Education and employment patterns of U.S. Ph.D.'s in the biomedical sciences

During most of the 1970s and 1980s, the number of biomedical Ph.D.'s conferred in the United States was fairly constant. From 1987 to 1995, however, there was an increase of almost 50% in the number of biomedical Ph.D.'s awarded by U.S. institutions; nearly 70% of this increase can be accounted for by the increase in the number of noncitizens receiving a Ph.D. in the U.S. Although unemployment among U.S. citizens with biomedical Ph.D.'s is now extremely low--less than 2.0%--there have been some important changes in the job market for biomedical Ph.D.'s. The total number of biomedical scientists has grown, whereas the number of faculty positions has remained stable, causing a decline in faculty positions as a percentage of total employment for biomedical scientists. Jobs in industry have increased, and in the future might surpass academic jobs as the most prevalent form of employment for U.S. biomedical scientists.

Discrete start sites for DNA synthesis in the yeast ARS1 origin

Sites of DNA synthesis initiation have been detected at the nucleotide level in a yeast origin of bidirectional replication with the use of replication initiation point mapping. The ARS1 origin of Saccharomyces cerevisiae showed a transition from discontinuous to continuous DNA synthesis in an 18-base pair region (nucleotides 828 to 845) from within element B1 toward B2, adjacent to the binding site for the origin recognition complex, the putative initiator protein.

Replication initiation point mapping

Replication in eukaryotes is bidirectional and semi-discontinuous. This asymmetry provides the basis for mapping the origin of bidirectional replication (OBR), which is the transition point from discontinuous to continuous synthesis. The regions of each DNA strand complementary to the leading strand or lagging strand can be measured by the methods of imbalanced DNA synthesis or Okazaki fragment distribution, respectively. The resolution of both of these hybridization-based procedures is a few hundred base pairs. Nucleotide resolution was previously achieved for viral origins by mapping the initiation sites of Okazaki fragments on sequencing gels. To overcome the background caused by nicked DNA, all DNA ends were phosphorylated, RNA primers were removed from the Okazaki fragments by NaOH hydrolysis, and the hydroxyl ends thus created were phosphorylated with 32P. Unfortunately, this method was not sensitive enough to map eukaryotic cellular origins. A new method, replication initiation point (RIP) mapping, that is 1000-fold more sensitive and has been applied to yeast ARS1 where the OBR is mapped to and 18-bp region from within element B1 toward B2 is described here. RIP mapping utilizes Vent (exo-) polymerase to extend from a labeled primer to the DNA/RNA junctions of nascent strand template in an asynchronous population of replicating molecules. The DNA is digested with lambda-exonuclease prior to primer extension to remove nicked contaminating DNA.

U3 snoRNA may recycle through different compartments of the nucleolus

A model is proposed in which U3 small nucleolar RNA (snoRNA) is recruited from an inactive, stored form in the dense fibrillar component (DFC) of the nucleolus to an active form that is associated with the initial ribosomal RNA (rRNA) precursor. The initial steps of rRNA processing occur in the DFC, and then it is proposed that the U3 snoRNA moves with intermediates in rRNA processing from the DFC to the granular component (GC) of the nucleolus. The nucleolar protein fibrillarin is located primarily in the DFC, and it is suggested that the complex of fibrillarin and U3 snoRNA dissociates when U3 snoRNA transits to the GC. Finally, when U3 snoRNA is released from the processed rRNA, the tether holding the rRNA in the nucleolus is broken and rRNA can then be exported from the nucleolus to the cytoplasm. U3 snoRNA is hypothesized to recycle back from the GC to the DFC where it is stored until future association with another initial rRNA precursor. Data supporting this model are summarized. U3 snoRNA is also stored in the coiled body of interphase cells and in the nucleolar remnants and prenucleolar bodies of mitotic cells, and there may be some similarity in the binding sites for stored U3 snoRNA in the DFC and in these structures.

Delocalization of some small nucleolar RNPs after actinomycin D treatment to deplete early pre-rRNAs

Retention of some components within the nucleolus correlates with the presence of rRNA precursors found early in the rRNA processing pathway. Specifically, after most 40S, 38S and 36S pre-rRNAs have been depleted by incubation of Xenopus kidney cells in 0.05 microg/ml actinomycin D for 4 h, only 69% U3 small nucleolar RNA (snoRNA), 68% U14 snoRNA and 72% fibrillarin are retained in the nucleolus as compared with control cells. These nucleolar components are important for processing steps in the pathway that gives rise to 18S rRNA. In contrast, U8 snoRNA, which is used for 5.8S and 28S rRNA production, is fully retained in the nucleolus after actinomycin D treatment. Therefore, U8 snoRNA is in a different category than U3 and U14 snoRNA and fibrillarin. It is proposed that U3 and U14 snoRNA and fibrillarin, but not U8 snoRNA, bind to the external transcribed spacer or internal transcribed spacer 1, and when these binding sites are lost after actinomycin D treatment some of these components cannot be retained in the nucleolus. Other binding sites may also exist, which would explain why only some and not all of these components are lost from the nucleolus.

Small nucleolar RNA

A growing list of small nucleolar RNAs (snoRNAs) has been characterized in eukaryotes. They are transcribed by RNA polymerase II or III; some snoRNAs are encoded in the introns of other genes. The nonintronic polymerase II transcribed snoRNAs receive a trimethylguanosine cap, probably in the nucleus, and move to the nucleolus. snoRNAs are complexed with proteins, sometimes including fibrillarin. Localization and maintenance in the nucleolus of some snoRNAs requires the presence of initial precursor rRNA (pre-rRNA). Many snoRNAs have conserved sequence boxes C and D and a 3' terminal stem; the role of these features are discussed. Functional assays done for a few snoRNAs indicate their roles in rRNA processing for cleavage of the external and internal transcribed spacers (ETS and ITS). U3 is the most abundant snoRNA and is needed for cleavage of ETS1 and ITS1; experimental results on U3 binding sites in pre-rRNA are reviewed. 18S rRNA production also needs U14, U22, and snR30 snoRNAs, whereas U8 snoRNA is needed for 5.8S and 28S rRNA production. Other snoRNAs that are complementary to 18S or 28S rRNA might act as chaperones to mediate RNA folding. Whether snoRNAs join together in a large rRNA processing complex (the "processome") is not yet clear. It has been hypothesized that such complexes could anchor the ends of loops in pre-rRNA containing 18S or 28S rRNA, thereby replacing base-paired stems found in pre-rRNA of prokaryotes.

Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method

The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.

Developmental progression of DNA puffs in Sciara coprophila: amplification and transcription

DNA amplification for two major DNA puffs (II/2B and II/9A) of the fungus fly Sciara coprophila increases steeply from 17 to 19 days after hatching (18 degrees C), resulting in almost 20-fold more DNA at these loci in mature larval salivary glands than in adult tissues. At 19 days after hatching when gene amplification reaches a plateau, there is a burst in the amount of mRNA encoded by these two DNA puffs. Expansion of the two puffs coincides with the increase in transcription rather than reinitiation of DNA replication. In contrast, an RNA puff (III/9B) undergoes no DNA amplification, and the burst in RNA produced by this locus occurs slightly later, at 20 days after hatching. The progression of cytological puffing and associated molecular events of DNA amplification and transcription correlate with features of the external phenotype of the larvae, especially the number of pigment granules in the eyespots that are the anlage to the adult eyes. The sequential and coordinated regulation of DNA puff replication and transcription is discussed.

Replication initiates at a confined region during DNA amplification in Sciara DNA puff II/9A

Two independent two-dimensional (2D) gel methods were used to map an origin of replication that is developmentally regulated by the steroid hormone ecdysone, namely an origin for DNA puff amplification in the fungus fly Sciara coprophila. Initiation of replication was found to occur within a small region of no larger than 6 kb by use of the neutral/neutral 2D gel method. Neutral/alkaline 2D gel analyses support the results of the neutral/neutral 2D gels and further define within the origin region an approximately 1-kb area where the majority of replication initiates. This is the first example of an origin of replication in multicellular eukaryotes that has been mapped by 2D gels to such a small defined region. Moreover, replication can be seen by the neutral/alkaline 2D gel method to proceed bidirectionally outward from this replication origin region. These data are consistent with an onion-skin mechanism whereby multiple rounds of DNA replication initiate at a specific origin of replication for Sciara DNA puff amplification.

Genes for Xenopus laevis U3 small nuclear RNA

Genomic Southern blots showed there are only 14 to 20 copies of U3 snRNA genes per somatic genome in Xenopus laevis, unlike the highly repetitive, tandem arrangement of other snRNA genes in this organism. Sequencing of two U3 snRNA genes from lambda clones of a genomic library revealed striking similarity upstream, but much more divergence downstream. Consensus motifs common to other U snRNA genes were also found: a distal sequence element (DSE, octamer motif at -222 to -215), a proximal sequence element (PSE, at -62 to -52) and a 3' Box (15 or 16 bp downstream of the U3 genes). The DSE of mammals also has an inverted CCAAT motif specific for U3 snRNA genes, and we find this is conserved in the amphibian U3 snRNA genes. The Xenopus inverted CCAAT motif is exactly one helical turn further upstream of the octamer motif than its mammalian counterpart, suggesting interaction of putative transcription factors bound to these motifs. Mutation of the inverted CCAAT motif and part of an adjacent Sp1 site greatly depresses transcription of the mutant U3 snRNA gene in Xenopus oocytes, implying a role in transcriptional efficiency. Electrophoretic mobility shift assays implicate transcription factor binding to this region.

Chorion gene cis-regulatory DNA restricts tissue specificity of reporter gene expression in transformed Drosophila

P element mediated germ-line transformation was used to study the developmental specificity of Drosophila chorion gene regulatory sequences directing expression of the bacterial reporter genes for chloramphenicol acetyltransferase (CAT) and beta-galactosidase (lacZ). DNA fragments containing 5' flanking plus the entire 5' untranslated and the beginning of the coding region of either the s36 or the s15 chorion gene are able to confer on the reporter genes normal tissue as well as temporal specificity of expression, exclusively in the ovary of transformed female flies. However, if 5' untranslated and coding regions are omitted, normal ovarian expression is maintained but tissue specificity is relaxed: expression of the reporter gene is detected both in the ovary and in specific non-ovarian tissues of transformed females and males. The evidence suggests that the missing 5' untranslated and coding sequences may include negative elements that normally suppress expression in non-ovarian tissues, and that these putative elements are distinct from those that prevent premature expression in the ovarian follicles. The exact location of ectopic lacZ expression within the internal male genitalia depends on the constellation of 5' flanking chorion regulatory sequences included in the P element constructs. Ectopic expression of the CAT gene in the male genitalia under s15 promoter control can be abolished by mutating the hexamer TCACGT, a sequence previously shown to be essential for the normal expression of this chorion gene in the ovary.

The promoter of DNA puff gene II/9-1 of Sciara coprophila is inducible by ecdysone in late prepupal salivary glands of Drosophila melanogaster

DNA puffs occur in Sciarid salivary gland chromosomes; they are sites of DNA amplification and intense transcription and they appear to encode secreted structural proteins needed for pupation. In this report we have used P-element transformation of Drosophila to study regulation of a Sciara DNA puff gene. We found that a 718-bp promoter fragment of DNA puff gene II/9-1 from Sciara coprophila directs expression of the bacterial reporter gene CAT in late prepupal salivary glands of transgenic Drosophila melanogaster. The identical tissue and analogous stage specificity indicate that some aspects of the ecdysone response are evolutionarily conserved between Drosophila and Sciara. When transgenic salivary glands are cultured in vitro, CAT activity is rapidly induced by ecdysone, suggesting direct control of gene expression by the ecdysone receptor. Putative stage-specific factors limit expression of the chimeric Sciara-CAT gene in transgenic Drosophila to late prepupae but not to third instar larvae when ecdysone titers are also high.

Preribosomal RNA processing in Xenopus oocytes does not include cleavage within the external transcribed spacer as an early step

Recently it has been reported that U3 snRNA is necessary for: (a) internal cleavage at +651/+657 within the external transcribed spacer (ETS) of mouse precursor ribosomal RNA (pre-rRNA); and (b) cleavage at the 5' end of 5.8S rRNA in Xenopus oocytes. To study if U3 snRNA plays a role at more than one processing site in the same system, we have investigated whether internal cleavage sites exist within the ETS of Xenopus oocyte pre-rRNA. The ETS of Xenopus pre-rRNA contains the consensus sequence for the mammalian early processing site (+651/+657 in mouse pre-rRNA), but freshly prepared RNA from Xenopus oocytes has no cuts in this region. The only putative cleavage sites we found in the ETS of Xenopus oocyte pre-rRNA are a cluster further downstream of the mouse early processing site consensus sequence. This cluster is not homologous to the mouse +651/+657 sites because unlike the latter it is (a) not abolished by disruption of U3 snRNA, (b) not cleaved during early steps of pre-rRNA processing, and (c) lacks sequence similarity to the +651/+657 consensus. Therefore, pre-rRNA of Xenopus oocytes does not cleave within the ETS as an early step in rRNA processing. We conclude that cleavage within the ETS is not an obligatory early step needed for the rest of rRNA maturation.

Changes in 7SL RNA conformation during the signal recognition particle cycle

The structure of 7SL RNA has been probed by chemical modification followed by primer extension, using four substrates: (i) naked 7SL RNA; (ii) free signal recognition particle (SRP); (iii) polysome bound SRP; and (iv) membrane bound SRP. Decreasing sensitivity to chemical modification between these different substrates suggests regions on 7SL RNA that: bind proteins associated with SRP might interact with ribosomes; and are protected by binding to membranes. Other areas increase in chemical sensitivity, exemplified by a tertiary interaction present in naked 7SL RNA but not in free SRP. Such changes suggest that 7SL RNA changes its conformation during the SRP cycle. These conformational changes could be a necessary component to move through the SRP cycle from one stage to the next.

Structural analysis of the peptidyl transferase region in ribosomal RNA of the eukaryote Xenopus laevis

Accessible single-strand bases in Xenopus laevis 28 S ribosomal RNA (rRNA) Domain V, the peptidyl transferase region, were determined by chemical modification with dimethylsulfate, 1-cyclohexyl-3-(2-morpholinoethyl-carbodiimide metho-p-toluene sulfonate and kethoxal, followed by primer extension. The relative accessibilities of three rRNA substrates were compared: deproteinized 28 S rRNA under non-denaturing conditions (free 28 S rRNA), 60 S subunits and 80 S ribosomes. Overall, our experimental results support the theoretical secondary structure model of Domain V derived by comparative sequence analysis and compensatory base-pair changes, and support some theoretical tertiary interactions previously suggested by covariation. The 60 S subunits and 80 S ribosomes generally show increasing resistance to chemical modification. Bases which are sensitive in free 28 S rRNA but protected in 60 S subunits may be sites for ribosomal protein binding or induced structural rearrangements. Another class of nucleotides is distinguished by its sensitivity in 60 S subunits but protection in 80 S ribosomes; these nucleotides may be involved in subunit-subunit interactions or located at the interface of the ribosome. We found a third class of bases, which is protected in free 28 S rRNA but sensitive in 60 S subunits and/or 80 S ribosomes, suggesting that structural changes occur in Domain V as a result of subunit assembly and ribosome formation. One such region is uniquely hypersensitive in eukaryotic ribosomes but is absent in Escherichia coli ribosomes. Sites that we determined to be accessible on empty 80 S ribosomes could serve as recognition sites for translation components.

In vivo disruption of Xenopus U3 snRNA affects ribosomal RNA processing

DNA oligonucleotide complementary to sequences in the 5' third of U3 snRNA were injected into Xenopus oocyte nuclei to disrupt endogenous U3 snRNA. The effect of this treatment on rRNA processing was examined. We found that some toads have a single rRNA processing pathway, whereas in other toads, two rRNA processing pathways can coexist in a single oocyte. U3 snRNA disruption in toads with the single rRNA processing pathway caused a reduction in 20S and '32S' pre-rRNA. In addition, in toads with two rRNA processing pathways, an increase in '36S' pre-rRNA of the second pathway is observed. This is the first in vivo demonstration that U3 snRNA plays a role in rRNA processing. Cleavage site #3 is at the boundary of ITS 1 and 5.8S and links all of the affected rRNA intermediates: 20S and '32S' are the products of site #3 cleavage in the first pathway and '36S' is the substrate for cleavage at site #3 in the second pathway. We postulate that U3 snRNP folds pre-rRNA into a conformation dictating correct cleavage at processing site #3.

Molecular characterization of DNA puff II/9A genes in Sciara coprophila

A cDNA clone, pSDII/9, that hybridizes in situ to ecdysone-regulated DNA puff II/9A in Sciara coprophila was used as a probe to isolate a Sciara genomic clone. lambda pSDII/9, which contains a 14.7 x 10(3) base-pair DNA insert. The full-length cDNA insert was sequenced and mapped to gene II/9-1 on the genomic clone. A second gene (II/9-2), transcribed in the same direction as II/9-1, was also mapped to lambda pSDII/9, and its nucleic acid sequence was found to be 85% similar to that of gene II/9-1. An RNase protection assay demonstrates that gene II/9-1 contains a single intron that also exists in gene II/9-2 according to sequencing analysis and primer extensions of RNA encoded by this gene. Computer analyses of the deduced amino acid sequences of genes II/9-1 and II/9-2 indicate that the two DNA puff-encoded proteins are mostly alpha-helical coiled-coils. The 5'-flanking sequences of both genes contain regions that are similar to other ecdysone-regulated genes from Drosophila melanogaster.

Isolation and characterization of ribosomal DNA variants from Sciara coprophila

The ribosomal RNA multigene family in the fungus fly Sciara coprophila contains a total of only 65 to 70 repeat units. We explored the types and frequencies of variant repeats in this small multigene family by characterizing different cloned rDNA variants from Sciara. Although we did not observe any intergenic spacer length variants in Sciara, we found a variant due to the insertion of a putative mobile element (lambda Bc11), and variants containing ribosomal insertion elements. By DNA sequence analysis of rDNA/non-rDNA junctions, there are three distinct types of ribosomal insertion elements found in Sciara rDNA: two correspond to the R1 and R2 insertion elements found in other dipterans (clones lambda Bc5 and pBc1L1, respectively), and one is a novel class of ribosomal insertion elements (R3, exemplified by clone pBc6D6) which so far is unique to Sciara. Together, the several different rDNA variants make up from 12 to 20% of the rDNA in Sciara. These results are discussed in the context of evolution of the ribosomal RNA multigene family.

Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA

Using a combination of RNA sequencing and construction of cDNA clones followed by DNA sequencing, we have determined the primary nucleotide sequence of U3 snRNA in Xenopus laevis and Xenopus borealis. This molecule has a length of 219 nucleotides. Alignment of the Xenopus sequences with U3 snRNA sequences from other organisms reveals three evolutionarily conserved blocks. We have probed the secondary structure of U3 snRNA in intact Xenopus laevis nuclei using single-strand specific chemical reagents; primer extension was used to map the positions of chemical modification. The three blocks of conserved sequences fall within single-stranded regions, and are therefore accessible for interaction with other molecules. Models of U3 snRNA function are discussed in light of these data.

The evolution of eukaryotic ribosomal DNA

Mutations occur randomly throughout the ribosomal DNA (rDNA) sequence. Molecular drive (unequal crossing-over, gene conversion, and transposition) spreads these variations through the multiple copies of rDNA. Forces of selection act upon the variants to favor and fix them or disfavor and eliminate them. Selection has not permitted changes in regions within rRNA vital for its function; these sequences are evolutionarily conserved between diverse species. Possible functions for some of these conserved sequences are discussed. The secondary structure of rRNA is also highly conserved during evolution. However, eukaryotic rRNA is larger than prokaryotic rRNA due to blocks of "expansion segments". Arguments are put forward that expansion segments might not play any functional role. Other examples are reviewed of rDNA sequence insertion or deletion, including introns and the internal transcribed spacer 2.

rRNA processing: removal of only nineteen bases at the gap between 28S alpha and 28S beta rRNAs in Sciara coprophila

We have determined the sequence of the rDNA region between the 28S alpha and 28S beta rRNA coding segments (termed a "gap") in the insect Sciara coprophila, and have used S1 nuclease mapping and cDNA primer extension to define the 5' and 3' boundaries of the gap. Only 19 bases found in rDNA at the gap region are absent from mature 28S rRNA. Eukaryotic rRNAs contain stretches of nucleotides ("expansion segments") which are absent in E. coli rRNA. The gap region in Sciara is located within expansion segment V. Therefore, the excision of 19 bases in the Sciara gap suggests that a large portion of expansion segment V plays no function in mature ribosomes. Specific sequences conserved in Sciara and Drosophila are considered as candidates for recognition signals for the excision of the gap transcript.

Xenopus laevis 28S ribosomal RNA: a secondary structure model and its evolutionary and functional implications

Based upon the three experimentally derived models of E. coli 23S rRNA (1-3) and the partial model for yeast 26S rRNA (4), which was deduced by homology to E. coli, we derived a secondary structure model for Xenopus laevis 28S rRNA. This is the first complete model presented for eukaryotic 28S rRNA. Compensatory base changes support the general validity of our model and offer help to resolve which of the three E. coli models is correct in regions where they are different from one another. Eukaryotic rDNA is longer than prokaryotic rDNA by virtue of introns, expansion segments and transcribed spacers, all of which are discussed relative to our secondary structure model. Comments are made on the evolutionary origins of these three categories and the processing fates of their transcripts. Functionally important sites on our 28S rRNA secondary structure model are suggested by analogy for ribosomal protein binding, the GTPase center, the peptidyl transferase center, and for rRNA interaction with tRNA and 5S RNA. We discuss how RNA-RNA interactions may play a vital role in translocation.

Processing of the large rRNA precursor: two proposed categories of RNA-RNA interactions in eukaryotes

The 5.8S RNA gene of eukaryotes is separated from the 26-28S rRNA gene by the internal transcribed spacer 2 (ITS 2). A compilation of known ITS 2 sequences is presented here. Four characteristic features of the ITS 2 primary structure are shared by all vertebrates. In contrast, lower eukaryotes lack most of these features, suggesting that the excision of the ITS 2 transcript during processing may differ between vertebrates and lower eukaryotes. Since the transcripts of rRNA ITS 2 and mRNA introns share some similarity, analogies have been made between the mechanisms of their removal during RNA maturation. A model is proposed for hydrogen-bonding of U3 snRNA with the 5' end of the vertebrate ITS 2 transcript. This U3 snRNA-ITS 2 RNA interaction does not appear to be used in ITS 2 processing in lower eukaryotes. Instead, in lower eukaryotes a region within the ITS 2 itself has the potential to hydrogen-bond to the 5' end of the ITS 2 transcript.

Sequence analysis of 28S ribosomal DNA from the amphibian Xenopus laevis

We have determined the complete nucleotide sequence of Xenopus laevis 28S rDNA (4110 bp). In order to locate evolutionarily conserved regions within rDNA, we compared the Xenopus 28S sequence to homologous rDNA sequences from yeast, Physarum, and E. coli. Numerous regions of sequence homology are dispersed throughout the entire length of rDNA from all four organisms. These conserved regions have a higher A + T base composition than the remainder of the rDNA. The Xenopus 28S rDNA has nine major areas of sequence inserted when compared to E. coli 23S rDNA. The total base composition of these inserts in Xenopus is 83% G + C, and is generally responsible for the high (66%) G + C content of Xenopus 28S rDNA as a whole. Although the length of the inserted sequences varies, the inserts are found in the same relative positions in yeast 26S, Physarum 26S, and Xenopus 28S rDNAs. In one insert there are 25 bases completely conserved between the various eukaryotes, suggesting that this area is important for eukaryotic ribosomes. The other inserts differ in sequence between species and may or may not play a functional role.

Structure of 1.71 lb gm/cm(3) bovine satellite DNA: evolutionary relationship to satellite I

The Eco RI fragments from the 2600 bp repeating unit of 1.711b gm/Cm(3) bovine satellite DNA were cloned in pBR322. The structure of the repeat unit was determined and compared to bovine satellite I DNA (rho CsCl = 1.715 gm/cm(3)). All of the DNA in the 1402 bp repeat of satellite I is represented in the sequence of the 2600 bp 1.711b gm/cm(3) repeat. The difference between the two repeats is due to a 1200 bp piece of DNA (INS) residing in the middle of the 1.711b gm/cm(3) repeat. The INS is AT-rich and has some repetitive components; it bears only limited similarity to the structure of eukaryotic transposable elements. We propose that the 1.711b gm/cm(3) satellite DNA arose via the amplification of a 1.715 gm/cm(3) satellite repeat altered by a 1200 bp insertion of DNA.

The basic repeat unit of a Chironomus Balbiani ring gene

A clone derived from the Balbiani ring b (BRb) gene of Chironomus thummi has been used to study the internal organization of that gene. Much of the gene consists of approximately 80 copies of a ca. 300 bp repeat unit, which are tandemly organized. The BRb clone contains a major part of that unit (242 bp). Sequence analysis shows that approximately 60% of the unit corresponds to short, tandemly organized subsequences, which encode peptides 8 to 11 residues long. In turn, each subsequence consists of even shorter internal repeats, corresponding to a tripeptide (consensus Proline. Serine. Lysine.). The remainder of the ca. 300 bp unit probably does not have obvious repetitive substructure.

Sequence analysis of bovine satellite I DNA (1.715 gm/cm3)

The 1402 bp Eco RI repeating unit of bovine satellite I DNA (rho CsCl = 1.715 gm/cm3) has been cloned in pBR322. The sequence of this cloned repeat has been determined and is greater than 97% homologous to the sequence reported for another clone of satellite I (48) and for uncloned satellite I DNA (49). The internal sequence structure of the Eco RI repeat contains imperfect direct and inverted repeats of a variety of lengths and frequencies. The most outstanding repeat structures center on the hexanucleotide CTCGAG which, at a stringency of greater than 80% sequence homology, occurs at 26 locations within the RI repeat. Two of these 6 bp units are found within the 31 bp consensus sequence of a repeating structure which spans the entire length of the 1402 bp repeat (49). The 31 bp consensus sequence contains an internal dodecanucleotide repeat, as do the consensus sequences of the repeat units determined for 3 other bovine satellite DNAs (rho CsCl = 1.706, 1.711a, 1.720 gm/cm3). Based on this evidence, we present a model for the evolutionary relationship between satellite I and the other bovine satellites.

Two distinct intervening sequences in different ribosomal DNA repeat units of Sciara coprophila

We have prepared a partial gene library of sheared DNA from the fungus fly, Sciara coprophila, by dA-T tailing and insertion into pBR322. Two ribosomal DNA clones which differ from the usual ribosomal DNA organization in this organism were studied in detail. Clone pBc 1L-1 has an intervening sequence of 1.4 kb, and clone pBc 6D-6 has an intervening sequence of 0.9 kb. These intervening sequences occur in about the same position in 28S rDNA, but do not appear to share sequence homology with one another. Previously we found that 90% of Sciara ribosomal DNA is homogenous and lacks an intervening sequence, and our present data explains the size heterogeneity found in most of the remaining 10%. We have found no evidence of size heterogeneity in the nontranscribed spacer.

Spermatogenesis in Sciara coprophila. I. Chromosome orientation on the monopolar spindle of meiosis I

Meiosis I of spermatogenesis in the fungus fly, Sciara coprophila, has a monopolar spindle which collects the maternal and supernumerary L chromosome sets, while the paternal chromosomes migrate away from the single pole to be excluded in a bud. By inspection, the metacentric paternal chromosome IV moves with its centromere lagging rather than leading the direction of motion. Therefore, we wondered if all paternal homologues move in such a reverse orientation. To determine the orientation of the other homologues which are acrocentrics (chromosomes II, III, X), their centromeres were localized by use of the DAPI C-bonding technique. In addition, we characterized centromeric heterochromatin on polytene chromosomes by C-banding and in situ hybridization of satellite DNA isolated by Ag+-Cs2SO4 (rho CsC1 satellite I=1.698 g/ml; rho CsC1 satellite II=1.705 g/ml). The two satellite fractions were localized to the centromeric heterochromatin of all the chromosomes, and to a varying degree to all chromosome telomeres. By DAPI C-banding we could precisely locate each centromere band on polytene chromosomes, and these results agreed with those of satellite cRNA in situ hybridization. We then applied the DAPI C-banding technique to primary spermatocyte preparations, and determined that all paternal chromosomes migrate at anaphase I with their centromeres lagging rather than leading movement to the cell periphery. Since in polytene chromosomes the X chromosome contains a moderately fluorescent band on its noncentromeric end as well, in order to clarify its DAPI C-banding result in primary spermatocytes, we did in situ hybridization of (3)H nick-translated cloned rDNA, since rDNA is a convenient marker for the centromeric heterochromatin of the X. These data and the DAPI C-banding results indicate that the X as well as all th other paternal homologues display a reverse orientation (centromeres lag) as they migrate away from the single spindle pole to the cell periphery. - One model explaining this unusual paternal chromosome orientation is that there may be unique neocentromeric-like attachments to the non-centromeric free ends of these chromosomes. These attachments could serve to pull the paternal chromosomes to the cellular periphery as anaphase I progresses. In order to test this model, we analyzed anaphase I spermatocytes after a terminal block of heterochromatin had been removed from metacentric paternal chromosome IV by X-irradiation. We observed that when metacentric paternal chromosome IV is broken, it maintains its inverted "V" orientation rather than assuming a rod-like configuration. These data imply that there are no unique, terminal neocentromeric attachments to paternal chromosome IV as it progresses to the cellular periphery.

Spermatogenesis in Sciara coprophila. II. Precocious chromosome orientation in meiosis II

In the second meiotic division of spermatogenesis in Sciara coprophila the X dyad undergoes a directed nondisjunction appearing precociously at one pole. All other chromosomes behave in a normal fashion aligning on the metaphase plate and dividing. Crouse has determined that this directed nondisjunction is governed by a region of the X centromere heterochromatin known to contain the rDNA (Crouse et al., 1977; Crouse, 1979). In order to further characterize this system we have utilized DAPI c-banding and rDNA in situ hybridization to demonstrate that the precocious chromosome (X or translocation chromosome) orients at metaphase II with its centromere end juxtaposed to the pole. Even when the controlling region is not near the centromere as in the case of translocations T1 and T32, the precocious chromosome orients with the centromere end rather than the controlling region end adjacent to the pole. These data may argue that precocious positioning is established at telophase I and maintained throughout the second meiotic division. - We have examined the hypothesis that the controlling region is transcriptionally active at metaphase II and can find no evidence for this speculation. This argues that if an RNA product is related to precocious positioning it must be synthesized earlier in spermatogenesis. - An analysis of naturally occurring tetraploid spermatocytes demonstrates that the two independent precocious chromosomes of such cells are always associated with the same pole. This datum in conjunction with the observation that tetraploid primary spermatocytes have only one monopolar spindle and not two, further supports the notion that a precocious chromosome-pole interaction may be established in meiosis I and maintained throughout meiosis II.

Specific binding of a prokaryotic ribosomal protein to a eukaryotic ribosomal RNA: implications for evolution and autoregulation

Ribosomal protein L1 from the prokaryote Escherichia coli has been shown to form a specific complex with 26S ribosomal RNA from the eukaryote Dictyostelium discoideum. The segment of Dictyostelium rRNA protected from ribonuclease digestion by L1 and the corresponding region in Dictyostelium rDNA were investigated by nucleotide sequence analysis, and an analogous section in rDNA from Xenopus laevis was identified. When the L1-specific segments from eukaryotic rRNA were compared with those from prokaryotic rRNA, striking similarities in both primary and secondary structure were apparent. These conserved features suggest a common structural basis for protein recognition and indicate that such regions became fixed at a very early stage in rRNA evolution. In addition, certain structural elements of the L1 binding sites in rRNA are also found in the initial segment of the polycistronic L11-L1 mRNA, providing support for the hypothesis that L1 participates in the regulation of ribosomal protein synthesis by specific interaction with its own mRNA.

Fine structure of ribosomal RNA. IV. Extraordinary evolutionary conservation in sequences that flank introns in rDNA

By hybridization and DNA sequencing, we have defined a specific region in Xenopus rDNA that is extremely conserved between Tetrahymena, a protozoan, and Xenopus, a vertebrate. This highly conserved region is found at the site where an intron has been shown to interrupt Tetrahymena rDNA [1,2], although we have not detected introns in genomic or cloned Xenopus rDNA. We have noted that the sequences corresponding to nuclear rDNA interon-flanking regions show an intriguing complementarity to tRNAiMet. This suggests possible models for tRNA-rRNA interactions in protein synthesis and/or rRNA splicing.

Fine structure of ribosomal RNA. II. Distribution of methylated sequences within Xenopus laevis rRNA

The distribution of methyl groups in rRNA from Xenopus laevis was analyzed by hybridization of rRNA to subfragments of either of two cloned rDNA fragments, X1r11 and X1r12, which together constitute a complete rDNA repeat unit. Using a mixture of 3H-methyl plus 32P-labelled rRNA as probe, the molar yield of methyl groups per rRNA region in hybrid could be calculated. For this calculation the length of the rRNA coding region in each DNA subfragment is needed, which was determined for X1r11 subfragments by the nuclease S1 mapping method of Berk and Sharp. The results show that both in 18S and 28S rRNA the methyl groups are nonrandomly distributed. For 18S rRNA, clustering was found within a 3' terminal fragment of 310 nucleotides. For 28S rRNA, clustering of methyl groups was found within a region of 750 nucleotides in length, which ends 500 nucleotides from the 3' end. In contrast, the 28S rRNA 5' terminal region of 900 nucleotides is clearly undermethylated. The general position of methyl groups in 28S rRNA correlates with the location of evolutionarily conserved sequences in this molecule, as recently determined in our laboratory.

Ribosomal DNA of fly Sciara coprophila has a very small and homogeneous repeat unit

In this report we show by hybridization of restriction fragments and by Miller spreads that the unit repeat of the fly Sciara coprophila is only 8.4 kb which is the smallest known for a multicellular eukaryote. The 8.4 kb EcoR1 fragment containing a complete unit of Sciara rDNA was cloned in pBR322, and mapped by the method of Parker (1977) and also by double digestions. The coding regions for 28S, 18S, and 5.8S RNA were localized by the method of Berk and Sharp (1977). From these data we conclude that the nontranscribed spacer, external transcribed spacer, and internal transcribed spacer are all shorter than in other organisms, thereby giving rise to the shorter overall rDNA repeat unit of Sciara. At least 90% of the Sciara rDNA repeats are homogeneous, with a length of 8.4 kb, but a 700 bp ladder of minor bands can also be found in digestions of total genome DNA. This profile of major and minor bands is identical between the X and X' chromosomes, as seen by a comparison of several genotypes. There are only 45 rRNA genes per X chromosome of Sciara (Gerbi and Crouse, 1976). These can easily be counted by low magnification Miller spreads which show that virtually all gene copies are actively being transcribed in the stage of spermatogenesis examined. This is the first demonstration for any reiterated gene family where all copies are shown to be simultaneously active.

Further studies on the ribosomal RNA cistrons of Sciara coprophila (Diptera)

Additional experiments with homologous as well as heterologous hybridization confirmed our previous finding in Sciara coprophila that XX females have nearly twice the number of ribosomal RNA cistrons as XO males. A comparison between two different X' chromosomes revealed that only the one carrying the irradiation-induced Wavy mutation has a deletion of 70% of its ribosomal RNA cistrons as compared to the standard X. The deletion is relatively stable, and the remaining ribosomal RNA cistrons donot appear to undergo disproportionate replication or magnification as in Drosophila. Homologous hybridization experiments revealed an unusually low reiteration of ribosomal RNA cistrons in this fly, 45 gene copies per X chromosome. The question is raised as to whether such a low number of cistrons may be related to the unusual nucleolar condition encountered in the Sciaridae.