Differential chromosomal distribution of ribonucleoprotein antigens in nuclei of Drosophila spermatocytes

The regulation and potential functions of intronic satellite DNA

Satellite DNAs are arrays of tandem repeats found in the eukaryotic genome. They are mainly found in pericentromeric heterochromatin and have been believed to be mostly inert, leading satellite DNAs to be erroneously regarded as junk. Recent studies have started to elucidate the function of satellite DNA, yet little is known about the peculiar case where satellite DNA is found within the introns of protein coding genes, resulting in incredibly large introns, a phenomenon termed intron gigantism. Studies in Drosophila demonstrated that satellite DNA-containing introns are transcribed with the gene and require specialized mechanisms to overcome the burdens imposed by the extremely long stretches of repetitive DNA. Whether intron gigantism confers any benefit or serves any functional purpose for cells and/or organisms remains elusive. Here we review our current understanding of intron gigantism: where it is found, the challenges it imposes, how it is regulated and what purpose it may serve.

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.

Gene regulation in Drosophila spermatogenesis: analysis of protein binding at the translational control element TCE

We have previously identified a 12 nucleotide long sequence element, the TCE, that was demonstrated to be necessary for translational control of expression in the male germ line of Drosophila melanogaster (Schäfer et al., 1990). It is conserved among all seven members of the Mst(3)CGP gene family, that encode structural proteins of the sperm tail. The TCE is invariably located in the 5' untranslated region (UTR) at position +28 relative to the transcription start site. In this paper we analyse the mode of action of this element. We show that protein binding occurs at the TCE after incubation with testis protein extracts from Drosophila melanogaster. While several proteins are associated with the translational control element in the RNA, only one of these proteins directly crosslinks to the sequence element. The binding activity is exclusively observed with testis protein extracts but can be demonstrated with testis extracts from other Drosophila species as well, indicating that regulatory proteins involved in translational regulation in the male germ line are conserved. Although binding to the TCE can occur independent of its position relative to the transcription start site of the in vitro transcripts, its function in vivo is not exerted when shifted further downstream within the 5' UTR of a fusion gene. In addition to being a translational control element the TCE also functions as a transcriptional regulator. Consequently, a DNA-protein complex is also formed at the TCE. In contrast to the RNA-protein complexes we find DNA-protein complexes with protein extracts of several tissues of Drosophila melanogaster.

Isolation of hnRNP complexes from Drosophila melanogaster

Nascent RNA polymerase II transcripts, heterogeneous nuclear RNAs (hnRNAs), become associated with nuclear proteins (hnRNP Proteins), and their processing into mRNAs takes place in these hnRNP complexes. hnRNP complexes have previously been purified from vertebrate cells. Here we report the isolation of hnRNP complexes from an invertebrate organism, the fruitfly Drosophila melanogaster. Candidate hnRNP proteins were purified from D. melanogaster embryos by ssDNA affinity chromatography, and mAbs were produced to many of the major proteins. Genuine hnRNP proteins were identified by several criteria, including nucleoplasmic localization, association with nascent transcripts, crosslinking to poly(A)-containing RNA in living cells, and amino acid sequence. In addition, mAbs that cross-react between the fruitfly and human hnRNP proteins were obtained. Most importantly, using hnRNP-specific mAbs we have purified the hnRNP complexes from D. melanogaster cells. These RNAase-sensitive complexes contain at least 10 major proteins designated hrps, the most abundant proteins having apparent molecular masses of 36, 38, 39, 40, 44, 48, 54, 62, 70, and 75 kD. cDNAs and complete sequences for several of these proteins have been obtained and are presented in the accompanying paper (Matunis, E. L., M. J. Matunis, and G. Dreyfuss. 1992. J. Cell Biol. 116:257-269). The purification of D. melanogaster hnRNP complexes will facilitate genetic and cytological studies on the function of hnRNA-binding proteins and on the posttranscriptional regulation of gene expression.

Genetic and cytogenetic analysis of the "Th-Ps" region of the Y chromosome of Drosophila hydei: evidence for dual functions of the lampbrush loop-forming fertility genes?

Two competing hypotheses have been proposed for the function of the Y chromosomal fertility factors in Drosophila, which form giant lampbrush loops during the primary spermatocyte stage. The first hypothesis suggests a conventional coding function, the second proposes an unconventional gene function mediated through protein binding by nascent transcripts. Therefore, we studied the genetics and cytogenetics of the two Y chromosomal fertility genes A and C of Drosophila hydei (which form the lampbrush loops threads and pseudonucleolus) in order to test the validity of these different hypotheses. Both lampbrush loops bind specific proteins, which are recognized by different antisera. Absence of either of the lampbrush loops does not interfere with the synthesis of the antigens but completely prevents the binding of the particular antigen to other lampbrush loops. Absence of the loops also does not interfere with the postmeiotic presence and localization of the particular antigen. Deletion (or inactivation) of either of the lampbrush loops threads or pseudonucleolus causes sterility of the male flies as do other male-sterile alleles of both fertility genes, which do not affect the morphology of the lampbrush loops. The phenotypic effects of these mutations on sperm morphogenesis are identical for all various male-sterile alleles of each of the fertility genes A and C, regardless of whether a particular allele leaves the loop intact, modifies that loop, or deletes (or inactivates) the loop completely. Finally, the isolation of fertile Y chromosomal mutations which modify the morphology of the lampbrush loops demonstrates that it is possible to uncouple loop morphology and genetic function. These findings do not support the hypothesis that the binding of proteins to a lampbrush loop has a substantial impact on spermiogenesis.

Higher order structure of Balbiani ring premessenger RNP particles depends on certain RNase A sensitive sites

Specific premessenger ribonucleoprotein (RNP) particles, the Balbiani ring (BR) granules from Chironomus tentans salivary glands, were treated with RNase A to study the effect of RNA strand breaks on the higher order structure of the particles. Isolated, radioactively labeled BR granules, known to sediment at 300 S, were digested with RNase A and centrifuged in sucrose gradients. The fractionated particles were subsequently analyzed using electron microscopy and caesium chloride centrifugation. At a low RNase concentration, most of the 300 S particles disintegrated completely, and no metastable degradation products were observed. At intermediate RNase concentrations, no 300 S particles were left, but a minor fraction of the BR granules had unfolded and sedimented at 160 S. These granules could represent particles modified during the RNase treatment or represent a more slowly degrading subfraction of the particles. At a high RNase concentration, no RNP particles at all remained in the gradient. The rapid disintegration of the majority of the BR granules was investigated further by electrophoretic analysis of RNA in the remaining particles. During the RNase treatment BR granules, still sedimenting at 300 S, accumulated strand breaks; in fact, as many as 50 to 100 nicks in the 37 kb RNA could be tolerated. It was concluded from RNA analyses that the disintegration of the BR granules was not dependent on any single nick in the RNA, nor on the accumulation of a certain number of nicks, but rather on one or a few critical strand breaks. We propose that there are organizing sequences essential for particle integrity; once these sequences are nicked, the premessenger RNP particles are rapidly and completely degraded.

Multiple modifications in the phosphoproteins bound to stored messenger RNA in Xenopus oocytes

Messenger RNA molecules accumulated in amphibian oocytes are stabilized and blocked from translation through association with a defined set of phosphoproteins. Phosphoproteins of 60 kDa and 56 kDa (pp60 and pp56) isolated from messenger ribonucleoprotein particles of Xenopus laevis oocytes can be bound in vitro to mRNA sequences. After phospholabelling in vitro, both pp60 and pp56 show a range of ionic forms, which resolve on two-dimensional gel electrophoresis as a series of pairs with identical charge. The similarities between pp60 and pp56 in their ionic properties suggest a common protein primary structure. This suggestion gains further support from proteinase digestion analysis of pp60 and pp56: practically identical size patterns of phospholabelled fragments are generated using a range of different proteinases. However, in spite of their structural similarities, pp60 and pp56 are recognised as antigenically distinct from each other by using polyclonal antibodies. It is concluded from these, and other, observations that pp60 and pp56 are members of a family of structurally similar polypeptides which are subjected to multiple secondary modifications. Of these modifications, phosphorylation appears to be instrumental in establishing tight binding to mRNA, while antigenicity appears to be determined by some other modification. The role of microheterogeneity in the structure of RNA-binding proteins is discussed in relation to the differential activation of mRNA sequences for translation during early development.

Molecular organization of RNP complexes containing P11 antigen in heat-shocked and non-heat-shocked Drosophila cells

Immunofluorescence analysis of polytene chromosomes of Drosophila melanogaster using the monoclonal antibody P11 has shown that after heat-shock the 38-kDa P11 antigen almost exclusively localizes at heat-shock puff 93D where it is part of giant puff-specific RNP granules. The biochemical experiments reported here show that, independent of growth temperature, the P11 antigen is a component of nuclear 10S RNP particles. The P11-containing 10S snRNPs can be stabilized in CsCl with 20 mM Mg2+ and possess a buoyant density of rho = 1.4 g/cm3. Sucrose gradient analysis of nuclear RNP extracts of heat-shocked Schneider's S-3 tissue culture cells shows that, after a 37 degree C heat-shock, the 10S RNPs associate with large RNP complexes sedimenting at 170-220S. The change in distribution is a temperature-dependent process with intermediate forms at 29 degrees C and 33 degrees C. In thermotolerant cells this observed change in distribution is strongly reduced. DEAE-Sephacel column chromatography and sucrose gradient analysis of nuclear RNP, followed by Northern blot analysis using 93D-specific probes of the TaqI repeat and immunoblotting experiments, show that the P11-containing 10S snRNPs are distinct from the RNP complexes formed by the 93D transcripts, suggesting an indirect association after heat-shock. Our experiments demonstrate that, despite the fact that a 37 degrees C heat-shock does not affect the overall integrity of nuclear RNP, it imposes changes on the general organization and interaction of the nuclear RNP population, resulting in the formation of large nuclear RNP aggregates and complexes. Such changes may be important for the survival strategy of the cell and for hnRNA processing and storage events which are effected by heat-shock.

Ribonucleoproteins package 700 nucleotides of pre-mRNA into a repeating array of regular particles

An assay for the in vitro assembly of HeLa cell 40S nuclear ribonucleoprotein particles (hnRNP particles) has been developed. The substrates were single-stranded nucleic acid polymers of defined length and sequence prepared in vitro and the six major core particle proteins from isolated 40S hnRNP. The fidelity of in vitro assembly was evaluated on various physical parameters, including sedimentation, salt dissociation, polypeptide stoichiometry, UV-activated protein-RNA cross-linking, and overall morphology. Correct particle assembly depended on RNA length and on the input protein/RNA ratio but not on the concentration of the reactant mixture nor on the presence or absence of internal RNA processing signals, a 5'-cap structure, a 3'-poly(A) moiety, or ATP as energy source. RNA lengths between 685 and 726 nucleotides supported correct particle assembly. Dimers and oligomeric complexes that possessed the same polypeptide stoichiometry as native hnRNP assembled on RNA chains that were integral multiples of 700 nucleotides. Intermediate-length RNA supported the assembly of nonstoichiometric complexes lacking structural homogeneity. An analysis of these complexes indicates that proteins A1 and A2 may be the first proteins to bind RNA during particle assembly. We conclude that the major proteins of 40S hnRNP particles contain the necessary information for packaging nascent transcripts into a repeating "ribonucleosomal" structure possessing a defined RNA length and protein composition but do not themselves contain the information for modulating packaging that may be required for RNA splicing.

Ribonucleoproteins package 700 nucleotides of pre-mRNA into a repeating array of regular particles

An assay for the in vitro assembly of HeLa cell 40S nuclear ribonucleoprotein particles (hnRNP particles) has been developed. The substrates were single-stranded nucleic acid polymers of defined length and sequence prepared in vitro and the six major core particle proteins from isolated 40S hnRNP. The fidelity of in vitro assembly was evaluated on various physical parameters, including sedimentation, salt dissociation, polypeptide stoichiometry, UV-activated protein-RNA cross-linking, and overall morphology. Correct particle assembly depended on RNA length and on the input protein/RNA ratio but not on the concentration of the reactant mixture nor on the presence or absence of internal RNA processing signals, a 5'-cap structure, a 3'-poly(A) moiety, or ATP as energy source. RNA lengths between 685 and 726 nucleotides supported correct particle assembly. Dimers and oligomeric complexes that possessed the same polypeptide stoichiometry as native hnRNP assembled on RNA chains that were integral multiples of 700 nucleotides. Intermediate-length RNA supported the assembly of nonstoichiometric complexes lacking structural homogeneity. An analysis of these complexes indicates that proteins A1 and A2 may be the first proteins to bind RNA during particle assembly. We conclude that the major proteins of 40S hnRNP particles contain the necessary information for packaging nascent transcripts into a repeating "ribonucleosomal" structure possessing a defined RNA length and protein composition but do not themselves contain the information for modulating packaging that may be required for RNA splicing.

Protein kinase activity associated with stored messenger ribonucleoprotein particles of Xenopus oocytes

As the oocytes of Xenopus laevis grow and develop they accumulate vast stores of mRNA for use during early embryogenesis. The stored mRNA is stabilized and may be prevented from being translated in oocytes by the binding of a defined set of oocyte-specific proteins to form messenger RNP (mRNP) particles. A key event in the interaction of protein with mRNA is the phosphorylation of those few polypeptides that bind directly to all classes of polyadenylated mRNA. In this study we show that the phosphorylating enzyme (protein kinase), in addition to its target phosphoproteins, is an integral component of the mRNP particles. This association extends through various stages in the formation and use of the mRNP particles. Examination of material from oocytes of an early developmental stage (early stage 1), when the level of accumulated mRNA is low, reveals an excess of protein particles free of RNA, sedimenting at 6-18 S, and containing protein kinase activity and mRNA-binding phosphoproteins. At stages of maximum rate of mRNA accumulation (stages 1 and 2), the phosphoproteins and kinase are found primarily in individual mRNP particles that sediment at 40-80 S. As ribosomes become abundant (stages 2 and 3), the mRNP particles tend to interact with ribosomal subunits, at least in vitro, to form blocked translation initiation complexes that sediment at 80-110 S. These results are compared with observation on stored mRNP in other developmental systems.

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.

Phosphorylation of a 60 kDa polypeptide from Xenopus oocytes blocks messenger RNA translation

The stored mRNP particles of Xenopus oocytes contain protein kinase activity and two major phosphoproteins of 60 kDa (pp60) and 56 kDa (pp56). These proteins can be phospholabelled in the particles either in vivo or in vitro and then isolated by SDS-PAGE. On renaturing pp60 in the presence of globin mRNA, a stable RNA-protein complex is formed. The complex has a uniform density in Cs salt gradients, corresponding to the binding of about 10 protein molecules to each mRNA, probably at the poly(A) sequence. Compared with uncomplexed mRNA, the RNP complex is translated poorly both in vitro and in vivo. Translation of the complex can be regained after treatment with protein phosphatase. It is shown that dephosphorylation destabilizes the binding of protein to RNA, making the mRNA accessible for translation. Studies with native mRNP particles show that their translation also can be enhanced by dephosphorylation.

The 19S ring-type particles of Drosophila. Cytological and biochemical analysis of their intracellular association and distribution

The intracellular distribution and interaction of 19S ring-type particles from D. melanogaster have been analysed. Immunological and biochemical analyses show that the 19S particles are of a predominant cytoplasmic origin. Immunofluorescence experiments, using the particle-specific antibody Dm28K2, reveal a characteristic speckled cytoplasmic fluorescence pattern. Investigation of different biochemically isolated, cytoplasmic subfractions by sucrose gradient centrifugation and immunoblotting show that the 19S particles can exist as 'free' unbound structures as well as in association with Triton-X-100-extractable polyribosomal fractions. The tight association with the polyribosomes can only be broken by extraction of the polysomes in EDTA, which releases the particles as whole entities. The data suggest that the 19S ring-type particles of Drosophila may represent a new class of scRNPs involved in translational processes.