The organization of highly repeated DNA sequences in Drosophila melanogaster chromosomes

The Singular Evolution of Olea Genome Structure

The current view of plant genome evolution proposes that genome size has mainly been determined by polyploidisation and amplification/loss of transposons, with a minor role played by other repeated sequences, such as tandem repeats. In cultivated olive (Olea europaea subsp. europaea var. europaea), available data suggest a singular model of genome evolution, in which a massive expansion of tandem-repeated sequences accompanied changes in nuclear architecture. This peculiar scenario highlights the importance of focusing on Olea genus evolution, to shed light on mechanisms that led to its present genomic structure. Next-generation sequencing technologies, bioinformatics and in situ hybridisation were applied to study the genomic structure of five related Olea taxa, which originated at different times from their last common ancestor. On average, repetitive DNA in the Olea taxa ranged from ~59% to ~73% of the total genome, showing remarkable differences in terms of composition. Among repeats, we identified 11 major families of tandem repeats, with different abundances in the analysed taxa, five of which were novel discoveries. Interestingly, overall tandem repeat abundance was inversely correlated to that of retrotransposons. This trend might imply a competition in the proliferation of these repeat classes. Indeed, O. paniculata, the species closest to the Olea common ancestor, showed very few tandem-repeated sequences, while it was rich in long terminal repeat retrotransposons, suggesting that the amplification of tandem repeats occurred after its divergence from the Olea ancestor. Furthermore, some tandem repeats were physically localised in closely related O. europaea subspecies (i.e., cultivated olive and O. europaea subsp. cuspidata), which showed a significant difference in tandem repeats abundance. For 4 tandem repeats families, a similar number of hybridisation signals were observed in both subspecies, apparently indicating that, after their dissemination throughout the olive genome, these tandem repeats families differentially amplified maintaining the same positions in each genome. Overall, our research identified the temporal dynamics shaping genome structure during Olea speciation, which represented a singular model of genome evolution in higher plants.

Identification and characterization of centromeric sequences in Xenopus laevis

Centromeres play an essential function in cell division by specifying the site of kinetochore formation on each chromosome for mitotic spindle attachment. Centromeres are defined epigenetically by the histone H3 variant Centromere Protein A (Cenpa). Cenpa nucleosomes maintain the centromere by designating the site for new Cenpa assembly after dilution by replication. Vertebrate centromeres assemble on tandem arrays of repetitive sequences, but the function of repeat DNA in centromere formation has been challenging to dissect due to the difficulty in manipulating centromeres in cells. Xenopus laevis egg extracts assemble centromeres in vitro, providing a system for studying centromeric DNA functions. However, centromeric sequences in Xenopus laevis have not been extensively characterized. In this study, we combine Cenpa ChIP-seq with a k-mer based analysis approach to identify the Xenopus laevis centromere repeat sequences. By in situ hybridization, we show that Xenopus laevis centromeres contain diverse repeat sequences, and we map the centromere position on each Xenopus laevis chromosome using the distribution of centromere-enriched k-mers. Our identification of Xenopus laevis centromere sequences enables previously unapproachable centromere genomic studies. Our approach should be broadly applicable for the analysis of centromere and other repetitive sequences in any organism.

Bundling up DNA

Structures known as chromocenters, comprising satellite DNA and proteins such as D1 or HMGA1, help to contain DNA inside the nucleus between cell divisions.

Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster

Highly repetitive satellite DNA (satDNA) repeats are found in most eukaryotic genomes. SatDNAs are rapidly evolving and have roles in genome stability and chromosome segregation. Their repetitive nature poses a challenge for genome assembly and makes progress on the detailed study of satDNA structure difficult. Here, we use single-molecule sequencing long reads from Pacific Biosciences (PacBio) to determine the detailed structure of all major autosomal complex satDNA loci in Drosophila melanogaster, with a particular focus on the 260-bp and Responder satellites. We determine the optimal de novo assembly methods and parameter combinations required to produce a high-quality assembly of these previously unassembled satDNA loci and validate this assembly using molecular and computational approaches. We determined that the computationally intensive PBcR-BLASR assembly pipeline yielded better assemblies than the faster and more efficient pipelines based on the MHAP hashing algorithm, and it is essential to validate assemblies of repetitive loci. The assemblies reveal that satDNA repeats are organized into large arrays interrupted by transposable elements. The repeats in the center of the array tend to be homogenized in sequence, suggesting that gene conversion and unequal crossovers lead to repeat homogenization through concerted evolution, although the degree of unequal crossing over may differ among complex satellite loci. We find evidence for higher-order structure within satDNA arrays that suggest recent structural rearrangements. These assemblies provide a platform for the evolutionary and functional genomics of satDNAs in pericentric heterochromatin.

Correlated variation and population differentiation in satellite DNA abundance among lines of Drosophila melanogaster

Tandemly repeating satellite DNA elements in heterochromatin occupy a substantial portion of many eukaryotic genomes. Although often characterized as genomic parasites deleterious to the host, they also can be crucial for essential processes such as chromosome segregation. Adding to their interest, satellite DNA elements evolve at high rates; among Drosophila, closely related species often differ drastically in both the types and abundances of satellite repeats. However, due to technical challenges, the evolutionary mechanisms driving this rapid turnover remain unclear. Here we characterize natural variation in simple-sequence repeats of 2-10 bp from inbred Drosophila melanogaster lines derived from multiple populations, using a method we developed called k-Seek that analyzes unassembled Illumina sequence reads. In addition to quantifying all previously described satellite repeats, we identified many novel repeats of low to medium abundance. Many of the repeats show population differentiation, including two that are present in only some populations. Interestingly, the population structure inferred from overall satellite quantities does not recapitulate the expected population relationships based on the demographic history of D. melanogaster. We also find that some satellites of similar sequence composition are correlated across lines, revealing concerted evolution. Moreover, correlated satellites tend to be interspersed with each other, further suggesting that concerted change is partially driven by higher order structure. Surprisingly, we identified negative correlations among some satellites, suggesting antagonistic interactions. Our study demonstrates that current genome assemblies vastly underestimate the complexity, abundance, and variation of highly repetitive satellite DNA and presents approaches to understand their rapid evolutionary divergence.

Accessible DNA and relative depletion of H3K9me2 at maize loci undergoing RNA-directed DNA methylation

RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2. The data revealed that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but that lacks RdDM. The minority of the genome marked by RdDM was predominantly near genes, and its overall chromatin structure appeared more similar to euchromatin than to heterochromatin. These and other data indicate that the densely staining chromatin defined as heterochromatin differs fundamentally from RdDM-targeted chromatin. We propose that small interfering RNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production.

Simple quantitative PCR approach to reveal naturally occurring and mutation-induced repetitive sequence variation on the Drosophila Y chromosome

Heterochromatin is a significant component of the human genome and the genomes of most model organisms. Although heterochromatin is thought to be largely non-coding, it is clear that it plays an important role in chromosome structure and gene regulation. Despite a growing awareness of its functional significance, the repetitive sequences underlying some heterochromatin remain relatively uncharacterized. We have developed a real-time quantitative PCR-based method for quantifying simple repetitive satellite sequences and have used this technique to characterize the heterochromatic Y chromosome of Drosophila melanogaster. In this report, we validate the approach, identify previously unknown satellite sequence copy number polymorphisms in Y chromosomes from different geographic sources, and show that a defect in heterochromatin formation can induce similar copy number polymorphisms in a laboratory strain. These findings provide a simple method to investigate the dynamic nature of repetitive sequences and characterize conditions which might give rise to long-lasting alterations in DNA sequence.

Distinct chromatin features characterize different classes of repeat sequences in Drosophila melanogaster

Background

Repeat sequences are abundant in eukaryotic genomes but many are excluded from genome assemblies. In Drosophila melanogaster classical studies of repeat content suggested variability between individuals, but they lacked the precision of modern high throughput sequencing technologies. Genome-wide profiling of chromatin features such as histone tail modifications and DNA-binding proteins relies on alignment to the reference genome and hence excludes highly repetitive sequences.

Results

By analyzing repeat libraries, sequence complexity and k-mer counts we determined the abundances of different D. melanogaster repeat classes in flies in two public datasets, DGRP and modENCODE. We found that larval DNA was depleted of all repeat classes relative to adult and embryonic DNA, as expected from the known depletion of repeat-rich pericentromeric regions during polytenization of larval tissues. By applying a method that is independent of alignment to the genome assembly, we found that satellite repeats associate with distinct H3 tail modifications, such as H3K9me2 and H3K9me3 for short repeats and H3K9me1 for 359 bp repeats. Short AT-rich repeats however are depleted of nucleosomes and hence all histone modifications and associated chromatin proteins.

Conclusions

The total repeat content and association of repeat sequences with chromatin modifications can be determined despite repeats being excluded from genome assemblies, revealing unexpected distinctions in chromatin features based on sequence composition.

Genetic analysis of the heterochromatin of chromosome 3 in Drosophila melanogaster. I. Products of compound-autosome detachment

The heterochromatin of the third chromosome is the largest uncharacterized region of the Drosophila melanogaster genome, and the last major block of D. melanogaster heterochromatin to be thoroughly analyzed. In the present study, this region was genetically dissected by generating and analyzing a series of attached, detached and reattached third chromosomes. Separate detachment experiments were conducted for all 12 possible combinations of four newly synthesized sister-strand compound-3L and three newly synthesized sister-strand compound-3R chromosomes. A total of 443 recessive lethal detachment products carrying putative heterochromatic deficiencies were tested for complementation in a several-stage complementation analysis. The results revealed the presence of seven separable vital regions in the heterochromatin of chromosome 3. Attempts to reattach deficiency-carrying detachment products established that six of these vital regions are on the left arm, but only one is on the right arm. An analysis of the types and frequencies of detachment-product deficiencies generated in each detachment experiment permitted the genetic characterization of the progenitor compounds. It was also possible to determine the proximal-distal orientation of the genes on each arm, and to identify possible breakpoints for each lethal detachment product produced. The results of this study suggest that vital genes in the heterochromatin of the third chromosome are not randomly distributed between, nor within, the heterochromatic blocks of the left and right arms.

Similarities in the chromosomal distribution of AG and AC repeats within and between Drosophila, human and barley chromosomes

Two simple sequence repeats (SSRs), AG and AC, were mapped directly in the metaphase chromosomes of man and barley (Hordeum vulgare L.), and in the metaphase and polytene chromosomes of Drosophila melanogaster. To this end, synthetic oligonucleotides corresponding to (AG)(12) and (AC)(8) were labelled by the random primer technique and used as probes in fluorescent in situ hybridisation (FISH) under high stringency and strict washing conditions. The distribution and intensity of the signals for the repeat sequences were found to be characteristic of the chromosomes and genomes of the three species analysed. The AC repeat sites were uniformly dispersed along the euchromatic segments of all three genomes; in fact, they were largely excluded from the heterochromatin. The Drosophila genome showed a high density of AC sequences on the X chromosome in both mitotic and polytene nuclei. In contrast, the AG repeats were associated with the euchromatic regions of the polytene chromosomes (and in high density on the X chromosome), but were only seen in specific heterochromatic regions in the mitotic chromosomes of all three species. In Drosophila, the AG repeats were exclusively distributed on the tips of the Y chromosome and near the centromere on both arms of chromosome 2. In barley and man, AG repeats were associated with the centromeres (of all chromosomes) and nucleolar organizer regions, respectively. The conserved chromosome distribution of AC within and between these three phylogenetically distant species, and the association of AG in specific chromosome regions with structural or functional properties, suggests that long clusters of these repeats may have some, as yet unknown, role.

Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster

Heterochromatin in Drosophila has unusual genetic, cytological and molecular properties. Highly repeated DNA sequences (satellites) are the principal component of heterochromatin. Using probes from cloned satellites, we have constructed a chromosome map of 10 highly repeated, simple DNA sequences in heterochromatin of mitotic chromosomes of Drosophila melanogaster. Despite extensive sequence homology among some satellites, chromosomal locations could be distinguished by stringent in situ hybridizations for each satellite. Only two of the localizations previously determined using gradient-purified bulk satellite probes are correct. Eight new satellite localizations are presented, providing a megabase-level chromosome map of one-quarter of the genome. Five major satellites each exhibit a multi-chromosome distribution, and five minor satellites hybridize to single sites on the Y chromosome. Satellites closely related in sequence are often located near one another on the same chromosome. About 80% of Y chromosome DNA is composed of nine simple repeated sequences, in particular (AAGAC)n (8 Mb), (AAGAG)n (7 Mb) and (AATAT)n (6 Mb). Similarly, more than 70% of the DNA in chromosome 2 heterochromatin is composed of five simple repeated sequences. We have also generated a high resolution map of satellites in chromosome 2 heterochromatin, using a series of translocation chromosomes whose breakpoints in heterochromatin were ordered by N-banding. Finally, staining and banding patterns of heterochromatic regions are correlated with the locations of specific repeated DNA sequences. The basis for the cytochemical heterogeneity in banding appears to depend exclusively on the different satellite DNAs present in heterochromatin.

RNA mapping on Drosophila mitochondrial DNA: precursors and template strands

Drosophila melanogaster mitochondrial DNA (mtDNA) is closely related to the mammalian and amphibian mtDNA except for gene organization. In Drosophila, genes are distributed in clusters alternatively coded on each strand. Besides the eleven major foreseeable transcripts previously described (MERTEN and PARDUE, 1981, J. Mol. Biol., 153, 1-21), we have characterized two poly A+ transcripts, one major and one minor which could correspond respectively to the ND3 and ND6 reading frames, and 27 poly A+ minor transcripts (0.2 to greater than 3.2 kb) which are distributed along the mtDNA except in the rRNAs, ND 1 and A+ T rich regions. The mapping and length of 25 of these transcripts strongly suggest a precursor role. They would be processed at the level of tRNA or tRNA-like sequences. Most of them are transcribed from the template strand of each gene cluster and their distribution is in agreement with the hypothesis of several transcription origins and terminations located near the extremities of each gene cluster. Quantitatively our results show a large variation in each presumptive mature transcript compared to the other, even in a given gene cluster, suggesting a specific degradation of some of the mature transcripts.

Multiplicity of satellite DNA sequences in Drosophila melanogaster

Three Drosophila melanogaster satellite DNAs (1.672, 1.686, and 1.705 g/ml in CsCl), each containing a simple sequence repeated in tandem, were cloned in pBR322 as small fragments about 500 base pairs long. This precaution minimized deletions, since inserts of the same size as the fragments used for cloning were recovered in a stable form. A homogeneous tandem array of one sequence type usually extended the length of the insert. Eleven distinct repeat sequences were discovered, but only one sequence was predominant in each satellite preparation. The remaining classes were minor in amount. The repeat unit lengths were restricted to 5, 7, or 10 base pairs, with sequences closely related. Each sequence conforms to the expression (RRN)m(RN)n, where R is A or G. The multiplicity of simple repeated sequences revealed despite the small sample size suggests that numerous repeat sequences reside in heterochromatin and that particular rules apply to the structure of the repeating sequence.

The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code

The sequence of the 16,019 nucleotide-pair mitochondrial DNA (mtDNA) molecule of Drosophila yakuba is presented. This molecule contains the genes for two rRNAs, 22 tRNAs, six identified proteins [cytochrome b, cytochrome c oxidase subunits I, II, and III (COI-III), and ATPase subunits 6 and 8] and seven presumptive proteins (URF1-6 and URF4L). Replication originates within a region of 1077 nucleotides that is 92.8% A + T and lacks any open reading frame larger than 123 nucleotides. An equivalent to the sequence found in all mammalian mtCDNAs that is associated with initiation of second-strand DNA synthesis is not present in D. yakuba mtDNA. Introns are absent from D. yakuba mitochondrial genes and there are few (0-31) intergenic nucleotides. The genes found in D. yakuba and mammalian mtDNAs are the same, but there are differences in their arrangement and in the relative proportions of the complementary strands of the molecule that serve as templates for transcription. Although the D. yakuba small and large mitochondrial rRNA genes are exceptionally low in G and C and are shorter than any other metazoan rRNA genes reported, they can be folded into secondary structures remarkably similar to the secondary structures proposed for mammalian mitochondrial rRNAs. D. yakuba mitochondrial tRNA genes, like their mammalian counterparts, are more variable in sequence than nonorganelle tRNAs. In mitochondrial protein genes ATG, ATT, ATA, and in one case (COI) ATAA appear to be used as translation initiation codons. The only termination codon found in these genes is TAA. In the D. yakuba mitochondrial genetic code, AGA, ATA, and TGA specify serine, isoleucine, and tryptophan, respectively. Fifty-nine types of sense condon are used in the D. yakuba mitochondrial protein genes, but 93.8% of all codons end in A or T. Codon-anticodon interactions may include both G-A and C-A pairing in the wobble position. Evidence is summarized that supports the hypothesis that A and T nucleotides are favored at all locations in the D. yakuba mtDNA molecule where these nucleotides are compatible with function.

A constitutively transcribed actin gene is associated with the nuclear matrix in a Drosophila cell line

The relationship between transcriptional activity and gene association with the nuclear matrix has been investigated in Drosophila melanogaster. The nuclear matrix of Schneider cell line 2 of Drosophila was isolated and observed to conform to expected dimensions in phase contrast and scanning electron microscopic preparations. This structure contains proteins that appear similar to the intact nucleus. High salt extracted nuclei digested with DNase I released 98% of the DNA, whereas digestion with Eco RI released a maximum of 80%. These and other nuclease digestions indicate that satellite DNA as well as some unique sequence DNA are bound to the nuclear matrix. A constitutively transcribed actin gene was enriched in the nuclear matrix bound DNA. Two other nontranscribed genes, a muscle-specific actin gene and the myosin heavy chain gene, showed no enrichment in nuclear matrix DNA.

The association of transcribed genes with the nuclear matrix of Drosophila cells during heat shock

Using the transcriptional modulation afforded by heat shock, we found that the association of active genes with the nuclear matrix was not dependent on their level of transcription. Heat shock genes were matrix associated both before heat shock (when transcription was relatively low), and during heat shock (when transcription was greatly increased). Conversely, the cytoplasmic actin gene was matrix associated during normal growth conditions (when transcription was high) and during heat shock (when transcription was greatly decreased). Removal of greater than 99.7% of nascent RNA during preparation of the matrices did not affect these findings. Detailed examination of the cytoplasmic actin gene revealed that its matrix association was apparently mediated by multiple interactions near the 5' end of the gene.

Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code

The sequence of a 4,869 base-pair fragment of Drosophila melanogaster mitochondrial DNA is presented. It contains genes for cytochrome oxidase subunits I, II and III, ATPase subunit 6 and six tRNAs together with two unassigned reading frames. The gene organization differs from that of mammalian mitochondrial DNAs. Evidence is provided for a genetic code in which AGA codes for serine and the quadruplet ATAA is used in initiation of translation.

Underreplication during polytenization? : Recent cytophotometric DNA determinations and related biochemical results concerning polytene salivary gland nuclei of Drosophila melanogaster

Recent cytophotometric DNA determinations and results of labeling experiments are compared with results of biochemical experiments concerning larval polytene salivary gland nuclei of Drosophila melanogaster. Recent publications (Dennhöfer 1981; 1982 a, b) demonstrate that methodological errors both in hydrolysis of the DNA before Feulgen reaction and in interpretation of the cytophotometric values give raise to the hypothesis of heterochromatic underreplication during polytenization. It is concluded also that methodological difficulties cause the absence of polytene SAT-DNA in biochemical centrifugation experiments since, because of different solubilities of eu- and heterochromatic DNA, the latter is not resolved in DNA isolation procedures from polytene nuclei.

Cytophotometric DNA determinations and autoradiographic studies in salivary gland nuclei from larvae with different karyotypes in Drosophila melanogaster

Cytophotometric DNA determinations in Feulgen stained mitotic diploid chromosome sets of neuroblasts from larvae of Drosophila melanogaster stocks, which possess different karyotypes, show significant differences between the 4C values, caused by an additional or deficient X- and Y-chromosome depending on the karyotype. The ranges of polytenic DNA size classes are theoretically expected to be doublings of the corresponding 4C mean value of each karyotype. The extinction integral data of nuclei with completely duplicated 4C quantities exclusively fall into the range of the expected size classes. Not all data falling into the range of a size class necessarily originate from duplicated nuclei, because the limits of the DNA size classes cannot be determined by measurements, but must be estimated from the confidence limits of the corresponding 4C mean value. The validity of the mitotic 4C values of the karyotypes X/X and X/Y is tested using data from non-labeled interphase nuclei, where extinction integral data accumulate in two groups. The larger values (= G2-nuclei) confirm the 4C values of mitotic chromosome sets, and the lower values (= G1-nuclei) are just half of these. Extinction integrals from individual, 3H-thymidine non-incorporating polytene salivary gland nuclei accumulate in distinct, non-overlapping groups which are always complete doublings of the preceding smaller group. In each karyotype, the most frequent data of each group are in accord with the 4C doublings. The data from labeled nuclei alternate with those from unlabeled nuclei. The measured DNA values of individual polytene nuclei that did not incorporate any 3H-thymidine, demonstrate that all chromosomal DNA replicates completely during polytenization of the chromosomes in the larval salivary gland nuclei of Drosophila melanogaster. Specifically, this would mean that the heterochromatic Y-chromosome replicates as well as the partially heterochromatic X-chromosome along with the autosomes. There is no indication of underreplicating heterochromatin.

Satellite DNA of Drosophila nasuta nasuta and D. n. albomicana: localization in polytene and metaphase chromosomes

The DNA from the two Drosophila nasuta races, D. n. nasuta and D. n. albomicana was investigated by CsCl density gradient centrifugation. D. n. nasuta has one major AT-rich satellite DNA sequence with a density of 1.664 g/cm3, while D. n. albomicana has at least three satellites with densities of 1.674 g/cm3, 1.665 g/cm3 and 1.661 g/cm3. The isolated satellite sequences hybridize in situ to all heterochromatic regions of all metaphase chromosomes of both races. In polytene chromosomes the satellite sequences hybridize exclusively to the chromocenter. All chromosomal regions hybridizing with the satellites show also bright quinacrine fluorescence.

The satellite DNAs of Drosophila simulans

The resolution of antibiotic-CsCl gradients enabled an examination of the satellite DNAs in the nuclear DNA of Drosophila simulans. Of the eight distinct satellite DNAs which were detected, four band at almost the same buoyant density in CsCl but can be resolved in netropsin sulphate-CsCl gradients. Each consists of a repeated sequence which, in five of the satellites, is shown to be arranged in tandem for long regions of the chromosomal DNA. One satellite (1·697 g/ml in CsCl) contains repeated sequences interspersed with other sequences. The satellite DNAs were compared with the satellite DNAs known to be present in the sibling species, D. melanogaster. The two species have different overall complements of satellite DNAs, but one satellite (1·672 g/ml) may be identical.

Non-random position of the A-T rich DNA sequences in early embryos of Drosophila virilis

Examination of early embryos of Drosophila virilis by light and electron microscopy has shown that the A-T rich satellite DNA sequences have a non-random distribution within the nuclei. As observed by 33258 Hoechst staining and fluorescent microscopy, these sequences are consistently found to be located on the sides of the nuclei nearest to the vitelline membrane. This arrangement of the A-T rich sequences has been observed from the syncytial balstoderm stage into the gastrula stage where, in each nucleus, the satellite DNA sequences remain at a point nearest the topological outside of the organism.

Hoechst 33258 induced uncondensed sites in marsupial chromosomes

The fluorochrome Hoechst 33258 induces pronounced uncondensed regions at mitosis at one or more specific sites on the X chromosomes of all eighteen species of marsupials belonging to the family Macropodidae which have been examined. The Y chromosomes of nearly all of these species also show sensitive sites. Autosomal regions which respond to this chemical were observed in only five species and there is evidence of polymorphism for two of these. The regions which respond usually show C-banding, but not all C-banding regions are affected. No specific effect was found in the chromosomes of eleven other species examined which are representative of 5 different Australian marsupial families. The implications of the apparent restriction of sex chromosome sensitive sites to macropods are discussed.

Restriction enzyme analysis of a highly diverged satellite DNA from Drosophila nasutoides

The satellite II DNA of Drosophila nasutoides is a highly diverged repetitive DNA, showing about 17% base changes between repeat units (Cordeiro-Stone and Lee, 1976). This DNA is cleaved by four different restriction enzymes to produce multimeric fragmentation patterns, indicating that their restriction sites are regularly arranged. Moreover, all four enzymes produce identical fragment lengths, the size of a monomer being 96 base pairs. Such multimeric patterns are expected for a diverged repetitive DNA, since many restriction sequences could have undergone changes during sequence divergence. Further restriction analyses of this DNA by double digestions and cloning reveal that there are three different sequences in satellite II DNA with respect to the presence and the arrangement of various restriction sites (Fig. 7). As an example, one sequence contains many EcoRI sites and fewer HinfI sites (20% of EcoRI sites), which are arranged regularly. These observations suggest that satellite II DNA of D. nasutoides might have evolved through different modes of sequence divergence.

The distribution of two highly repeated DNA sequences within Drosophila melanogaster chromosomes

In situ hybridization using 3H-RNA probes has been used to localize the sequences found in two satellites of density 1.705 g/cc and 1.672 g/cc to specific sites within the chromosomal complement. A detailed analysis of the sites on the S chromosome was carried out using the acute series of inversions to relate the heterochromatic breakpoint relative to the location of the sequence on this chromosome. It has also been possible to establish the order of arrangement of 1.705 and 1.672 DNA at the heterochromatic-euchromatic junction on chromosome 3(R). A mitotic map is provided. The Tm of hybrids formed in situ showed that the hybrids were representative of the sequences being analyzed. The two satellites also were traced through a number of purification procedures to show that a covalent linkage may be likely between the 1.705 g/cc and 1.672 g/cc satellite as predicted from in situ hybridization analyses.

The number of genes on the second chromosome of Drosophila melanogaster and a comment on the genetic structure of eukaryotes

Recessive lethals on the second chromosome were extracted from genetically isolated populations in Australia and the U.K. The frequency of allelism, used in a manner analogous to capture-recapture of animal populations, indicated that the number of genes capable of mutating to lethal had a 95 per cent probability of being in the range 247 to 1140, although excluding possible heterotic and synthetic lethals altered this to 309 to 3568. Possible sources of bias are discussed. The disagreement between these values and those obtained the direct measurements of DNA (more than 10 times greater) is clear. It is suggested that many of the genes of eukaryotes have been duplicated by unequal exchange during recombination and occur in functionally related groups or in supergenes. Some consequences of this hypothesis to population genetics are noted.

Chromosomal distribution of the major insert in Drosophila melanogaster 28S rRNA genes

The major type I insert sequence for the 28S rRNA genes ofDrosophila melanogasterhas been mapped within the chromosomes using a probe synthesized from a cloned sequence containing the entire 5·4 kb segment. The genomic distribution was shown to be complex in that the insert sequence occurred next to many different types of sequences, in addition to occurring as an insert in the 28S rRNA genes of theXchromosome.In situhybridization of mitotic chromosomes showed most of the insert units not contained in the ribosomal genes to be located near the ribosomal gene cluster on theXchromosome. Additional sites were detected in polytene chromosomes in region 102C, 8–12 and in the hetero-chromatin of the autosomes.

Fluorescence patterns of heterochromatin in mitotic and polytene chromosomes in seven members of three sub-groups of the melanogaster species group of Drosophila

A comparative study of fluorescence patterns of heterochromatin in mitotic and polytene chromosomes of seven species belonging to 3 subgroups (melanogaster sub-group: D. melanogaster and D. simulans; montium sub-group: D. kikkawai and D. jambulina; ananassae sub-group: D. ananassae. D. malerkotliana and D. bipectinata) of the melanogaster species group of Drosophila (Sophophora) has been made. Hoechst 33258 (H) fluorescence patterns of mitotic chromosomes reveal differences correlated to the taxonomic groupings of these species. The melanogaster sub-group species have H-bright regions on heterochromatin of all chromosomes; the montium subgroup species have H-bright regions mainly on the 4th and Y-chromosomes; in the ananassae sub-group, while D. ananassae chromosomes do not show any H-bright regions. D. malerkotliana and D. bipectinata have small H-bright segments only on their 4th chromosomes. The H- and quinacrine mustard (QM) fluorescence patterns of larval salivary gland polytene chromocentre in these species, however, do not show the same taxonomic correlation. While D. ananassae and D. kikkawai polytene nuclei lack any H- or QM-bright region in the chromocentre, the remaining species have prominent H- and/or QM-bright region(s). In D. jambulina, the QM-bright regions are generally bigger than H-bright regions, while in D. malerkotliana and D. bipectinata the situation is reversed. Actinomycin D counterstaining prior to H-staining of polytene preparations of each species confirms that the H-bright region/s in the chromocentre are composed of A-T rich sequences. In vivo labelling of salivary gland polytene nuclei with 5-bromo-deoxyuridine for 24 to 48 h and subsequent H-staining reveals that in all the species, the H-bright regions do not replicate in 3rd instar stage and presumably represent the non-replicating alpha heterochromatin. Significantly, in all the species (excepting D. kikkawai and D. ananassae), the size, location and the number of H- and/or QM-bright regions were seen to vary in different polytene nuclei in the same gland. It seems that the organization and the extent of under-replication of alpha heterochromatin varies in different polytene nuclei. Present studies also show that even closely related species differ in the content and organization of H-bright heterochromatin. The 81F band at the base of 3R in D. melanogaster, but not in D. simulans, appears to contain non-replicating H-bright sequences in addition to replicating chromatin.

DNA-protein interactions in the Drosophila melanogaster mitochondrial genome as deduced from trimethylpsoralen crosslinking patterns

The location of proteins on the mitochondrial DNA (mtDNA) of Drosophila melanogaster was investigated by trimethylpsoralen photoreaction of embryos disrupted by gentle homogenization. After photoreaction, the mtDNA was isolated and the pattern of DNA crosslinking was determined by electron microscopy of the DNA under totally denaturing conditions. In contrast to nuclear DNA, which showed periodic crosslinks indicative of a nucleosome structure, most of each mtDNA molecule exhibited uniformly heavy crosslinking. A 10% region of the mtDNA was, however, protected from psoralen crosslinking in a distinctive manner: five uncrosslinked segments were closely clustered in the mtDNA. Four were 394 +/- 13 (SD) base pairs in size, while the fifth measured about 200 base pairs. These protected segments mapped within the A+T-rich region of the mtDNA, extending from the end of the A+T-rich region near the Bg1 II cleavage site to the center of the A+T-rich region. Protection of this part of the mtDNA from crosslinking was interpreted to be the result of association with proteins in the mitochondrion because mtDNA that was deproteinized before the photoreaction was uniformly crosslinked over its entire length. The origin of replication of the mtDNA is also located at the center of the A+T-rich region, which suggests that the protection from the psoralen photoreaction may be due to proteins involved in membrane attachment or replication.

Segmental amplification in a satellite DNA: restriction enzyme analysis of the major satellite of Macropus rufogriseus

The 1.708 g/cc satellite DNA of the red necked wallaby is shown to consist of a number of related families of sequences arranged in tandem arrays. Particular families are subpopulations of other families; their distribution supports a model of successive amplification events during the generation of the satellite. In each amplification episode one 2,500 bp unit is multiplied into a tandemly repeated array of that unit (segmental amplification). The 1.708 g/cc sequences can be detected in related kangaroo species in much reduced amount, and with changes to the long order periodicity of the repeat units.

Similarity of centromeric heterochromatin in strains of drosophila melanogaster which interact to produce hybrid dysgenesis

Many long-established laboratory strains of D. melanogaster interact with recently-collected wild-type strains, so that the progeny show sterility, enhanced mutation, male recombination and other degenerative traits, a syndrome known collectively as "hybrid dysgenesis". Tests have been made for differences in centromeric heterochromatin between interacting strains, by comparing homologues in mitotic preparations from hybrid individuals. Differences between homologues have not been revealed, either qualitatively by C-banding or quantitatively by in situ hybridisation to RNA transcripts from satellites 1.705 and 1.686. However, the sensitivities of the techniques are such that quantitative differences of less than 50% between strains could escape detection.

Isolation, properties and cellular distribution of D1, a chromosomal protein of Drosophila

The protein D1 was obtained from nuclei of Drosophila melanogaster embryos and purified by perchloric acid fractionation and preparative gel electrophoresis. In nuclei its amount is approximately 1% of the amount of DNA by weight. D1 is soluble in 5% perchloric acid and extractable from nuclei by solutions of moderate ionic strength (0.35 M NaCl). Amino acid analysis shows that it is rich in both basic (20%) and acidic (27%) aminoacids. In all these properties D1 resembles HMG proteins (high mobility group; Johns et al., 1975) of vertebrates; however, its apparent molecular weight (approximately 50,000) is much higher. The distribution of D1 in salivary gland polytene chromosomes was investigated by immunofluorescence. Two levels of fluorescence intensity were observed: 1) Very bright fluorescence at chromosomal positions 81F, 83E, 101F, 102C and 102F; these sites are shown, by double labeling techniques, to coincide with quinacrine bright sites. 2) Medium to low fluorescence at many sites widely distributed throughout all chromosomes. In order to interpret these results and to relate them to the in vivo distribution of D1, we have investigated the pattern of immunofluorescence staining as a function of the methods of chromosome preparation and salivary gland fixation. The immunological specificity of the anti-D1 serum was studied by comparing its reactivity with D. melanogaster and D. virilis chromosome spreads and whole salivary glands, and by using reagents that minimize non-specific antibody interactions. We conclude that D1 is widely distributed throughout cytoplasm and nucleus, present in many chromomeres but most abundant in chromosomal sites that contain the AT-rich satellite DNA of density 1.672. This distribution, together with available evidence about the nucleotide sequences present in this satellite, suggests that D1 binds preferentially to chromatin containing sequences AATAT and/or AATATAT.

Hybridization of tRNAs of Drosophila melanogaster to polytene chromosomes

Highly purified tRNAs from Drosophila melanogaster were iodinated with 125I and hybridized to squashes of polytene chromosomes of Drosophila silivary glands followed by autoradiography to localize binding sites. Most tRNAs hybridize strongly to more than one site and weakly to one or more additional sites. The major sites for various tRNAs are the following: tRNA2Arg, 42A, 84F1,2; tRNA2Asp, 29DE; tRNA3Gly, 22BC, 35BC, 57BC, tRNA2Lys, 42A, 42E; tRNA5Lys, 84AB, 87B; tRNA2Met, 48B5-7, 72F1-2, 83F-84A; tRNA3Met, 46A1-2, 61D1-2, 70F1-2; tRNA4Ser, 12DE, 23E; tRNA7Ser, 12DE, 23E; tRNA3aVal, 64D; tRNA3bVal, 84d3-4, 92b1-9; tRNA4Val, 56D3-7, 70BC.