Molecular cloning of microdissected lampbrush loop DNA sequences of Drosophila hydei

Association of RB97D, an RRM protein required for male fertility, with a Y chromosome lampbrush loop in Drosophila spermatocytes

The Y chromosome of Drosophila melanogaster, which is required only for male fertility, contains six loci that are essential for spermatogenesis. In primary spermatocytes, three of these loci form large lampbrush loops containing RNA transcripts and associated proteins. The identities and functions of these Y chromosome loop-binding proteins are largely unknown. This report demonstrates that the RB97D protein, which is essential for spermatogenesis, bound to a specific lampbrush loop. RB97D contains two copies of a well-characterized RNA binding domain, the RNA recognition motif, followed by a proline-glutamine rich domain. Immunohistochemical and immunofluorescence experiments showed that in the testis, RB97D was found only in primary spermatocyte nuclei and associated with the C loop from the ks-1 fertility locus in an RNAse-sensitive manner. The anti-RB97D antibodies also bound a single Y chromosome loop in D. hydei, suggesting that the protein and its loop-binding function have been evolutionarily conserved. These results demonstrate that the proteins that bind lampbrush loops can be essential for fertility. Since RB97D was present only premeiotically, its function is likely to be directly related to the metabolism of the C loop transcripts.

Localized expression of a novel micropia-like element in the blastoderm of Drosophila melanogaster is dependent on the anterior morphogen bicoid

We have identified a novel transposon-like element of Drosophila melanogaster that is present in approximately 20 copies in the genome. It codes for a polyprotein containing the diagnostic sequence motifs for a nucleic acid binding CCHC protein, a proteinase, a reverse transcriptase and an integrase as typically found in retroviruses. Owing to its early expression in the blastoderm embryo, and its close relationship to micropia, a previously identified Drosophila retrotransposon, we termed the novel element "blastopia". The spatially restricted expression of blastopia transcripts in head anlagen of the blastoderm embryo is under the direct or indirect control of the Drosophila morphogen bicoid, which is normally required to establish the anterior pattern elements in the embryo. Our results suggest that a blastopia element acts as an "enhancer trap", and thereby participates in the control of an as yet unidentified gene normally expressed in the head anlagen of the embryo.

Partial reconstruction of the lampbrush loop pair Nooses on the Y chromosome of Drosophila hydei

We present the analysis of genomic DNA fragments that were isolated as potential segments of the lampbrush loop pair Nooses on the short arm of the Y chromosome of Drosophila hydei. More than 300 kb of DNA were recovered in BamHI lambda and cosmid clone groups. This DNA is composed of the Y-specific ay1 family of repetitive DNA sequences, and of other repetitive DNA sequences, which at least in part are also located elsewhere in the genome (Y-associated sequences). Two additional classes of DNA fragments were obtained from an EcoRI library. One of them consists of ay1 repeats without apparent interspersion, including a total of more than 300 kb of DNA. The other is composed of tandemly repeated YsI sequences, a Y-specific sequence derived from ay1. This class includes more than 400 kb of DNA, which is also not interspersed by other sequences. Our results show that only the ay1 repeats interspersed by Y-associated DNA sequences can represent parts of the 260 kb transcription unit forming the lampbrush loop, whereas the ay1 and YsI repeats without interspersion form separate and nontranscribed clusters of repetitive DNA.

Towards a physical map of the fertility genes on the heterochromatic Y chromosome of Drosophila hydei: families of repetitive sequences transcribed on the lampbrush loops Nooses and Threads are organized in extended clusters of several hundred kilobases

The understanding of structure and function of the so-called fertility genes of Drosophila is very limited due to their unusual size--several megabases--and their location on the heterochromatic Y chromosome. Since mapping of these genes has mainly been done by classical cytogenetic analyses using a small number of cytologically visible lampbrush loops as the sole markers for particular fertility genes, the resolution of the genetic map of the Y chromosome is restricted to 3-5 Mb. Here we demonstrate that a substantially finer subdivision of the megabase-sized fertility genes in the subtelomeric regions of the Y chromosome of Drosophila hydei can be achieved by a combination of digestion with restriction enzymes having 6 bp recognition sequences, and pulsed field gel electrophoresis. The physical subdivision is based upon large conserved fragments of repetitive DNA in the size range from 50 up to 1600 kb and refers to the long-range organization of several families of repetitive DNA involved in Y chromosomal transcription processes in primary spermatocytes. We conclude from our results that at least five different families of repetitive DNA specifically transcribed on the lampbrush loops nooses and threads are organized as extended clusters of several hundred kb, essentially free of interspersed non-repetitive sequences.

Drosophila spermatogenesis as a model system

Spermatogenesis is very similar throughout the animal kingdom and is probably based on very old evolutionarily principles. Drosophila can serve as a suitable model system to understand the underlying processes. The molecular and ultrastructural data obtained for Drosophila germ cell development can be applied to understanding spermatogenesis in other organisms, including humans. Various methods used in studies of Drosophila spermatogenesis are presented together with observations which exemplify this conclusion.

Microdissection and cloning of DNA from landmark loops of amphibian lampbrush chromosomes

Microdissection of the "globular" and "granular" landmark loops of Pleurodeles lampbrush chromosomes and subsequent cloning of their DNA yielded several recombinant clones. The 6.6-kb insert of one of them was subcloned and the 600 bp of one subclone was characterized by Southern and slot hybridizations as well as by sequencing. This sequence, designated p130B, was shown to belong to a class of moderately repetitive DNA. RNA expression of this sequence was investigated by in situ hybridization of p130B to the nascent transcripts of lateral loops. Results showed that: (1) the same transcripts were not always found in matrices of landmarks exhibiting the same morphological features; (2) the same transcripts were expressed in loops of different morphological types. Based on these results we suggest that even if there is a morphological similarity of landmark loops, this does not reflect total similarity of their transcripts.

Structural organization of Acheta rDNA. Evidence for differential amplification of soma and germ-line-specific rDNA sequences

Amplification is one of the mechanisms whereby the expression of genes can be specifically reinforced. Ribosomal gene amplification in amphibian and insect oocytes is a particularly well documented case. We studied heterogeneity, amplification and size of Acheta domesticus (insects; Orthoptera) ribosomal DNA and characteristics of male and female somatic or germ line rDNAs by analysis of genomic clones from a conventional and a microclone library. The length of the Acheta rDNA repeat unit (transcription unit and non-transcribed spacer (NTS] varied from 47 x 10(3) to 60 x 10(3) base-pairs, with highest variability within the NTS region. Deletions, fragment length heterogeneity and size variability in small steps of individual NTS segments are responsible for the observed size variation. The number of rDNA repeat units per haploid genome of Acheta was determined as 190(+/- 10%). The rDNA is amplified 14(+/- 10%)-fold in the oocyte, producing about 10,000 gene copies per cell. Our results show that the amplification mechanism does not favor individual fragments within the repeat unit. Thus, it can be concluded that amplification does not change the chromosomal characteristics of the rDNA pool. Two fragments specific for oocyte rDNA suggest that the rearrangements accompanying amplification are preferentially located in one distinct EcoRI fragment. Certain regions of Acheta rDNA contain cell-type-specific fragments: it was thus possible to characterize one purely male fragment and a second one specific for male and female soma but not for germ line rDNA. We show that Acheta rDNA reveals a combination of many features reported from different organisms and novel tissue-specific alterations on an extremely large repeat unit. The tissue-specific alterations indicate sexual and soma/germ line differentiation events that are derived by as yet unknown mechanisms.

Poly[d(C-A)].poly[d(G-T)] is highly transcribed in the testes of Drosophila hydei

Microdissection of the lampbrush loops "threads" and "pseudonucleolus" of Y chromosomes from primary spermatocytes of Drosophila hydei and subsequent microcloning of the DNA yielded several recombinant DNA clones which cross-hybridized in screening the different clone banks. By DNA sequencing we found that the inserts of these cross-hybridizing clones contain blocks of poly[d(C-A].poly[d(G-T)]. Testis RNA contains a large fraction of transcripts with this simple repeated nucleotide sequence. With the aid of transcript in situ hybridization we discovered that the "cones" and "pseudonucleolus" lampbrush loops are the primary sites of transcription of poly[d(C-A)].poly[d(G-T)] in spermatocytes. In addition, we found a strand-specific transcription of (CA/GT)n. In both the "cones" and "pseudonucleolus" the (CA)n strand is transcribed, while in the "pseudonucleolus" (GT)n is also transcribed. Labelled (CA)n probes also react with the protein bodies in spermatid nuclei. These observations are discussed in the context of possible functions of (CA/GT)n transcripts in spermatogenesis.

DNA sequence comparison of micropia transposable elements from Drosophila hydei and Drosophila melanogaster

Members of the retrotransposon family micropia were discovered as constituents of wild-type Y chromosomal fertility genes from Drosophila hydei. Several members of the micropia family have subsequently been recovered from Drosophila melanogaster and four micropia elements, micropia-DhMiF2, -DhMiF8, -Dm11 and -Dm2, two each from D. hydei and D. melanogaster, have been totally sequenced (17 kb of micropia sequences and 6.8 kb from insertions). Comparative analysis of micropia sequences revealed a complex pattern of divergence within a single Drosophila genome. The divergence includes deletions, possibly by a slipped mispairing mechanism, insertions of a retroposon, and of another retrotransposon (copia) and "positional nucleotide shuffling" within the tandem repeats of the 3' non-protein-coding region of micropia elements. A 10 bp long sequence of each repeat unit of the 3' tandem repeats of micropia elements is highly conserved and is therefore a candidate of functional importance either in transposition events or in regulatory activity on flanking DNA sequences.

Telomeric sequences derived from laser-microdissected polytene chromosomes

Telomeric fragments from salivary gland squashes of Drosophila melanogaster Oregon R. were produced by a new microdissection technique, UV laser microbeam dissection. Microdissection, an essential step in microcloning procedures, is usually performed using micromanipulators and microneedles. Recently it has been shown that microdissection can be improved to very high precision if a laser coupled into a microscope is used. A laser microbeam, generated by an excimer pumped dye laser, allows chromosomes to be cut into slices of less than 0.5 micron. Here it is shown, that single copy DNA probes prepared from Drosophila chromosomes by laser microdissection and microcloning relocalize to the chromosomal regions from which they are derived. The combination of laser technique and microcloning provides an advantageous approach for rapid genetic analysis with potential for the study of genetic diseases and genome mapping.

Characterization of the long terminal repeats of micropia elements microdissected from the Y-chromosomal lampbrush loops "threads" of Drosophila hydei

Four micropia elements from Drosophila melanogaster and D. hydei have been analysed by sequencing. Two elements, from D. hydei, micropia-DhMiF8 and -DhMiF2, were recovered by cloning microdissected Y-chromosomal lampbrush loops "threads". This method allows isolation of repetitive sequences from defined chromosomal positions, but recovery of large and overlapping inserts is difficult. In case of the Y-chromosomal micropia elements it was not possible to define the endpoints of their long terminal repeat sequences precisely. Comparison of these locus-defined micropia elements to complete micropia elements isolated from D. melanogaster allowed identification of micropia-DhMiF8 and micropia-DhMiF2 long terminal repeats (LTRs). LTR sequences from the two Drosophila species are not conserved except for a few short sequences found at comparable positions that are believed to have functional significance. In contrast, the Leu-tRNA primer binding site and plus strand primer binding site are conserved between D. melanogaster and D. hydei.

An abundant testis RNA species shows sequence similarity to Y chromosomal and other genomic sites in Drosophila hydei

A cDNA clone bank was constructed from testis poly(A)+ RNA of Drosophila hydei and screened for clones which hybridize to Y chromosomal DNA sequences. The insert of clone cDhT14 hybridizes to a family of repeated DNA sequences with members distributed within the Y chromosome and elsewhere in the genome. This type of sequence has earlier been described as the Y-associated class of DNA. Southern blot analysis of DNA from different wild-type strains of D. hydei suggests that members of the T14 family of repeated DNA sequences are parts of a family of transposable elements. The genomic localization of the T14 family of repeated DNA sequences was revealed by in situ hybridization to metaphase and polytene chromosomes, and to transcripts of Y chromosomal lampbrush loops. Approximately 10-15 members (20%-30%) of the T14 sequence family reside in 8.3 kb PstI restriction fragments. A genomic clone of one of these DNA fragments, DhT14-8.3, hybridizes to transcripts on the Y chromosomal lampbrush loop "cones", and in conventional in situ hybridization experiments to region 12D/13A of the X chromosome and to region 112 of chromosome 5. The cDNA clone cDhT14 represents a part of an abundant testis RNA species of 5.0 kb. This RNA is also present in ovaries and in 0-3 h, 3-6 h and 6-12 h embryos, but less abundantly than in testes. Both the Y chromosomal site of the 8.3 kb PstI fragments and sites elsewhere in the genome are actively transcribed. At least one of the latter genomic sites is transcribed into the 5.0 kb RNA species.(ABSTRACT TRUNCATED AT 250 WORDS)

Micropia: a retrotransposon of Drosophila combining structural features of DNA viruses, retroviruses and non-viral transposable elements

The retrotransposon micropia was first described from Y-chromosomal fertility genes of Drosophila hydei. Screening a Drosophila melanogaster genomic library yielded several clones representing micropia elements in D. melanogaster. The DNA sequences of two elements from D. hydei (micropia-DhMiF2 and micropia-DhMiF8) and two elements from D. melanogaster (micropia-Dm2 and micropia-Dm11) permitted a detailed analysis of the spatial organization of micropia constituents. Micropia represents the typical gene organization represented by "core"-protein domains followed by a protease, reverse transcriptase, RNase and integrase domain. New features of the micropia family compared with other retrotransposons are: (1) a region of similarity to class I major histocompatibility complex antigens of mammals; (2) only one main open reading frame of about 4000 bases length; (3) a non-protein-coding region of about 500 base-pairs length between the 3' end of the open reading frame and the 5' start of the 3' long terminal repeat. This region includes 32 base-pair tandem repeats; (4) within the long terminal repeats, 82 base-pair tandem repeats with four potential ecdysteroid receptor binding sites. Because micropia combines many evolutionary features of different viruses, non-viral transposable elements, chromosomal genes and repetitive sequence organizations, this retrotransposon may be seen as a "minigenome" reflecting evolutionary principles of the construction of genomic components.

Retrotransposon-like sequences are expressed in Y chromosomal lampbrush loops of Drosophila hydei

The DNA sequence family micropia consists of repeated DNA sequences that occur dispersed in the genome of Drosophila hydei. Members of this DNA sequence family were recovered from two recombinant DNA clone banks obtained by microdissection of the two Y chromosomal lampbrush loop threads and pseudonucleolus from primary spermatocyte nuclei. Nucleotide sequence analysis of two of the recombinant DNA clones revealed homology to the DNA region coding for a reverse transcriptase-like protein in retroviruses and retrotransposons. Homologous tissue-specific transcripts of a size of 1.2 x 10(3) base-pairs were found in testes. Transcript in-situ hybridization shows that at least parts of these transcripts are synthesized in these Y chromosomal lampbrush loops, which were originally used for microdissection. Also the cytoplasm of primary spermatocytes contains homologous RNA species. These observations are discussed in the context of lampbrush loop function and evolution.

Structure and function of Y chromosomal DNA. II. Analysis of lampbrush loop associated transcripts in nuclei of primary spermatocytes of Drosophila hydei by in situ hybridization using asymmetric RNA probes of four different families of repetitive DNA

pSP64/65 subclones of four different families of repetitive sequences on the Y chromosome of Drosophila hydei were used for in vitro synthesis of labelled RNA. Pairs of RNA probes of opposite strand polarity were employed to analyse RNAs transcribed on, or associated with, various Y chromosomal lampbrush loops in nuclei of primary spermatocytes of D. hydei. The results of RNA filter analysis and in situ hybridization experiments can be generalized as follows: (1) Y-specific transcripts are heterogeneous in length and are synthesized on lampbrush loops. (2) Transcription of tandemly repeated sequences is usually strand specific. (3) Members of the same sequence family can be found in transcripts from different lampbrush loops. (4) Transcripts not coded by the Y chromosome are accumulated on different subregions of Y chromosomal lampbrush loops.

Structure and function of Y chromosomal DNA. I. Sequence organization and localization of four families of repetitive DNA on the Y chromosome of Drosophila hydei

The sequence organization of four different families of Y chromosomal repetitive DNA is characterized at three levels of spatial extension along the Y chromosome of Drosophila hydei. At the lowest level of resolution, DNA blot analysis of Y chromosomal fragments of different lengths and in situ hybridization experiments on metaphase chromosomes demonstrate the clustering of each particular sequence family within one defined region of the chromosome. At a higher level of resolution, family specific repeats can be detected within these clusters by crosshybridization within 10-20 kb long continuous stretches of cloned DNA in EMBL3 phages. At the highest level of resolution, detailed sequence analysis of representative subclones about 1 kb in length reveals a satellite-like head to tail arrangement of family specific degenerated subrepeats as the building scheme common to all four families. Our results provide the first comparative sequence analysis of three novel families of repetitive DNA on the long arm of the Y chromosome of D. hydei. Additional data are presented which support the existence of two related subfamilies of repetitive DNA on the short arm of the Y chromosome.

Evolution of Y chromosomal lampbrush loop DNA sequences of Drosophila

The evolutionary conservation of Y chromosomal DNA sequences of Drosophila hydei in different species of the genus Drosophila was studied by in situ hybridization and on genomic DNA blots of restriction enzyme digested DNA. We demonstrated that Y specific DNA sequences, which form major parts of lampbrush loops related to the male fertility genes, are only retained in a few closely related species during evolution. Other Y chromosomal DNA sequences, also present in lampbrush loops but with homology to autosomal and X chromosomal locations, were found in distant species. We propose a model for the evolution of the Y chromosomal lampbrush loops.