species of bird is described with reference to chromomeres, loops and transcription units. Unlike the situation described in lampbrush chromosomes of amphibians, the lampbrush chromosomes of birds end in a terminal chromosome with conspicuous loops emerging from it. The fine-scale morphology of the ribonuclear protein matrix of these terminal loops is different from that of the majority of loops elsewhere on the chromosomes. In many cases the loops associated with the terminal chromomere are open ended, emerging from the chromomere but not returning to it at the other end. The distal ends of terminal open-ended loops therefore represent the true ends of the chromatids that make up a lampbrush half-bivalent. The pattern of binding of three telomeric DNA sequence probes to the terminal regions of bird lampbrush chromosomes, under conditions of DNA/DNA and DNA/RNA transcript in situ hybridization has been investigated by fluorescence in situ hybridization. All three probes gave the same results. With DNA/DNA and DNA/RNA transcript hybridization, three classes of structure were labelled: the terminal chromomere, a small number of interstitial chromomeres and the terminal transcription unit on telomere loops. Labelling of telomere loops, but not of terminal or interstitial chromomeres, was eliminated by ribonuclease treatment before in situ hybridization. The labelled regions of telomere loops were spaced away from the labelled terminal chromomere by an unlabelled sub telomeric transcription unit. After DNA/DNA in situ hybridization, no labelled loops were seen. DNA/RNA transcript in situ hybridization with single-stranded hexamers of each strand of telomeric DNA showed that the terminal transcription unit on telomere loops represents transcription exclusively from the C-rich strand of the repeat outwards towards the end of the chromosome. It is concluded that transcription specifically of the C-rich strand of strictly terminal clusters of telomere repeats is an obligatory event on the lampbrush chromosomes of birds and is unlikely to represent indiscriminate readthrough from proximally located gene elements.

Avian sex chromosomes in the lampbrush form: the ZW lampbrush bivalents from six species of bird.

The ZW bivalent has been identified and characterized in detail in its lampbrush form in oocytes of chicken, quail, turkey, pigeon, chaffinch and sparrow. The sex bivalent in all six species looks like a single highly asymmetrical chromosome. Most of it has the typical lampbrush organization. The terminal one-fifth is relatively thick and condensed and bears only a few pairs of lateral loops: this condensed terminal region is the W chromosome; the part with normal lampbrush morphology is the Z. The two are connected by a single near terminal chiasma. The fine scale morphology and arrangement of loops and markers on Z and W chromosomes are described for each species and lampbrush maps have been constructed. The identification of the lampbrush sex bivalent is based on the following criteria. The asymmetrical chromosome has two centromere regions. In the interstitial region of the asymmetrical chromosome where the junction between Z and W chromosomes is supposed to be, there are telomere-specific loops and telomeric DNA sequences and there is good morphological evidence for the presence of a chiasma. There are W chromosome specific DNA sequences in the region of the asymmetrical lampbrush chromosome that is thought to represent the W. Breed-specific variations in the morphology of the chicken W chromosome with respect to the sizes, numbers and arrangements of axial chromomeres and distributions of specified repeated DNA sequence families have been identified, offering one of the first examples of definitive correlation between a repeat family and a single chromomere. The lampbrush chromosomes of all the birds examined, except quail, terminate in distinctive free hanging loops. These are a novel feature in the sense that at the end of each chromatid there is a large transcription unit terminating in a cluster of telomeric DNA sequences.

A novel structure associated with a lampbrush chromosome in the chicken, Gallus domesticus.

At a site near the end of the short arms of lampbrush bivalent 2 in the chicken (Gallus domesticus) there is always a marker structure that appears in the phase-contrast light microscope as a solid object with diffuse edges measuring about 4 microns across. When examined by transmission electron microscopy in thin section, this object appears as a loose bundle of fibres. In some preparations individual fibres appear 15-16 nm thick, smooth in outline and solid in cross-section. In other preparations they are 32-38 nm thick, rougher in outline and ring-like in cross-section. High-resolution scanning electron micrographs of the chromosome 2 marker show it to be a loose bundle of spaghetti-like fibres that is quite unlike anything previously seen on a lampbrush chromosome of any organism. As with the sectioned material, fibres in some preparations were smooth and 15-16 nm in diameter, whereas those in others were more knobbly and about 35 nm thick. The fibres appear to branch and in some cases it is clear that the daughter strands of a branch have the same dimensions as the parent strand. Free ends are rare. Total length of fibre material present at one marker locus is estimated to be between 500 and 2000 microns. Similar structures are not present on the lampbrush chromosomes of quail, wood pigeon or chaffinch. The nature of this fibrous marker, referred to in this paper as the "spaghetti marker", is discussed in relation to lampbrush chromosome function and to events that take place during the lampbrush phase of oogenesis in chicken. Evidence is discussed in relation to the possibility that the chromosome 2 marker represents a novel form of nuclear RNP or the specific association of some structural protein with one chromosome locus.

Amplification of ribosomal genes and formation of extrachromosomal nucleoli in oocytes of starfish Henricia hayashi (Asteroidea: Echinasteridae).

DNA and RNA specific dyes, Ag-NOR staining and in situ hybridization were used for studying the nucleolar apparatus in the growing oocytes of Henricia hayashi (Asteroidea: Echinasteridae). A plasmid containing ribosomal genes of Drosophila melanogaster (Kolchinsky et al., 1980) labelled with 3H by nick-translation served as an rDNA probe. Multiple extrachromosomal nucleoli are formed by the cascade type as a result of growth and subsequent fragmentation of the chromosomal (primary) rDNA body and its derivative extrachromosomal (secondary) rDNA bodies. Ribosomal genes were shown in all nucleolar structures. Argentophilia of the primary and secondary DNA bodies appears to be due to the dense packing of the rDNA-containing material. Ag(+) NORs were detected in the extrachromosomal multiple nucleoli and NOR complexes. Amplification of rDNA is a highly probable conclusion from the existing data.